[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.13.2-1-3-g9e1fbef
Charles Plessy
plessy at debian.org
Sat Oct 29 02:27:10 UTC 2011
The following commit has been merged in the meta branch:
commit 4a4d85b69e016b03083d9057ef3d154fb3b4d7e5
Author: Charles Plessy <plessy at debian.org>
Date: Sat Oct 29 11:16:47 2011 +0900
Collected build logs for 2.13.3-1.
diff --git a/armel.log b/armel.log
index 81e8b39..20b62bd 100644
--- a/armel.log
+++ b/armel.log
@@ -1,68 +1,75 @@
-From buildd at antheil.debian.org Sat Sep 24 04:06:10 2011
-Return-path: <buildd at antheil.debian.org>
+From buildd at ancina.debian.org Wed Oct 05 09:58:28 2011
+Return-path: <buildd at ancina.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
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- (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
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-Received: from antheil.islands.arm.com ([217.140.96.60]
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+ CN=ancina.debian.org, EMAIL=hostmaster at ancina.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>)
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-Date: Sat, 24 Sep 2011 04:06:07 +0000
-Message-Id: <E1R7JV9-0003re-N0 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_2.13.2-1 on armel (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+ (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
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+Received: from buildd by ancina.debian.org with local (Exim 4.69)
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+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
+Date: Wed, 5 Oct 2011 09:58:26 +0000
+From: Build Daemon <buildd at ancina.debian.org>
+To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.3-1 on armel (dist=sid)
+Key-Id: 534B6930
+Message-Id: <E1RBOF8-0002ZS-Ha at ancina.debian.org>
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 ancina.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (armel) 24 Sep 2011 03:39 ║
+║ bedtools 2.13.3-1 (armel) 05 Oct 2011 09:35 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: armel
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5773 kB]
+Get:1 http://ftp.de.debian.org sid InRelease [146 kB]
+Get:2 http://incoming.debian.org sid InRelease [146 kB]
+Get:3 http://ftp.de.debian.org sid/main Sources/DiffIndex [2038 B]
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 [5783 kB]
-Get:6 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:7 http://incoming.debian.org unstable/non-free Sources [102 kB]
-Get:8 http://incoming.debian.org unstable/main armel Packages [7567 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib Sources [56.5 kB]
-Get:10 http://ftp.uk.debian.org unstable/non-free Sources [102 kB]
-Get:11 http://ftp.uk.debian.org unstable/main armel Packages [7559 kB]
-Get:12 http://incoming.debian.org unstable/contrib armel Packages [54.7 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:13 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:14 http://incoming.debian.org Release [1604 B]
-Get:15 http://incoming.debian.org Sources [32.8 kB]
-Get:16 http://incoming.debian.org Packages [562 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
+Get:4 http://ftp.de.debian.org sid/main armel Packages/DiffIndex [2038 B]
+Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
+Ign http://ftp.de.debian.org sid/contrib TranslationIndex
+Get:5 http://ftp.de.debian.org sid/main TranslationIndex [2045 B]
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://ftp.de.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:8 http://ftp.de.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
+Get:9 http://ftp.de.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:10 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:11 http://incoming.debian.org sid/main armel Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Get:12 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Get:13 http://incoming.debian.org Release [1604 B]
+Get:14 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:15 http://incoming.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
+Get:16 http://ftp.de.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
+Ign http://ftp.de.debian.org sid/contrib Translation-en
+Get:17 http://incoming.debian.org Sources [36.7 kB]
+Get:18 http://incoming.debian.org Packages [271 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Get:17 http://ftp.uk.debian.org unstable/contrib armel Packages [54.7 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:18 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Fetched 28.0 MB in 1min 20s (346 kB/s)
+Get:19 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:20 http://incoming.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
+Fetched 632 kB in 24s (26.0 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,10 +91,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 1s (624 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 1s (502 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +114,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 26 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 26 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -129,14 +136,14 @@ dash: already installed (0.5.7-1)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+e2fsprogs: already installed (1.42~WIP-2011-09-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -145,138 +152,51 @@ tar: already installed (1.26-2)
bsdutils: already installed (1:2.19.1-5)
mount: already installed (2.19.1-5)
util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-18)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
-debhelper: missing
-Using default version 8.9.7
+debhelper: already installed (8.9.8 >= 8 is satisfied)
quilt: missing
-zlib1g-dev: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs quilt
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ devscripts procmail graphviz
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 26 not upgraded.
-Need to get 9369 kB of archives.
-After this operation, 28.1 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-3 [33.8 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-2 [990 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.08-1 [245 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.08-1 [51.2 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-4 [139 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-4 [815 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.6-1 [1535 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-4 [409 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-4 [1984 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.54-1 [27.7 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9369 kB in 5s (1846 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10521 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_armel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_armel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_armel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.08-1_armel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_armel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_armel.deb) ...
+ cdbs diffstat quilt
+0 upgraded, 3 newly installed, 0 to remove and 38 not upgraded.
+Need to get 0 B/461 kB of archives.
+After this operation, 1215 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
+(Reading database ... 28011 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_armel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_armel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_armel.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Processing triggers for man-db ...
Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 26 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.31-rc9 armel (armv5tel)
+Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
+Package versions: adduser_3.113 apex-nslu2_1.6.10 apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 bc_1.06.95-2 bf-utf-source_0.05-0.1 binutils_2.21.53.20110910-1 bison_1:2.4.1.dfsg-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 cramfsprogs_1.1-6 dash_0.5.7-1 dbus_1.4.16-1 dbus-x11_1.4.16-1 dctrl-tools_2.18 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debiandoc-sgml_1.2.25 debianutils_4.0.2 devio_1.2-1+b1 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 dns323-firmware-tools_0.3-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.16.0.3 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-16-1 e2fsprogs_1.42~WIP-2011-09-16-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.6_4.6.1-13 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gconf2_2.32.4-1 gconf2-common_2.32.4-1 genext2fs_1.4.1-3 genisoimage_9:1.1.11-2 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gir1.2-atk-1.0_2.2.0-1 gir1.2-freedesktop_0.10.8-2+b1 gir1.2-gdkpixbuf-2.0_2.24.0-1 gir1.2-glib-2.0_0.10.8-2+b1 gir1.2-pango-1.0_1.28.4-3 gnome-mime-data_2.18.0-1 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gvfs_1.6.4-4 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libart-2.0-2_2.3.21-1 libasound2_1.0.24.1-4 libaspell15_0.60.7~20110707-1 libatasmart4_0.17+git20100219-3 libatk1.0-0_2.2.0-1 libatk1.0-data_2.2.0-1 libatk1.0-dev_2.2.0-1 libattr1_1:2.4.46-3 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common3_0.6.30-5 libavahi-glib1_0.6.30-5 libblas3gf_1.2.20110419-2 libblkid1_2.19.1-5 libbluetooth-dev_4.96-2 libbluetooth3_4.96-2 libbogl-dev_0.1.18-5 libbogl0_0.1.18-5 libbonobo2-0_2.24.3-1 libbonobo2-common_2.24.3-1 libbonoboui2-0_2.24.3-1 libbonoboui2-common_2.24.3-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-pic_2.13-21 libcairo-gobject2_1.10.2-6.1 libcairo-script-interpreter2_1.10.2-6.1 libcairo2_1.10.2-6.1 libcairo2-dev_1.10.2-6.1 libcanberra0_0.28-1 libcomerr2_1.42~WIP-2011-10-01-2 libcroco3_0.6.2-1 libcups2_1.5.0-8 libdatrie1_0.2.4-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdbus-glib-1-2_0.98-1 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.1 libdrm2_2.4.26-1 libenchant1c2a_1.6.0-3 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfam0_2.7.0-17 libffi-dev_3.0.10-1 libffi5_3.0.10-1 libfontconfig1_2.8.0-3 libfontconfig1-dev_2.8.0-3 libfontenc1_1:1.1.0-1 libfreetype6_2.4.6-2 libfreetype6-dev_2.4.6-2 libgail18_2.24.6-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgconf2-4_2.32.4-1 libgcrypt11_1.5.0-3 libgd2-noxpm_2.0.36~rc1~dfsg-5.1+b1 libgdbm3_1.8.3-10 libgdk-pixbuf2.0-0_2.24.0-1 libgdk-pixbuf2.0-dev_2.24.0-1 libgdu0_2.32.1-1 libgfortran3_4.6.1-13 libgirepository-1.0-1_0.10.8-2+b1 libgl1-mesa-glx_7.11-6 libglade2-0_1:2.6.4-1 libglapi-mesa_7.11-6 libglib2.0-0_2.28.6-1 libglib2.0-bin_2.28.6-1 libglib2.0-data_2.28.6-1 libglib2.0-dev_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnome-keyring0_3.2.0-2 libgnome2-0_2.32.1-1 libgnome2-common_2.32.1-1 libgnomecanvas2-0_2.30.3-1 libgnomecanvas2-common_2.30.3-1 libgnomeui-0_2.24.5-2 libgnomeui-common_2.24.5-2 libgnomevfs2-0_1:2.24.4-1 libgnomevfs2-common_1:2.24.4-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgpm2_1.20.4-4 libgssapi-krb5-2_1.9.1+dfsg-3 libgtk2.0-0_2.24.6-1 libgtk2.0-common_2.24.6-1 libgtk2.0-dev_2.24.6-1 libgtkspell0_2.0.16-1 libgudev-1.0-0_172-1 libhtml-parser-perl_3.68-1+b1 libhtml-tagset-perl_3.20-2 libhunspell-1.2-0_1.2.14-4 libice-dev_2:1.0.7-2 libice6_2:1.0.7-2 libidl0_0.8.14-0.2 libidn11_1.22-3 libjasper1_1.900.1-10 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1+b1 libldap-2.4-2_2.4.25-3 libltdl7_2.4-4 liblvm2app2.2_2.02.86-1 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libmysqlclient16_5.1.58-1 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-1 libnewt-dev_0.52.11-2.1 libnewt-pic_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libogg0_1.2.2~dfsg-1 liborbit2_1:2.14.18-0.2 libp11-kit0_0.7-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-4 libpango1.0-0_1.28.4-3 libpango1.0-dev_1.28.4-3 libparted0debian1_2.3-8 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpisock-dev_0.12.5-4 libpisock9_0.12.5-4 libpisync1_0.12.5-4 libpixman-1-0_0.22.2-1 libpixman-1-dev_0.22.2-1 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpolkit-gobject-1-0_0.102-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1 libpthread-stubs0-dev_0.3-2.1 libpython2.6_2.6.7-4 libpython2.7_2.7.2-5 libreadline5_5.2-10 libreadline6_6.2-6 libroman-perl_1.23-1 libruby1.8_1.8.7.352-2 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libsgmls-perl_1.03ii-32 libsgutils2-2_1.32-1 libsigsegv2_2.9-4 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libslang2-pic_2.2.4-3 libsm-dev_2:1.2.0-2 libsm6_2:1.2.0-2 libsp1c2_1.3.4-1.2.1-47.1 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-09-25-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtasn1-3_2.9-4 libtdb1_1.2.9-4+b1 libtext-format-perl_0.53-1 libthai-data_0.1.15-2 libthai0_0.1.15-2 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libudev0_172-1 libunistring0_0.9.3-4 liburi-perl_1.59-1 libusb-0.1-4_2:0.1.12-19 libusb-dev_2:0.1.12-19 libuuid1_2.19.1-5 libvolume-id1_0.141-2 libvorbis0a_1.3.2-1 libvorbisfile3_1.3.2-1 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libx11-dev_2:1.4.4-2 libxau-dev_1:1.0.6-3 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb-render0_1.7-3 libxcb-render0-dev_1.7-3 libxcb-shape0_1.7-3 libxcb-shm0_1.7-3 libxcb-shm0-dev_1.7-3 libxcb1_1.7-3 libxcb1-dev_1.7-3 libxcomposite-dev_1:0.4.3-2 libxcomposite1_1:0.4.3-2 libxcursor-dev_1:1.1.12-1 libxcursor1_1:1.1.12-1 libxdamage-dev_1:1.1.3-2 libxdamage1_1:1.1.3-2 libxdmcp-dev_1:1.1.0-3 libxdmcp6_1:1.1.0-3 libxext-dev_2:1.3.0-3 libxext6_2:1.3.0-3 libxfixes-dev_1:5.0-4 libxfixes3_1:5.0-4 libxft-dev_2.2.0-3 libxft2_2.2.0-3 libxi-dev_2:1.4.3-3 libxi6_2:1.4.3-3 libxinerama-dev_2:1.1.1-3 libxinerama1_2:1.1.1-3 libxml2_2.7.8.dfsg-4 libxml2-utils_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxmuu1_2:1.1.0-2 libxpm4_1:3.5.9-1 libxrandr-dev_2:1.3.2-2 libxrandr2_2:1.3.2-2 libxrender-dev_1:0.9.6-2 libxrender1_1:0.9.6-2 libxslt1.1_1.1.26-8 libxt6_1:1.1.1-2 libxtst6_2:1.2.0-3 libxv1_2:1.0.6-2 libxxf86dga1_2:1.1.2-1 libxxf86vm1_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 m4_1.4.16-2 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 mklibs_0.1.33 mklibs-copy_0.1.33 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-18 mysql-common_5.1.58-1 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 nullmailer_1:1.05-1 openssl_1.0.0d-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.14-1 python_2.7.2-7 python-all_2.7.2-7 python-all-dev_2.7.2-7 python-cairo_1.8.8-1+b2 python-central_0.6.17 python-dateutil_1.5-1 python-dev_2.7.2-7 python-egenix-mx-base-dev_3.2.1-1 python-egenix-mxdatetime_3.2.1-1 python-egenix-mxtools_3.2.1-1 python-gconf_2.28.1-3 python-glade2_2.24.0-2 python-gnome2_2.28.1-3 python-gobject_2.28.6-5 python-gobject-dev_2.28.6-5 python-gtk2_2.24.0-2 python-gtk2-dev_2.24.0-2 python-gtkspell_2.25.3-10.1 python-imaging_1.1.7-4 python-minimal_2.7.2-7 python-mysqldb_1.2.2-10+b3 python-numpy_1:1.5.1-2+b1 python-pisock_0.12.5-4 python-pyorbit_2.24.0-6+b1 python-pyparsing_1.5.2-2 python-reportlab_2.5-1.1 python-support_1.0.14 python-tz_2011h-0.1 python-vobject_0.8.1c-4 python2.6_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-5 python2.7-dev_2.7.2-5 python2.7-minimal_2.7.2-5 quilt_0.48-8 readline-common_6.2-4 ruby1.8_1.8.7.352-2 scons_2.1.0-1 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sgmlspl_1.03ii-32 shared-mime-info_0.90-1 slugimage_1:0.0+r104-5 sp_1.3.4-1.2.1-47.1 sudo_1.8.2-1 swig_2.0.4-4 swig2.0_2.0.4-4 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 ttf-dejavu-core_2.33-2 tzdata_2011k-1 u-boot-tools_2011.06-4 uboot-mkimage_2011.06-4 ucf_3.0025+nmu2 udev_172-1 udisks_1.0.4-1 util-linux_2.19.1-5 wget_1.13-1 x11-common_1:7.6+9 x11-utils_7.6+3 x11proto-composite-dev_1:0.4.2-2 x11proto-core-dev_7.0.22-1 x11proto-damage-dev_1:1.2.1-2 x11proto-fixes-dev_1:5.0-2 x11proto-input-dev_2.0.2-2 x11proto-kb-dev_1.0.5-2 x11proto-randr-dev_1.3.2-2 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.2.0-3 x11proto-xinerama-dev_1.2.1-2 xml-core_0.13 xorg-sgml-doctools_1:1.8-2 xsltproc_1.1.26-8 xtrans-dev_1.2.6-2 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +207,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -302,30 +222,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -338,21 +258,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3/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_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -370,7 +290,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -430,6 +350,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -599,7 +523,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -642,14 +566,14 @@ dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/flankBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/multiBamCov contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/unionBedGraphs contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/multiBamCov contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bed12ToBed6 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/pairToBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bamToBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/fastaFromBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/overlap contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/coverageBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/overlap contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/closestBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/maskFastaFromBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedToBam contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
@@ -663,64 +587,64 @@ dpkg-shlibdeps: warning: debian/bedtools/usr/bin/mergeBed contains an unresolvab
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/nucBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedToIgv contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/windowBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/linksBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/tagBam contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/linksBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/slopBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/intersectBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/complementBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org> >../bedtools_2.13.2-1_armel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0406
+Build finished at 20111005-0958
-bedtools_2.13.2-1_armel.changes:
+bedtools_2.13.3-1_armel.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
-Maintainer: armel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org>
+Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- a8c7bb800b066e797774f4be2e9aa9407c552ce4 531992 bedtools_2.13.2-1_armel.deb
+ 6dffa715e001bd06b2d6b28414ecdbf56a3c6970 533770 bedtools_2.13.3-1_armel.deb
Checksums-Sha256:
- 79931b80ac9289b1af036337ad93b4302f2e815cc702bdc23277fa331fda2c4a 531992 bedtools_2.13.2-1_armel.deb
+ 701dd9294529c8cc82f74e9aa19200b76e2f4ce4d59558552327f80d215acc17 533770 bedtools_2.13.3-1_armel.deb
Files:
- 7b7615edcf85994a31d6cd0214146c5a 531992 science optional bedtools_2.13.2-1_armel.deb
+ 23bf2ca7e0bd482f6452b11b81e3d317 533770 science optional bedtools_2.13.3-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_armel.deb
+bedtools_2.13.3-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 531992 bytes: control archive= 1724 bytes.
+ size 533770 bytes: control archive= 1713 bytes.
835 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4116
+ Installed-Size: 3942
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
@@ -735,49 +659,7 @@ bedtools_2.13.2-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 04:05 ./
-drwxr-xr-x root/root 0 2011-09-24 04:05 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 04:05 ./usr/bin/
--rwxr-xr-x root/root 106224 2011-09-24 04:05 ./usr/bin/closestBed
--rwxr-xr-x root/root 55680 2011-09-24 04:05 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 240008 2011-09-24 04:05 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 104572 2011-09-24 04:05 ./usr/bin/subtractBed
--rwxr-xr-x root/root 129136 2011-09-24 04:05 ./usr/bin/sortBed
--rwxr-xr-x root/root 94316 2011-09-24 04:05 ./usr/bin/mergeBed
--rwxr-xr-x root/root 96416 2011-09-24 04:05 ./usr/bin/slopBed
--rwxr-xr-x root/root 102476 2011-09-24 04:05 ./usr/bin/flankBed
--rwxr-xr-x root/root 305588 2011-09-24 04:05 ./usr/bin/pairToBed
--rwxr-xr-x root/root 92288 2011-09-24 04:05 ./usr/bin/linksBed
--rwxr-xr-x root/root 104600 2011-09-24 04:05 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 220504 2011-09-24 04:05 ./usr/bin/tagBam
--rwxr-xr-x root/root 92464 2011-09-24 04:05 ./usr/bin/annotateBed
--rwxr-xr-x root/root 96428 2011-09-24 04:05 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 231836 2011-09-24 04:05 ./usr/bin/windowBed
--rwxr-xr-x root/root 183404 2011-09-24 04:05 ./usr/bin/bamToBed
--rwxr-xr-x root/root 289196 2011-09-24 04:05 ./usr/bin/intersectBed
--rwxr-xr-x root/root 113124 2011-09-24 04:05 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 186788 2011-09-24 04:05 ./usr/bin/bedToBam
--rwxr-xr-x root/root 88196 2011-09-24 04:05 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 159756 2011-09-24 04:05 ./usr/bin/pairToPair
--rwxr-xr-x root/root 227716 2011-09-24 04:05 ./usr/bin/coverageBed
--rwxr-xr-x root/root 240032 2011-09-24 04:05 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 75928 2011-09-24 04:05 ./usr/bin/overlap
--rwxr-xr-x root/root 92304 2011-09-24 04:05 ./usr/bin/complementBed
--rwxr-xr-x root/root 122220 2011-09-24 04:05 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 122580 2011-09-24 04:05 ./usr/bin/nucBed
-drwxr-xr-x root/root 0 2011-09-24 04:05 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 04:05 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 03:42 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
-drwxr-xr-x root/root 0 2011-09-24 04:04 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 04:05 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
+dpkg-deb: file `/var/lib/schroot/mount/sid-armel-sbuild-6403b615-c722-4314-b6b7-19773bad4d98/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools_2.13.3-1_armel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -791,27 +673,42 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-39014e0e-403f-470e-be93-a27e465ac1f7/build/buildd-bedtools_2.13.2-1-armel-ZXrRqH
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-armel-sbuild-6403b615-c722-4314-b6b7-19773bad4d98/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ cdbs* diffstat* quilt*
+0 upgraded, 0 newly installed, 3 to remove and 38 not upgraded.
+After this operation, 1215 kB disk space will be freed.
+(Reading database ... 28146 files and directories currently installed.)
+Removing cdbs ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 97864
-Build-Time: 1383
+Build-Space: 98156
+Build-Time: 1263
Distribution: sid
-Install-Time: 89
-Job: bedtools_2.13.2-1
+Install-Time: 29
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 1589
-Source-Version: 2.13.2-1
-Space: 97864
+Package-Time: 1344
+Source-Version: 2.13.3-1
+Space: 98156
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0406
-Build needed 00:26:29, 97864k disc space
-Signature with key '288B0753' requested:
-
+Finished at 20111005-0958
+Build needed 00:22:24, 98156k disc space
+Signature with key '534B6930' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index 7dc31fb..b155467 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,146 +1,111 @@
-From buildd at mozart.debian.net Sat Sep 24 06:38:53 2011
+From buildd at mozart.debian.net Wed Oct 05 12:11:40 2011
Return-path: <buildd at mozart.debian.net>
Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
- id 1R7Lsx-00046c-HV
- for logs at buildd.debian.org; Sat, 24 Sep 2011 06:38:53 +0000
+ id 1RBQK2-0004mT-UM
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 12:11:40 +0000
Received: from mozart.debian.net ([10.1.0.1])
by callisto.debian.net with esmtp (Exim 4.69)
(envelope-from <buildd at mozart.debian.net>)
- id 1R7Lss-00015N-4Y; Sat, 24 Sep 2011 07:38:46 +0100
+ id 1RBQJp-0006nQ-Va; Wed, 05 Oct 2011 13:11:26 +0100
Received: from buildd by mozart.debian.net with local (Exim 4.76)
(envelope-from <buildd at mozart.debian.net>)
- id 1R7Lsr-0001YB-4h; Sat, 24 Sep 2011 06:38:45 +0000
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.78; A2.07; B3.08; Q3.08)
-Date: Sat, 24 Sep 2011 06:38:44 +0000
+ id 1RBQJq-0002OF-8b; Wed, 05 Oct 2011 12:11:26 +0000
From: Build Daemon <buildd at mozart.debian.net>
To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of bedtools_2.13.2-1 on hurd-i386 (dist=sid)
-Message-Id: <E1R7Lsr-0001YB-4h at mozart.debian.net>
+Subject: Log for successful build of bedtools_2.13.3-1 on hurd-i386 (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1RBQJq-0002OF-8b at mozart.debian.net>
+Date: Wed, 05 Oct 2011 12:11:26 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on mozart.debian.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mozart.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (hurd-i386) 24 sept. 2011 06:23 ║
+║ bedtools 2.13.3-1 (hurd-i386) 05 oct. 2011 11:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
-Distribution: sid
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: hurd-i386
-
-I: NOTICE: Log filtering will replace 'build/bedtools-dLhWj9/bedtools-2.13.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bedtools-dLhWj9' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'home/buildd/build/chroot-sid' with '«CHROOT»'
-W: Stripped single quote from command for security:
- use strict;
- use warnings;
- use POSIX;
- use FileHandle;
-
- my $lockfile="/var/lock/sbuild";
- my $try = 0;
-
- repeat:
- if (!sysopen( F, $lockfile, O_WRONLY|O_CREAT|O_TRUNC|O_EXCL, 0644 )){
- if ($! == EEXIST) {
- # lock file exists, wait
- goto repeat if !open( F, "<$lockfile" );
- my $line = <F>;
- my ($job, $pid, $user);
- close( F );
- if ($line !~ /^(\S+)\s+(\S+)\s+(\S+)/) {
- print STDERR "Bad lock file contents ($lockfile) -- still trying\n";
- } else {
- ($job, $pid, $user) = ($1, $2, $3);
- if (kill( 0, $pid ) == 0 && $! == ESRCH) {
- # process doesn't exist anymore, remove stale lock
- print STDERR "Removing stale lock file $lockfile ".
- "(job $job, pid $pid, user $user)\n";
- if (!unlink($lockfile)) {
- if ($! != ENOENT) {
- print STDERR "Cannot remove chroot lock file $lockfile: $!\n";
- exit 1;
- }
- }
- }
- }
- ++$try;
- if ($try > 120) {
- print STDERR "Lockfile $lockfile still present after " .
- 120 * 5 . " seconds -- giving up\n";
- exit 1;
- }
- print STDERR "Another sbuild process (job $job, pid $pid by user $user) is currently using the build chroot; waiting...\n"
- if $try == 1;
- sleep 5;
- goto repeat;
- } else {
- print STDERR "Can't create lock file $lockfile: $!\n";
- exit 1;
- }
- }
-
- F->print("bedtools_2.13.2-1 3899 buildd\n");
- F->close();
-
- exit 0;
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Update chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Hit http://ftp.uk.debian.org sid InRelease
-Hit http://ftp.fr.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
-Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
+Get:1 http://ftp.uk.debian.org sid InRelease [146 kB]
+Get:2 http://ftp.fr.debian.org sid InRelease [146 kB]
Ign http://ftp.debian-ports.org unreleased InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://ftp.debian-ports.org unreleased Release.gpg [836 B]
+Get:4 http://ftp.debian-ports.org unreleased Release [25.8 kB]
+Get:5 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Ign http://incoming.debian.org InRelease
Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
+Get:6 http://ftp.uk.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:7 http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
+Get:8 http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
-Hit http://ftp.uk.debian.org sid/main TranslationIndex
+Get:9 http://ftp.uk.debian.org sid/main TranslationIndex [2045 B]
Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
-Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Get:2 http://incoming.debian.org Release [1604 B]
+Get:10 http://ftp.uk.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
+Get:11 http://ftp.uk.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
+Get:12 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
+Get:13 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
+Get:14 http://ftp.fr.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:15 http://ftp.debian-ports.org unreleased/main hurd-i386 Packages [49.7 kB]
+Get:16 http://incoming.debian.org Release.gpg [836 B]
+Get:17 http://ftp.uk.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
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.debian-ports.org unreleased Release
-Get:3 http://incoming.debian.org Sources [33.0 kB]
+Get:18 http://ftp.fr.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:19 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex
+Get:20 http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.fr.debian.org sid/main TranslationIndex
+Get:21 http://ftp.fr.debian.org sid/main TranslationIndex [2045 B]
Ign http://ftp.fr.debian.org sid/non-free TranslationIndex
-Get:4 http://incoming.debian.org Packages [592 kB]
+Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
+Get:22 http://incoming.debian.org Release [1604 B]
+Get:23 http://ftp.fr.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
+Get:24 http://ftp.uk.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
+Get:25 http://ftp.fr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
+Get:26 http://ftp.uk.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
+Get:27 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
+Get:28 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
+Get:29 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
+Get:30 http://ftp.uk.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
Ign http://ftp.uk.debian.org sid/contrib Translation-en
Ign http://ftp.uk.debian.org sid/non-free Translation-en
-Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
+Get:31 http://incoming.debian.org Sources [36.5 kB]
+Ign http://ftp.fr.debian.org sid/contrib Translation-en
+Ign http://ftp.fr.debian.org sid/non-free Translation-en
Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Get:32 http://incoming.debian.org Packages [279 kB]
+Get:33 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
+Get:34 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
Ign http://incoming.debian.org Translation-en
-Err http://ftp.fr.debian.org sid/contrib Translation-en
- Unable to connect to ftp.fr.debian.org:http:
-Err http://ftp.fr.debian.org sid/non-free Translation-en
- Unable to connect to ftp.fr.debian.org:http:
-Fetched 627 kB in 4min 48s (2174 B/s)
-W: Failed to fetch http://ftp.fr.debian.org/debian/dists/sid/contrib/i18n/Translation-en Unable to connect to ftp.fr.debian.org:http:
-
-W: Failed to fetch http://ftp.fr.debian.org/debian/dists/sid/non-free/i18n/Translation-en Unable to connect to ftp.fr.debian.org:http:
-
-E: Some index files failed to download. They have been ignored, or old ones used instead.
+Get:35 http://ftp.fr.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
+Get:36 http://ftp.fr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
+Get:37 http://ftp.fr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
+Get:38 http://ftp.uk.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
+Get:39 http://ftp.fr.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Get:40 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
+Get:41 http://ftp.uk.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:42 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
+Get:43 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
+Get:44 http://ftp.uk.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Get:45 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
+Get:46 http://ftp.fr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
+Get:47 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
+Get:48 http://ftp.fr.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Get:49 http://ftp.fr.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:50 http://ftp.uk.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:51 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
+Get:52 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
+Get:53 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
+Get:54 http://ftp.fr.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:55 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
+Fetched 809 kB in 4min 6s (3275 B/s)
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -161,59 +126,84 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 3s (222 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 3s (181 kB/s)
Download complete and in download only mode
Check arch
──────────
-Merged Build-Depends: build-essential, fakeroot
-Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-R7p9eu/apt_archive/sbuild-build-depends-core-dummy.deb'.
-gpg: WARNING: using insecure memory!
-gpg: please see http://www.gnupg.org/faq.html for more information
-OK
-Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (apt-based resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Installing build dependencies
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.15.1-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
-The following NEW packages will be installed:
- sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 26 not upgraded.
-Need to get 0 B/716 B of archives.
-After this operation, 0 B of additional disk space will be used.
-WARNING: The following packages cannot be authenticated!
- sbuild-build-depends-core-dummy
-Authentication warning overridden.
-Selecting previously deselected package sbuild-build-depends-core-dummy.
-(Reading database ... 13809 files and directories currently installed.)
-Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, zlib1g-dev
-Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-bedtools-dummy' in `/«BUILDDIR»/resolver-oWVB2e/apt_archive/sbuild-build-depends-bedtools-dummy.deb'.
-gpg: WARNING: using insecure memory!
-gpg: please see http://www.gnupg.org/faq.html for more information
-OK
+0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+Removing negative dependencies:
Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install bedtools build dependencies (apt-based resolver) │
+│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Installing build dependencies
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
+bash: already installed (4.1-3+hurd.1)
+coreutils: already installed (8.5-1)
+dash: already installed (0.5.7-1)
+debianutils: already installed (4.0.2)
+diffutils: already installed (1:3.0-1)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+findutils: already installed (4.4.2-1+b1)
+grep: already installed (2.9-2)
+gzip: already installed (1.3.12-9)
+hostname: already installed (3.06)
+hurd: already installed (20110519-3)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-4)
+sed: already installed (4.2.1-9)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc0.3-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+hurd-dev: already installed (20110519-3)
+cdbs: missing
+debhelper: already installed (8.9.6 >= 8 is satisfied)
+quilt: missing
+zlib1g-dev: missing
+Checking for dependency conflicts...
+Installing positive dependencies: cdbs quilt zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
@@ -221,21 +211,21 @@ The following packages were automatically installed and are no longer required:
libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- cdbs diffstat quilt zlib1g-dev
+ diffstat
Suggested packages:
devscripts procmail graphviz
Recommended packages:
autotools-dev
The following NEW packages will be installed:
- cdbs diffstat quilt sbuild-build-depends-bedtools-dummy zlib1g-dev
-0 upgraded, 5 newly installed, 0 to remove and 26 not upgraded.
+ cdbs diffstat quilt zlib1g-dev
+0 upgraded, 4 newly installed, 0 to remove and 32 not upgraded.
Need to get 0 B/648 kB of archives.
After this operation, 1633 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs diffstat quilt zlib1g-dev sbuild-build-depends-bedtools-dummy
+ cdbs diffstat quilt zlib1g-dev
Authentication warning overridden.
Selecting previously deselected package cdbs.
-(Reading database ... 13809 files and directories currently installed.)
+(Reading database ... 13812 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
@@ -243,22 +233,23 @@ Selecting previously deselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
-Selecting previously deselected package sbuild-build-depends-bedtools-dummy.
-Unpacking sbuild-build-depends-bedtools-dummy (from .../sbuild-build-depends-bedtools-dummy.deb) ...
Processing triggers for man-db ...
Setting up cdbs (0.4.99) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Setting up sbuild-build-depends-bedtools-dummy (0.invalid.0) ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build environment │
-└──────────────────────────────────────────────────────────────────────────────┘
-
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.0.3 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 hurd-dev_20110519-3 libc0.3-dev_2.13-20 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-119 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-2 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-2 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-10 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-20 libc-dev-bin_2.13-20 libc0.3_2.13-20 libc0.3-dev_2.13-20 libc0.3-xen_2.13-20 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libept1_1.0.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libobjc2_4.5.3-8 libp11-kit0_0.4-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-4 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libuuid1_2.19.1-5 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-4 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-4 sbuild-build-depends-bedtools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 ttf-dejavu-core_2.33-2 type-handling_0.2.23 tzdata_2011i-2 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 hurd-dev_20110519-3 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-119 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-2 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-2 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-10 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 libept1_1.0.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncursesw5_5.9-2 libobjc2_4.5.3-8 libp11-kit0_0.4-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-4 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-5 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libuuid1_2.19.1-5 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-4 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 ttf-dejavu-core_2.33-2 type-handling_0.2.23 tzdata_2011i-2 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -269,71 +260,45 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
────────────────
-Sufficient free space for build
-
-User Environment
-────────────────
-
-FAKEROOTEGID=0
-FAKEROOTEUID=0
-FAKEROOTFGID=0
-FAKEROOTFUID=0
-FAKEROOTGID=0
-FAKEROOTSGID=0
-FAKEROOTSUID=0
-FAKEROOTUID=0
-HOME=/home/buildd
-LOGNAME=buildd
-OLDPWD=/
-PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin
-PWD=/«PKGBUILDDIR»
-SHELL=/bin/sh
-SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env'
-SUDO_GID=105
-SUDO_UID=60000
-SUDO_USER=buildd
-TERM=rxvt-unicode
-USER=buildd
-USERNAME=root
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/«PKGBUILDDIR»'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -346,21 +311,21 @@ rm -f debian/stamp-patch*
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3/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 `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -378,7 +343,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -438,12 +403,16 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
-- Building in src/utils/genomeFile
- * compiling genomeFile.cpp
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
+- Building in src/utils/genomeFile
+ * compiling genomeFile.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
@@ -459,9 +428,9 @@ bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wun
* linking bamToBed
- Building in src/bedToBam
- * compiling bedToBam.cpp
bedToBam.cpp: In function 'int main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+ * compiling bedToBam.cpp
* linking bedToBam
- Building in src/bedToIgv
@@ -523,12 +492,12 @@ mergeMain.cpp: In function 'int main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
* linking mergeBed
-
-- Building in src/multiBamCov
- * compiling multiBamCovMain.cpp
multiBamCovMain.cpp: In function 'int main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
* compiling multiBamCov.cpp
* linking multiBamCov
@@ -537,9 +506,9 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
* compiling nucBed.cpp
* linking nucBed
+- Building in src/overlap
overlap.cpp: In function 'int main(int, char**)':
overlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
-- Building in src/overlap
* compiling overlap.cpp
* linking overlap
@@ -555,9 +524,9 @@ pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-b
* linking pairToBed
- Building in src/pairToPair
+ * compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling pairToPairMain.cpp
* compiling pairToPair.cpp
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
@@ -580,16 +549,16 @@ pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but
* linking sortBed
- Building in src/subtractBed
- * compiling subtractMain.cpp
subtractMain.cpp: In function 'int main(int, char**)':
subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling subtractMain.cpp
* compiling subtractBed.cpp
* linking subtractBed
- Building in src/tagBam
+ * compiling tagBamMain.cpp
tagBamMain.cpp: In function 'int main(int, char**)':
tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling tagBamMain.cpp
* compiling tagBam.cpp
* linking tagBam
@@ -606,10 +575,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowMain.cpp
* compiling windowBed.cpp
* linking windowBed
- /usr/bin/fakeroot debian/rules binary-arch
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
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
@@ -652,34 +621,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../bedtools_2.13.2-1_hurd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0638
-
-Finished
-────────
-
-I: Built successfully
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bedtools_2.13.2-1_hurd-i386.changes:
-────────────────────────────────────
+Build finished at 20111005-1210
+bedtools_2.13.3-1_hurd-i386.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
@@ -687,34 +644,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- 4293c1dfdb6b5913c7d1ac6d5388e62c9f432379 676900 bedtools_2.13.2-1_hurd-i386.deb
+ b8f8978122b27a7402e9fa902685fc677d2ac7c4 678846 bedtools_2.13.3-1_hurd-i386.deb
Checksums-Sha256:
- 0d3e85b37766e5d9b9765485c7772dab94989b9a6b87bde7ec2ece682fd50311 676900 bedtools_2.13.2-1_hurd-i386.deb
+ 414f9666e227f4b4cba6047795d07ffa6f84bc158be12420a282019c5cf78d18 678846 bedtools_2.13.3-1_hurd-i386.deb
Files:
- 38163a5417e8269572bf984854590fd4 676900 science optional bedtools_2.13.2-1_hurd-i386.deb
+ d5b29d71b7eeb4ebba86cf64ceca6e87 678846 science optional bedtools_2.13.3-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_hurd-i386.deb
+bedtools_2.13.3-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 676900 bytes: control archive= 1723 bytes.
- 841 bytes, 18 lines control
+ size 678846 bytes: control archive= 1722 bytes.
+ 839 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4800
- Depends: libc0.3 (>= 2.2.6), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4638
+ Depends: libc0.3 (>= 2.4), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -728,68 +685,70 @@ bedtools_2.13.2-1_hurd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 06:36 ./
-drwxr-xr-x root/root 0 2011-09-24 06:36 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 06:37 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 06:36 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 06:37 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-24 06:37 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 06:30 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-09-24 06:37 ./usr/bin/
--rwxr-xr-x root/root 102836 2011-09-24 06:37 ./usr/bin/annotateBed
--rwxr-xr-x root/root 220432 2011-09-24 06:37 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96352 2011-09-24 06:37 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227624 2011-09-24 06:37 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121136 2011-09-24 06:37 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120912 2011-09-24 06:37 ./usr/bin/closestBed
--rwxr-xr-x root/root 105156 2011-09-24 06:37 ./usr/bin/complementBed
--rwxr-xr-x root/root 280916 2011-09-24 06:37 ./usr/bin/coverageBed
--rwxr-xr-x root/root 141940 2011-09-24 06:37 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 113920 2011-09-24 06:37 ./usr/bin/flankBed
--rwxr-xr-x root/root 297320 2011-09-24 06:37 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 347436 2011-09-24 06:37 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105300 2011-09-24 06:37 ./usr/bin/linksBed
--rwxr-xr-x root/root 109052 2011-09-24 06:37 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 106612 2011-09-24 06:37 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297308 2011-09-24 06:37 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 141988 2011-09-24 06:37 ./usr/bin/nucBed
--rwxr-xr-x root/root 88160 2011-09-24 06:37 ./usr/bin/overlap
--rwxr-xr-x root/root 366964 2011-09-24 06:37 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178280 2011-09-24 06:37 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129156 2011-09-24 06:37 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105028 2011-09-24 06:37 ./usr/bin/slopBed
--rwxr-xr-x root/root 142556 2011-09-24 06:37 ./usr/bin/sortBed
--rwxr-xr-x root/root 112712 2011-09-24 06:37 ./usr/bin/subtractBed
--rwxr-xr-x root/root 272740 2011-09-24 06:37 ./usr/bin/tagBam
--rwxr-xr-x root/root 59852 2011-09-24 06:37 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285020 2011-09-24 06:37 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-10-05 12:08 ./
+drwxr-xr-x root/root 0 2011-10-05 12:08 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 12:08 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 12:01 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/bin/
+-rwxr-xr-x root/root 104532 2011-10-05 12:09 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223448 2011-10-05 12:09 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96364 2011-10-05 12:09 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227776 2011-10-05 12:09 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121332 2011-10-05 12:09 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 120924 2011-10-05 12:09 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105476 2011-10-05 12:09 ./usr/bin/complementBed
+-rwxr-xr-x root/root 280928 2011-10-05 12:09 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142360 2011-10-05 12:09 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 114464 2011-10-05 12:09 ./usr/bin/flankBed
+-rwxr-xr-x root/root 297332 2011-10-05 12:09 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350580 2011-10-05 12:09 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105660 2011-10-05 12:09 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109572 2011-10-05 12:09 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 107068 2011-10-05 12:09 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297320 2011-10-05 12:09 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 142468 2011-10-05 12:09 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88172 2011-10-05 12:09 ./usr/bin/overlap
+-rwxr-xr-x root/root 366976 2011-10-05 12:09 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178292 2011-10-05 12:09 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129588 2011-10-05 12:09 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 105348 2011-10-05 12:09 ./usr/bin/slopBed
+-rwxr-xr-x root/root 143492 2011-10-05 12:09 ./usr/bin/sortBed
+-rwxr-xr-x root/root 113080 2011-10-05 12:09 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 272752 2011-10-05 12:09 ./usr/bin/tagBam
+-rwxr-xr-x root/root 59976 2011-10-05 12:09 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285032 2011-10-05 12:09 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
+│ Finished │
└──────────────────────────────────────────────────────────────────────────────┘
+Built successfully
+────────────────────────────────────────────────────────────────────────────────
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Cleanup │
+│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /«BUILDDIR»
+Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 26 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -797,17 +756,14 @@ The following packages were automatically installed and are no longer required:
libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* diffstat* quilt* sbuild-build-depends-bedtools-dummy*
- sbuild-build-depends-core-dummy* zlib1g-dev*
-0 upgraded, 0 newly installed, 6 to remove and 26 not upgraded.
+ cdbs* diffstat* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 4 to remove and 32 not upgraded.
After this operation, 1633 kB disk space will be freed.
-(Reading database ... 13980 files and directories currently installed.)
-Removing sbuild-build-depends-bedtools-dummy ...
+(Reading database ... 13983 files and directories currently installed.)
Removing cdbs ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
-Removing sbuild-build-depends-core-dummy ...
Removing zlib1g-dev ...
Processing triggers for man-db ...
@@ -816,17 +772,18 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 93836
-Build-Time: 489
+Build-Space: 94336
+Build-Time: 539
Distribution: sid
-Install-Time: 61
-Job: bedtools_2.13.2-1
+Install-Time: 31
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 869
-Source-Version: 2.13.2-1
-Space: 93836
+Package-Time: 863
+Source-Version: 2.13.3-1
+Space: 94336
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0638
-Build needed 00:14:29, 93836k disc space
+Finished at 20111005-1210
+Build needed 00:14:23, 94336k disc space
+
diff --git a/i386.log b/i386.log
index a31ca70..b558ff0 100644
--- a/i386.log
+++ b/i386.log
@@ -1,68 +1,71 @@
-From buildd at biber.debian.org Sat Sep 24 03:26:12 2011
-Return-path: <buildd at biber.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at murphy.debian.org Wed Oct 05 09:38:19 2011
+Return-path: <buildd at murphy.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1R7IsV-0001bo-TW
- for logs at buildd.debian.org; Sat, 24 Sep 2011 03:26:12 +0000
-Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
+ (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
+ id 1RBNvf-00073x-8c
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 09:38:19 +0000
+Received: from murphy.debian.org ([70.103.162.31])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
- 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 1R7IsU-0002Oe-SR; Sat, 24 Sep 2011 03:26:11 +0000
-Received: from buildd by biber.debian.org with local (Exim 4.72)
- (envelope-from <buildd at biber.debian.org>)
- id 1R7IsU-0002ak-1g; Sat, 24 Sep 2011 03:26:10 +0000
-Message-Id: <E1R7IsU-0002ak-1g at biber.debian.org>
+ CN=murphy.debian.org, EMAIL=hostmaster at murphy.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
+ id 1RBNve-0001OF-AO
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 09:38:18 +0000
+Received: from buildd by murphy.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at murphy.debian.org>)
+ id 1RBNvc-00013f-OA; Wed, 05 Oct 2011 09:38:16 +0000
+Message-Id: <E1RBNvc-00013f-OA at murphy.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 24 Sep 2011 03:26:09 +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_2.13.2-1 on i386 (dist=sid)
-Key-Id: E4786BDC
+Date: Wed, 5 Oct 2011 09:38:16 +0000
+From: buildd on murphy <buildd at murphy.debian.org>
+To: logs at buildd.debian.org,buildd-admin at murphy.debian.org
+Subject: Log for successful build of bedtools_2.13.3-1 on i386 (dist=sid)
+Key-Id: AC7BC9C1
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (i386) 24 Sep 2011 03:22 ║
+║ bedtools 2.13.3-1 (i386) 05 Oct 2011 09:34 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5773 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [56.5 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [102 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7735 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.5 kB]
-Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.gr.debian.org unstable/contrib Translation-en
+Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Hit http://ftp.us.debian.org sid InRelease
+Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
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 [5783 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7744 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [68.5 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [32.8 kB]
-Get:18 http://incoming.debian.org Packages [561 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.us.debian.org sid/main i386 Packages/DiffIndex
+Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
+Ign http://ftp.us.debian.org sid/contrib TranslationIndex
+Hit http://ftp.us.debian.org sid/main TranslationIndex
+Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:4 http://incoming.debian.org sid/main i386 Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Get:5 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Get:6 http://incoming.debian.org Release [1604 B]
+Get:7 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:8 http://incoming.debian.org sid/main i386 2011-10-05-0826.58.pdiff [5592 B]
+Get:9 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:10 http://incoming.debian.org Sources [36.7 kB]
+Ign http://ftp.us.debian.org sid/contrib Translation-en
+Get:11 http://incoming.debian.org Packages [271 kB]
+Get:12 http://incoming.debian.org sid/main i386 2011-10-05-0826.58.pdiff [5592 B]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.4 MB in 20s (1362 kB/s)
+Fetched 473 kB in 7s (64.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,10 +87,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 1s (412 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 2s (327 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +110,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -124,19 +127,19 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.13-1)
-dash: already installed (0.5.7-1)
+coreutils: already installed (8.13-2)
+dash: already installed (0.5.7-2)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-09-16-1)
+dpkg: already installed (1.16.1)
+e2fsprogs: already installed (1.42~WIP-2011-09-25-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -146,137 +149,49 @@ 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 (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
-debhelper: missing
-Using default version 8.9.7
+debhelper: already installed (8.9.8 >= 8 is satisfied)
quilt: missing
-zlib1g-dev: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Installing positive dependencies: cdbs quilt
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ devscripts procmail graphviz
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 4 not upgraded.
-Need to get 9547 kB of archives.
-After this operation, 28.7 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-3 [37.6 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-4 [223 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.3 [203 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.2-2 [1013 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.08-1 [248 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.08-1 [51.3 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-4 [133 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-4 [882 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.6-1 [1503 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-4 [431 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-4 [2024 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.54-1 [27.7 kB]
-Get:20 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+ cdbs diffstat quilt
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9547 kB in 1s (8258 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10637 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_i386.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.08-1_i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_i386.deb) ...
-Selecting previously deselected package cdbs.
+0 upgraded, 3 newly installed, 0 to remove and 15 not upgraded.
+Need to get 0 B/461 kB of archives.
+After this operation, 1215 kB of additional disk space will be used.
+Selecting previously unselected package cdbs.
+(Reading database ... 20082 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_i386.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_i386.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_i386.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Processing triggers for man-db ...
Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 libc6-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-09-16-1 e2fsprogs_1.42~WIP-2011-09-16-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-09-16-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-11 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-11 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-16-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011j-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.8 autoconf_2.68-1 automake_1:1.11.1-1 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20110502+nmu1 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 dconf-gsettings-backend_0.7.5-3 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool_0.41.1-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libasound2_1.0.24.1-4 libasound2-dev_1.0.24.1-4 libasyncns0_0.8-4 libatk1.0-0_2.2.0-1 libatk1.0-data_2.2.0-1 libattr1_1:2.4.46-3 libavahi-client-dev_0.6.30-5 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common-dev_0.6.30-5 libavahi-common3_0.6.30-5 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 libcaca-dev_0.99.beta17-2.1 libcaca0_0.99.beta17-2.1 libcairo-gobject2_1.10.2-6.1 libcairo2_1.10.2-6.1 libcap2_1:2.22-1 libcomerr2_1.42~WIP-2011-10-01-1 libcroco3_0.6.2-1 libcups2_1.5.0-8 libdatrie1_0.2.4-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdbus-1-dev_1.4.16-1 libdirectfb-1.2-9_1.2.10.0-4.2 libdirectfb-dev_1.2.10.0-4.2 libdirectfb-extra_1.2.10.0-4.2 libdpkg-perl_1.16.1 libdrm2_2.4.26-1 libencode-locale-perl_1.02-2 libexpat1_2.0.1-7 libfile-listing-perl_6.03-1 libflac8_1.2.1-5 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libfreetype6-dev_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgdk-pixbuf2.0-0_2.24.0-1 libgl1-mesa-dev_7.11-6 libgl1-mesa-glx_7.11-6 libglapi-mesa_7.11-6 libglib2.0-0_2.28.6-1 libglib2.0-bin_2.28.6-1 libglib2.0-data_2.28.6-1 libglib2.0-dev_2.28.6-1 libglu1-mesa_7.11-6 libglu1-mesa-dev_7.11-6 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgssapi-krb5-2_1.9.1+dfsg-3 libgtk-3-0_3.0.12-2 libgtk-3-common_3.0.12-2 libgtk2.0-0_2.24.6-1 libgtk2.0-common_2.24.6-1 libhtml-parser-perl_3.68-1+b1 libhtml-tagset-perl_3.20-2 libhtml-tree-perl_4.2-1 libhttp-cookies-perl_6.00-2 libhttp-date-perl_6.00-1 libhttp-message-perl_6.01-1 libhttp-negotiate-perl_6.00-2 libice-dev_2:1.0.7-2 libice6_2:1.0.7-2 libio-socket-ssl-perl_1.44-1 libjasper1_1.900.1-10 libjpeg8_8c-2 libjpeg8-dev_8c-2 libjson0_0.9-1 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblwp-mediatypes-perl_6.01-1 liblwp-protocol-https-perl_6.02-1 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-2 libnet-http-perl_6.01-1 libnet-ssleay-perl_1.41-1 libode-sp-dev_2:0.11.1-4 libode1sp_2:0.11.1-4 libogg0_1.2.2~dfsg-1 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpango1.0-0_1.29.4-1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpixman-1-0_0.22.2-1 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1 libpthread-stubs0-dev_0.3-2.1 libpulse-dev_1.0-3 libpulse-mainloop-glib0_1.0-3 libpulse0_1.0-3 libquadmath0_4.6.1-13 libreadline6_6.2-6 librsvg2-2_2.34.1-2 librsvg2-bin_2.34.1-2 librsvg2-common_2.34.1-2 libsamplerate0_0.1.8-1 libsdl-image1.2_1.2.10-2.1+b1 libsdl-image1.2-dev_1.2.10-2.1+b1 libsdl-ttf2.0-0_2.0.9-1.1 libsdl-ttf2.0-dev_2.0.9-1.1 libsdl1.2-dev_1.2.14-6.4 libsdl1.2debian_1.2.14-6.4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libsm-dev_2:1.2.0-2 libsm6_2:1.2.0-2 libsndfile1_1.0.25-3 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-10-01-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libsysfs-dev_2.1.0+repack-1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libthai-data_0.1.15-2 libthai0_0.1.15-2 libtiff4_3.9.5-2 libtiff4-dev_3.9.5-2 libtiffxx0c2_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libtool_2.4-4 libts-0.0-0_1.0-9 libunistring0_0.9.3-4 liburi-perl_1.59-1 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libvorbis0a_1.3.2-1 libvorbisenc2_1.3.2-1 libwrap0_7.6.q-21 libwww-perl_6.02-1 libwww-robotrules-perl_6.01-1 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libx11-dev_2:1.4.4-2 libx11-xcb1_2:1.4.4-2 libxau-dev_1:1.0.6-3 libxau6_1:1.0.6-3 libxcb-render0_1.7-3 libxcb-shm0_1.7-3 libxcb1_1.7-3 libxcb1-dev_1.7-3 libxcomposite1_1:0.4.3-2 libxcursor1_1:1.1.12-1 libxdamage1_1:1.1.3-2 libxdmcp-dev_1:1.1.0-3 libxdmcp6_1:1.1.0-3 libxext-dev_2:1.3.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxft2_2.2.0-3 libxi6_2:1.4.3-3 libxinerama1_2:1.1.1-3 libxml-parser-perl_2.41-1 libxml2_2.7.8.dfsg-4 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.6-2 libxt-dev_1:1.1.1-2 libxt6_1:1.1.1-2 libxtst6_2:1.2.0-3 libxxf86vm1_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 m4_1.4.16-2 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mesa-common-dev_7.11-6 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 openssl_1.0.0e-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 python_2.7.2-7 python-minimal_2.7.2-7 python2.7_2.7.2-6 python2.7-minimal_2.7.2-6 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 shared-mime-info_0.90-1 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tsconf_1.0-9 ttf-dejavu-core_2.33-2 tzdata_2011k-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 x11-common_1:7.6+9 x11proto-core-dev_7.0.22-1 x11proto-input-dev_2.0.2-2 x11proto-kb-dev_1.0.5-2 x11proto-xext-dev_7.2.0-3 xorg-sgml-doctools_1:1.8-2 xtrans-dev_1.2.6-2 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +202,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -302,30 +217,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -338,21 +253,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3/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_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -370,7 +285,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -430,6 +345,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -599,7 +518,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-i386-gjfied/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -644,57 +563,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.13.2-1_i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0326
+Build finished at 20111005-0938
-bedtools_2.13.2-1_i386.changes:
+bedtools_2.13.3-1_i386.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
+Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- 304f8da62a18c00aa99a23b4e7f8d9ab428c9962 676280 bedtools_2.13.2-1_i386.deb
+ fd9b0d36d582794ca0512453dae58a63b4f79730 676004 bedtools_2.13.3-1_i386.deb
Checksums-Sha256:
- d19c33388aeb98eea1478a8b2770f5961f84fae568e758a14c904737075db846 676280 bedtools_2.13.2-1_i386.deb
+ ac2ca581306581c962ebf435c0c85c5c41aa58a656305a86886b596ac2907a43 676004 bedtools_2.13.3-1_i386.deb
Files:
- c9995414483f78950cfdea99a9147c7c 676280 science optional bedtools_2.13.2-1_i386.deb
+ 7aa3403311f6bf782a997b633c70bb3c 676004 science optional bedtools_2.13.3-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_i386.deb
+bedtools_2.13.3-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 676280 bytes: control archive= 1716 bytes.
- 836 bytes, 18 lines control
+ size 676004 bytes: control archive= 1715 bytes.
+ 834 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4796
- Depends: libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4633
+ Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -708,49 +627,49 @@ bedtools_2.13.2-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 03:25 ./
-drwxr-xr-x root/root 0 2011-09-24 03:25 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 03:25 ./usr/bin/
--rwxr-xr-x root/root 141716 2011-09-24 03:25 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 59628 2011-09-24 03:25 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 96352 2011-09-24 03:25 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227624 2011-09-24 03:25 ./usr/bin/bedToBam
--rwxr-xr-x root/root 113760 2011-09-24 03:25 ./usr/bin/flankBed
--rwxr-xr-x root/root 142268 2011-09-24 03:25 ./usr/bin/sortBed
--rwxr-xr-x root/root 297308 2011-09-24 03:25 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 105076 2011-09-24 03:25 ./usr/bin/linksBed
--rwxr-xr-x root/root 141764 2011-09-24 03:25 ./usr/bin/nucBed
--rwxr-xr-x root/root 347308 2011-09-24 03:25 ./usr/bin/intersectBed
--rwxr-xr-x root/root 112712 2011-09-24 03:25 ./usr/bin/subtractBed
--rwxr-xr-x root/root 285020 2011-09-24 03:25 ./usr/bin/windowBed
--rwxr-xr-x root/root 108924 2011-09-24 03:25 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 272740 2011-09-24 03:25 ./usr/bin/tagBam
--rwxr-xr-x root/root 129156 2011-09-24 03:25 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 280916 2011-09-24 03:25 ./usr/bin/coverageBed
--rwxr-xr-x root/root 106484 2011-09-24 03:25 ./usr/bin/mergeBed
--rwxr-xr-x root/root 102708 2011-09-24 03:25 ./usr/bin/annotateBed
--rwxr-xr-x root/root 88160 2011-09-24 03:25 ./usr/bin/overlap
--rwxr-xr-x root/root 120912 2011-09-24 03:25 ./usr/bin/closestBed
--rwxr-xr-x root/root 176848 2011-09-24 03:25 ./usr/bin/pairToPair
--rwxr-xr-x root/root 104996 2011-09-24 03:25 ./usr/bin/complementBed
--rwxr-xr-x root/root 220336 2011-09-24 03:25 ./usr/bin/bamToBed
--rwxr-xr-x root/root 297320 2011-09-24 03:25 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 366964 2011-09-24 03:25 ./usr/bin/pairToBed
--rwxr-xr-x root/root 120976 2011-09-24 03:25 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 104868 2011-09-24 03:25 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-09-24 03:25 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 03:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 03:25 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-09-24 03:25 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 03:23 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/bin/
+-rwxr-xr-x root/root 121164 2011-10-05 09:38 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 297324 2011-10-05 09:38 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 272744 2011-10-05 09:38 ./usr/bin/tagBam
+-rwxr-xr-x root/root 96356 2011-10-05 09:38 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 142236 2011-10-05 09:38 ./usr/bin/nucBed
+-rwxr-xr-x root/root 143260 2011-10-05 09:38 ./usr/bin/sortBed
+-rwxr-xr-x root/root 285024 2011-10-05 09:38 ./usr/bin/windowBed
+-rwxr-xr-x root/root 120916 2011-10-05 09:38 ./usr/bin/closestBed
+-rwxr-xr-x root/root 280920 2011-10-05 09:38 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 109276 2011-10-05 09:38 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 103124 2011-10-05 09:38 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 142064 2011-10-05 09:38 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 129356 2011-10-05 09:38 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 366968 2011-10-05 09:38 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 106836 2011-10-05 09:38 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 105244 2011-10-05 09:38 ./usr/bin/complementBed
+-rwxr-xr-x root/root 297312 2011-10-05 09:38 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 88164 2011-10-05 09:38 ./usr/bin/overlap
+-rwxr-xr-x root/root 178284 2011-10-05 09:38 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 105332 2011-10-05 09:38 ./usr/bin/linksBed
+-rwxr-xr-x root/root 112848 2011-10-05 09:38 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 227628 2011-10-05 09:38 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 59648 2011-10-05 09:38 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 223440 2011-10-05 09:38 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 114232 2011-10-05 09:38 ./usr/bin/flankBed
+-rwxr-xr-x root/root 350572 2011-10-05 09:38 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105116 2011-10-05 09:38 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 09:34 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -764,26 +683,42 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-e5619fe0-6e60-42dd-bf35-69551e41b189/build/buildd-bedtools_2.13.2-1-i386-gjfied
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-i386-sbuild-20013937-43eb-4fc3-ac1e-54fde9be699d/build/buildd-bedtools_2.13.3-1-i386-PCGCnt
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ cdbs* diffstat* quilt*
+0 upgraded, 0 newly installed, 3 to remove and 15 not upgraded.
+After this operation, 1215 kB disk space will be freed.
+(Reading database ... 20217 files and directories currently installed.)
+Removing cdbs ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 93820
-Build-Time: 168
+Build-Space: 94292
+Build-Time: 204
Distribution: sid
-Install-Time: 39
-Job: bedtools_2.13.2-1
+Install-Time: 7
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 241
-Source-Version: 2.13.2-1
-Space: 93820
+Package-Time: 227
+Source-Version: 2.13.3-1
+Space: 94292
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0326
-Build needed 00:04:01, 93820k disc space
-Signature with key 'E4786BDC' requested:
+Finished at 20111005-0938
+Build needed 00:03:47, 94292k disc space
+Signature with key 'AC7BC9C1' requested:
diff --git a/ia64.log b/ia64.log
index d6c683f..a1374cd 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,28 +1,28 @@
-From buildd at alkman.debian.org Sat Sep 24 04:58:16 2011
+From buildd at alkman.debian.org Wed Oct 05 09:54:29 2011
Return-path: <buildd at alkman.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 alkman.debian.org>)
- id 1R7KJb-0005uf-RZ
- for logs at buildd.debian.org; Sat, 24 Sep 2011 04:58:16 +0000
+ id 1RBOBJ-0001t9-G3
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 09:54:29 +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=alkman.debian.org, EMAIL=hostmaster at alkman.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 alkman.debian.org>)
- id 1R7KJa-00019G-0v
- for logs at buildd.debian.org; Sat, 24 Sep 2011 04:58:14 +0000
+ id 1RBOBI-0002Tr-6m
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 09:54:28 +0000
Received: from buildd by alkman.debian.org with local (Exim 4.72)
(envelope-from <buildd at alkman.debian.org>)
- id 1R7KJX-00043i-K7; Sat, 24 Sep 2011 04:58:11 +0000
-Date: Sat, 24 Sep 2011 04:58:11 +0000
-Message-Id: <E1R7KJX-00043i-K7 at alkman.debian.org>
+ id 1RBOBF-0007bB-Vu; Wed, 05 Oct 2011 09:54:26 +0000
+Date: Wed, 05 Oct 2011 09:54:25 +0000
+Message-Id: <E1RBOBF-0007bB-Vu 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_2.13.2-1 on ia64 (dist=sid)
+Subject: Log for successful build of bedtools_2.13.3-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,38 +30,38 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (ia64) 24 Sep 2011 04:46 ║
+║ bedtools 2.13.3-1 (ia64) 05 Oct 2011 09:42 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: ia64
-Get:1 http://spohr.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://spohr.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://incoming.debian.org Release [1604 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5783 kB]
-Get:6 http://spohr.debian.org unstable/main Sources [5783 kB]
-Get:7 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:8 http://incoming.debian.org unstable/non-free Sources [102 kB]
-Get:9 http://incoming.debian.org unstable/main ia64 Packages [7461 kB]
-Get:10 http://incoming.debian.org unstable/contrib ia64 Packages [55.5 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:11 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:12 http://incoming.debian.org Sources [33.1 kB]
-Get:13 http://incoming.debian.org Packages [576 kB]
-Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Get:14 http://spohr.debian.org unstable/contrib Sources [56.5 kB]
-Get:15 http://spohr.debian.org unstable/non-free Sources [102 kB]
-Get:16 http://spohr.debian.org unstable/main ia64 Packages [7461 kB]
-Get:17 http://spohr.debian.org unstable/contrib ia64 Packages [55.5 kB]
+Get:3 http://spohr.debian.org unstable/main Sources [5816 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [5816 kB]
+Get:6 http://spohr.debian.org unstable/contrib Sources [57.1 kB]
+Get:7 http://spohr.debian.org unstable/non-free Sources [103 kB]
+Get:8 http://spohr.debian.org unstable/main ia64 Packages [7490 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [55.5 kB]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:18 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
+Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
Ign http://spohr.debian.org unstable/contrib Translation-en
-Fetched 27.8 MB in 25s (1108 kB/s)
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [7490 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [55.5 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [36.7 kB]
+Get:18 http://incoming.debian.org Packages [271 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 27.6 MB in 23s (1200 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,10 +83,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 0s (675 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 0s (677 kB/s)
Download complete and in download only mode
Check arch
@@ -100,7 +100,7 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
@@ -109,7 +109,7 @@ 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 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -117,7 +117,7 @@ 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 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -129,18 +129,18 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.3)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
+dpkg: already installed (1.16.1)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -150,14 +150,14 @@ tar: already installed (1.26-2)
bsdutils: already installed (1:2.19.1-5)
mount: already installed (2.19.1-5)
util-linux: already installed (2.19.1-5)
-libc6.1-dev: already installed (2.13-19)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+libc6.1-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.7
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -182,9 +182,9 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 11 not upgraded.
Need to get 11.4 MB of archives.
-After this operation, 43.2 MB of additional disk space will be used.
+After this operation, 42.4 MB of additional disk space will be used.
Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-3 [47.8 kB]
Get:2 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
Get:3 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
@@ -202,54 +202,54 @@ Get:14 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-4
Get:15 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-4 [2441 kB]
Get:16 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:17 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9 kB]
Get:20 http://spohr.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.4 MB in 6s (1768 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10607 files and directories currently installed.)
+Fetched 11.4 MB in 0s (14.4 MB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10538 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_ia64.deb) ...
-Selecting previously deselected package libpcre3.
+Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
-Selecting previously deselected package bsdmainutils.
+Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_ia64.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_ia64.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_ia64.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.08-1_ia64.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_ia64.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_ia64.deb) ...
-Selecting previously deselected package cdbs.
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_ia64.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_ia64.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_ia64.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_ia64.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
@@ -272,7 +272,7 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -283,11 +283,11 @@ 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 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6.1-dev_2.13-19 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-19 libc-dev-bin_2.13-19 libc6.1_2.13-19 libc6.1-dev_2.13-19 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-9 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-19 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6.1_2.13-21 libc6.1-dev_2.13-21 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-5 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -298,12 +298,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -313,30 +313,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS =
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -349,21 +349,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3/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_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -381,7 +381,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -441,6 +441,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -610,7 +614,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -656,22 +660,22 @@ dpkg-shlibdeps: warning: dependency on libm.so.6.1 could be avoided if "debian/b
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bedtools_2.13.2-1_ia64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0458
+Build finished at 20111005-0954
-bedtools_2.13.2-1_ia64.changes:
+bedtools_2.13.3-1_ia64.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
@@ -679,34 +683,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- 60341ce50ab66cbb47de7a44fed7dfd4e55d0bff 744034 bedtools_2.13.2-1_ia64.deb
+ dd23cfe6292d224600f7403762e8675aa10914d2 745358 bedtools_2.13.3-1_ia64.deb
Checksums-Sha256:
- 70d9c7fc8ab9a57c23984a31bffab2c3592fb8a99eef102011830d762b9c965e 744034 bedtools_2.13.2-1_ia64.deb
+ 359ac4198e69fb333ed8ecbc2a21f787a7a68fd4abd08d6e8e45007a0670f8e9 745358 bedtools_2.13.3-1_ia64.deb
Files:
- ff9d5d42aa8e89520c8637433db4c929 744034 science optional bedtools_2.13.2-1_ia64.deb
+ c47d2b2ce55524bafe7af5bcdee2a2f9 745358 science optional bedtools_2.13.3-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_ia64.deb
+bedtools_2.13.3-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 744034 bytes: control archive= 1725 bytes.
- 849 bytes, 18 lines control
+ size 745358 bytes: control archive= 1729 bytes.
+ 850 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 10272
- Depends: libc6.1 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
+ Installed-Size: 9504
+ Depends: libc6.1 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -720,49 +724,49 @@ bedtools_2.13.2-1_ia64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 04:57 ./
-drwxr-xr-x root/root 0 2011-09-24 04:57 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 04:57 ./usr/bin/
--rwxr-xr-x root/root 216544 2011-09-24 04:57 ./usr/bin/annotateBed
--rwxr-xr-x root/root 456592 2011-09-24 04:57 ./usr/bin/bamToBed
--rwxr-xr-x root/root 199440 2011-09-24 04:57 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 471744 2011-09-24 04:57 ./usr/bin/bedToBam
--rwxr-xr-x root/root 246744 2011-09-24 04:57 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 248720 2011-09-24 04:57 ./usr/bin/closestBed
--rwxr-xr-x root/root 219816 2011-09-24 04:57 ./usr/bin/complementBed
--rwxr-xr-x root/root 573176 2011-09-24 04:57 ./usr/bin/coverageBed
--rwxr-xr-x root/root 293648 2011-09-24 04:57 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 234008 2011-09-24 04:57 ./usr/bin/flankBed
--rwxr-xr-x root/root 605640 2011-09-24 04:57 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 725680 2011-09-24 04:57 ./usr/bin/intersectBed
--rwxr-xr-x root/root 220280 2011-09-24 04:57 ./usr/bin/linksBed
--rwxr-xr-x root/root 226280 2011-09-24 04:57 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 221000 2011-09-24 04:57 ./usr/bin/mergeBed
--rwxr-xr-x root/root 620256 2011-09-24 04:57 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 297448 2011-09-24 04:57 ./usr/bin/nucBed
--rwxr-xr-x root/root 178672 2011-09-24 04:57 ./usr/bin/overlap
--rwxr-xr-x root/root 770432 2011-09-24 04:57 ./usr/bin/pairToBed
--rwxr-xr-x root/root 377984 2011-09-24 04:57 ./usr/bin/pairToPair
--rwxr-xr-x root/root 270504 2011-09-24 04:57 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 216952 2011-09-24 04:57 ./usr/bin/slopBed
--rwxr-xr-x root/root 305632 2011-09-24 04:57 ./usr/bin/sortBed
--rwxr-xr-x root/root 234248 2011-09-24 04:57 ./usr/bin/subtractBed
--rwxr-xr-x root/root 564800 2011-09-24 04:57 ./usr/bin/tagBam
--rwxr-xr-x root/root 120416 2011-09-24 04:57 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 586936 2011-09-24 04:57 ./usr/bin/windowBed
-drwxr-xr-x root/root 0 2011-09-24 04:57 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 04:57 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 04:48 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-09-24 04:57 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 04:57 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-10-05 09:53 ./
+drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/bin/
+-rwxr-xr-x root/root 216544 2011-10-05 09:53 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 456976 2011-10-05 09:53 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 199440 2011-10-05 09:53 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 471856 2011-10-05 09:53 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 246744 2011-10-05 09:53 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 249488 2011-10-05 09:53 ./usr/bin/closestBed
+-rwxr-xr-x root/root 219880 2011-10-05 09:53 ./usr/bin/complementBed
+-rwxr-xr-x root/root 574072 2011-10-05 09:53 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 293648 2011-10-05 09:53 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 234456 2011-10-05 09:53 ./usr/bin/flankBed
+-rwxr-xr-x root/root 605816 2011-10-05 09:53 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 727904 2011-10-05 09:53 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 220280 2011-10-05 09:53 ./usr/bin/linksBed
+-rwxr-xr-x root/root 226280 2011-10-05 09:53 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 221064 2011-10-05 09:53 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 620624 2011-10-05 09:53 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 297768 2011-10-05 09:53 ./usr/bin/nucBed
+-rwxr-xr-x root/root 178672 2011-10-05 09:53 ./usr/bin/overlap
+-rwxr-xr-x root/root 767632 2011-10-05 09:53 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 378032 2011-10-05 09:53 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 270696 2011-10-05 09:53 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 217208 2011-10-05 09:53 ./usr/bin/slopBed
+-rwxr-xr-x root/root 305760 2011-10-05 09:53 ./usr/bin/sortBed
+-rwxr-xr-x root/root 234968 2011-10-05 09:53 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 564992 2011-10-05 09:53 ./usr/bin/tagBam
+-rwxr-xr-x root/root 120416 2011-10-05 09:53 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 587368 2011-10-05 09:53 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 09:44 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -776,7 +780,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-cef8bc2b-9c7d-4a3d-96ee-8d62ac3d15a1/build/buildd-bedtools_2.13.2-1-ia64-TgnPuD
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-4dfe5cf8-691a-4d39-abfe-e242ff2b1e0c/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -784,19 +788,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 161388
-Build-Time: 580
+Build-Space: 162092
+Build-Time: 585
Distribution: sid
-Install-Time: 69
-Job: bedtools_2.13.2-1
+Install-Time: 65
+Job: bedtools_2.13.3-1
Package: bedtools
Package-Time: 700
-Source-Version: 2.13.2-1
-Space: 161388
+Source-Version: 2.13.3-1
+Space: 162092
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0458
-Build needed 00:11:40, 161388k disc space
+Finished at 20111005-0954
+Build needed 00:11:40, 162092k disc space
Signature with key 'C6591CE9' requested:
diff --git a/info b/info
index 583aa9a..bf985a9 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-kfreebsd-amd64~1316834703~sid~successful
-i386~1316834772~sid~successful
-powerpc~1316834926~sid~successful
-s390~1316835803~sid~successful
-kfreebsd-i386~1316836045~sid~successful
-armel~1316837171~sid~successful
-mipsel~1316838555~sid~successful
-ia64~1316840296~sid~successful
-sparc~1316840547~sid~successful
-hurd-i386~1316846333~sid~successful
-mips~1316969457~sid~successful
+i386~1317807504~sid~successful
+powerpc~1317807719~sid~successful
+kfreebsd-amd64~1317807732~sid~successful
+kfreebsd-i386~1317807765~sid~successful
+ia64~1317808470~sid~successful
+armel~1317808708~sid~successful
+mipsel~1317809171~sid~successful
+mips~1317809615~sid~successful
+sparc~1317809672~sid~successful
+s390~1317811073~sid~successful
+hurd-i386~1317816700~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index e1c2e73..8f40470 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,81 +1,83 @@
-From buildd at fano.debian.org Sat Sep 24 03:25:03 2011
-Return-path: <buildd at fano.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at fasch.debian.org Wed Oct 05 09:42:04 2011
+Return-path: <buildd at fasch.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 fano.debian.org>)
- id 1R7IrO-0001Pz-Rb
- for logs at buildd.debian.org; Sat, 24 Sep 2011 03:25:02 +0000
-Received: from fano.debian.org ([206.12.19.110])
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1RBNzI-0007ii-3e
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 09:42:04 +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 kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1R7IrN-0002DY-CF; Sat, 24 Sep 2011 03:25:01 +0000
-Received: from buildd by fano.debian.org with local (Exim 4.72)
- (envelope-from <buildd at fano.debian.org>)
- id 1R7IrL-0007RP-1u; Sat, 24 Sep 2011 03:24:59 +0000
-Message-Id: <E1R7IrL-0007RP-1u at fano.debian.org>
+ CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1RBNzG-0001as-JR; Wed, 05 Oct 2011 09:42:02 +0000
+Received: from buildd by fasch.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fasch.debian.org>)
+ id 1RBNzF-0000nq-Hx; Wed, 05 Oct 2011 09:42:01 +0000
+Message-Id: <E1RBNzF-0000nq-Hx 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: Sat, 24 Sep 2011 03:24:58 +0000
-From: buildd on fano <buildd at fano.debian.org>
+Date: Wed, 5 Oct 2011 09:42:01 +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_2.13.2-1 on kfreebsd-amd64
+Subject: Log for successful build of bedtools_2.13.3-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 911EAB69
+Key-Id: 56BAE008
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 2.13.2-1 (kfreebsd-amd64) 24 Sep 2011 03:20 ║
+║ bedtools 2.13.3-1 (kfreebsd-amd64) 05 Oct 2011 09:36 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: kfreebsd-amd64
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
Get:1 http://incoming.debian.org sid InRelease [146 kB]
+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://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
+Ign http://ftp.gr.debian.org sid/contrib Translation-en
+Ign http://ftp.gr.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org InRelease
Get:2 http://incoming.debian.org Release.gpg [836 B]
Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-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
-Get:4 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Get:4 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:5 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Get:6 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex [2023 B]
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:5 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Get:7 http://incoming.debian.org sid/main TranslationIndex [2045 B]
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
-Get:6 http://incoming.debian.org Release [1604 B]
-Get:7 http://incoming.debian.org sid/main 2011-09-24-0213.05.pdiff [16.1 kB]
-Get:8 http://incoming.debian.org sid/main kfreebsd-amd64 2011-09-24-0213.05.pdiff [27.8 kB]
-Get:9 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [87.2 kB]
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Get:10 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:11 http://incoming.debian.org sid/main 2011-09-24-0213.05.pdiff [16.1 kB]
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages
-Get:12 http://incoming.debian.org sid/main kfreebsd-amd64 2011-09-24-0213.05.pdiff [27.8 kB]
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Get:13 http://incoming.debian.org Sources [32.8 kB]
-Get:14 http://incoming.debian.org Packages [561 kB]
+Get:8 http://incoming.debian.org Release [1604 B]
+Get:9 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:10 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Get:11 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-05-0826.58.pdiff [3796 B]
+Get:12 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:13 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [87.7 kB]
+Get:14 http://incoming.debian.org Sources [36.7 kB]
+Get:15 http://incoming.debian.org Packages [271 kB]
+Get:16 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Get:17 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-05-0826.58.pdiff [3796 B]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 882 kB in 7s (115 kB/s)
+Fetched 563 kB in 5s (102 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -97,10 +99,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 1s (549 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 2s (230 kB/s)
Download complete and in download only mode
Check arch
@@ -114,18 +116,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.17-1)
+fakeroot: already installed (1.18.1-1)
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 4 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 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -137,20 +139,20 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.3)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
+dpkg: already installed (1.16.1)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.2+ds2-5)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -159,13 +161,13 @@ tar: already installed (1.25-3)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.7
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -175,8 +177,8 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
procmail graphviz
@@ -185,55 +187,52 @@ Recommended packages:
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 20 newly installed, 0 to remove and 4 not upgraded.
-Need to get 0 B/9575 kB of archives.
-After this operation, 27.0 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 12212 files and directories currently installed.)
+0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/9350 kB of archives.
+After this operation, 25.8 MB of additional disk space will be used.
+Selecting previously unselected package libpipeline1.
+(Reading database ... 11972 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_kfreebsd-amd64.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../file_5.08-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-amd64.deb) ...
-Selecting previously deselected package cdbs.
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-amd64.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-amd64.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+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 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
Setting up groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
@@ -250,7 +249,7 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -258,11 +257,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.17-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-11 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-11 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011j-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111004-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libncursesw5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-13 libreadline6_6.2-6 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -273,12 +272,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -288,30 +287,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -324,21 +323,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3/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_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -356,7 +355,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -416,6 +415,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -585,7 +588,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -630,57 +633,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.13.2-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0324
+Build finished at 20111005-0941
-bedtools_2.13.2-1_kfreebsd-amd64.changes:
+bedtools_2.13.3-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.13.2-1
+Version: 2.13.3-1
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 (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- 50435c77bd6741c69eb8a5970314b1a9826c10f3 662608 bedtools_2.13.2-1_kfreebsd-amd64.deb
+ a5a804611be9905baa3aabfca216e3a04af2e3d3 667732 bedtools_2.13.3-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 88673de5bce8a407d46ff9c7c5431dc6830d97a4950f968b09cc9be2eef8ac4e 662608 bedtools_2.13.2-1_kfreebsd-amd64.deb
+ cd5c5e1cc10b11382c2a12636d9159aa8f765229cde743477f4893102d8de153 667732 bedtools_2.13.3-1_kfreebsd-amd64.deb
Files:
- 7b19d82dba03787d4568f67d83eeaae5 662608 science optional bedtools_2.13.2-1_kfreebsd-amd64.deb
+ bec7217b9b6137d5059c57125771f27f 667732 science optional bedtools_2.13.3-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_kfreebsd-amd64.deb
+bedtools_2.13.3-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 662608 bytes: control archive= 1724 bytes.
+ size 667732 bytes: control archive= 1723 bytes.
846 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4876
- Depends: libc0.1 (>= 2.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4660
+ Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -694,49 +697,49 @@ bedtools_2.13.2-1_kfreebsd-amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 03:21 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./usr/bin/
--rwxr-xr-x root/root 109992 2011-09-24 03:24 ./usr/bin/annotateBed
--rwxr-xr-x root/root 214848 2011-09-24 03:24 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101848 2011-09-24 03:24 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227560 2011-09-24 03:24 ./usr/bin/bedToBam
--rwxr-xr-x root/root 126472 2011-09-24 03:24 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126392 2011-09-24 03:24 ./usr/bin/closestBed
--rwxr-xr-x root/root 114160 2011-09-24 03:24 ./usr/bin/complementBed
--rwxr-xr-x root/root 272776 2011-09-24 03:24 ./usr/bin/coverageBed
--rwxr-xr-x root/root 147104 2011-09-24 03:24 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 118464 2011-09-24 03:24 ./usr/bin/flankBed
--rwxr-xr-x root/root 290784 2011-09-24 03:24 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 344552 2011-09-24 03:24 ./usr/bin/intersectBed
--rwxr-xr-x root/root 110032 2011-09-24 03:24 ./usr/bin/linksBed
--rwxr-xr-x root/root 115240 2011-09-24 03:24 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 114104 2011-09-24 03:24 ./usr/bin/mergeBed
--rwxr-xr-x root/root 291976 2011-09-24 03:24 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 147128 2011-09-24 03:24 ./usr/bin/nucBed
--rwxr-xr-x root/root 93656 2011-09-24 03:24 ./usr/bin/overlap
--rwxr-xr-x root/root 356344 2011-09-24 03:24 ./usr/bin/pairToBed
--rwxr-xr-x root/root 179688 2011-09-24 03:24 ./usr/bin/pairToPair
--rwxr-xr-x root/root 134928 2011-09-24 03:24 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110048 2011-09-24 03:24 ./usr/bin/slopBed
--rwxr-xr-x root/root 148216 2011-09-24 03:24 ./usr/bin/sortBed
--rwxr-xr-x root/root 266856 2011-09-24 03:24 ./usr/bin/tagBam
--rwxr-xr-x root/root 118184 2011-09-24 03:24 ./usr/bin/subtractBed
--rwxr-xr-x root/root 65024 2011-09-24 03:24 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 278472 2011-09-24 03:24 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-10-05 09:40 ./
+drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 09:37 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/bin/
+-rwxr-xr-x root/root 110000 2011-10-05 09:40 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 215992 2011-10-05 09:40 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101856 2011-10-05 09:40 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 229232 2011-10-05 09:40 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 126480 2011-10-05 09:40 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 126400 2011-10-05 09:40 ./usr/bin/closestBed
+-rwxr-xr-x root/root 114168 2011-10-05 09:40 ./usr/bin/complementBed
+-rwxr-xr-x root/root 274440 2011-10-05 09:40 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 147112 2011-10-05 09:40 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 119160 2011-10-05 09:40 ./usr/bin/flankBed
+-rwxr-xr-x root/root 291216 2011-10-05 09:40 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 346336 2011-10-05 09:40 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 110096 2011-10-05 09:40 ./usr/bin/linksBed
+-rwxr-xr-x root/root 118328 2011-10-05 09:40 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 114112 2011-10-05 09:40 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 294864 2011-10-05 09:40 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 147136 2011-10-05 09:40 ./usr/bin/nucBed
+-rwxr-xr-x root/root 93664 2011-10-05 09:40 ./usr/bin/overlap
+-rwxr-xr-x root/root 357216 2011-10-05 09:40 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 180072 2011-10-05 09:40 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 135520 2011-10-05 09:40 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 110176 2011-10-05 09:40 ./usr/bin/slopBed
+-rwxr-xr-x root/root 150952 2011-10-05 09:40 ./usr/bin/sortBed
+-rwxr-xr-x root/root 268040 2011-10-05 09:40 ./usr/bin/tagBam
+-rwxr-xr-x root/root 118192 2011-10-05 09:40 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 65032 2011-10-05 09:40 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 279240 2011-10-05 09:40 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -750,21 +753,21 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1316834455-26488/build/buildd-bedtools_2.13.2-1-kfreebsd-amd64-o7Kzsl
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1317807374-99849/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 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* libglib2.0-0* libmagic1* libpcre3*
+ html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 4 not upgraded.
-After this operation, 27.0 MB disk space will be freed.
-(Reading database ... 13574 files and directories currently installed.)
+0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
+After this operation, 25.8 MB disk space will be freed.
+(Reading database ... 13328 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -787,8 +790,6 @@ Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
@@ -802,18 +803,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 135456
-Build-Time: 167
+Build-Space: 136132
+Build-Time: 197
Distribution: sid
-Install-Time: 37
-Job: bedtools_2.13.2-1
+Install-Time: 79
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 223
-Source-Version: 2.13.2-1
-Space: 135456
+Package-Time: 295
+Source-Version: 2.13.3-1
+Space: 136132
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0324
-Build needed 00:03:43, 135456k disc space
-Signature with key '911EAB69' requested:
+Finished at 20111005-0941
+Build needed 00:04:55, 136132k disc space
+Signature with key '56BAE008' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 0a9886a..232d49c 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,30 +1,30 @@
-From buildd at field.debian.org Sat Sep 24 03:47:24 2011
+From buildd at field.debian.org Wed Oct 05 09:42:44 2011
Return-path: <buildd at field.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1R7JD2-0004I6-KE
- for logs at buildd.debian.org; Sat, 24 Sep 2011 03:47:24 +0000
+ id 1RBNzw-0007kN-Mv
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 09:42:44 +0000
Received: from field.debian.org ([194.177.211.210])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ 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 1R7JD1-0003D6-OO; Sat, 24 Sep 2011 03:47:23 +0000
+ id 1RBNzw-0001b7-0O; Wed, 05 Oct 2011 09:42:44 +0000
Received: from buildd by field.debian.org with local (Exim 4.72)
(envelope-from <buildd at field.debian.org>)
- id 1R7JD0-0004D1-Vi; Sat, 24 Sep 2011 03:47:23 +0000
-Message-Id: <E1R7JD0-0004D1-Vi at field.debian.org>
+ id 1RBNzv-000HGc-5s; Wed, 05 Oct 2011 09:42:43 +0000
+Message-Id: <E1RBNzv-000HGc-5s at field.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 24 Sep 2011 03:47:22 +0000
+Date: Wed, 5 Oct 2011 09:42:42 +0000
From: buildd on field <buildd at field.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.13.2-1 on kfreebsd-i386
+Subject: Log for successful build of bedtools_2.13.3-1 on kfreebsd-i386
(dist=sid)
Key-Id: 6B8016EE
Delivered-To: logs at buildd.debian.org
@@ -32,17 +32,16 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (kfreebsd-i386) 24 Sep 2011 03:41 ║
+║ bedtools 2.13.3-1 (kfreebsd-i386) 05 Oct 2011 09:37 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: kfreebsd-i386
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 sid InRelease [146 kB]
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
@@ -51,25 +50,42 @@ 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]
+Get:2 http://ftp.gr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
+Get:3 http://ftp.gr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
+Get:4 http://ftp.gr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
+Get:5 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-05-0214.30.pdiff [14.9 kB]
+Ign http://incoming.debian.org InRelease
+Get:6 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-05-0214.30.pdiff [54 B]
Ign http://ftp.gr.debian.org sid/contrib Translation-en
Ign http://ftp.gr.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Get:9 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:10 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Get:11 http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex [2023 B]
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
+Get:12 http://incoming.debian.org sid/main TranslationIndex [2045 B]
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://incoming.debian.org Sources
-Get:3 http://incoming.debian.org Packages [562 kB]
+Get:13 http://ftp.gr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
+Get:14 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-05-0214.30.pdiff [14.9 kB]
+Get:15 http://incoming.debian.org Release [1604 B]
+Get:16 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:17 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Get:18 http://incoming.debian.org sid/main kfreebsd-i386 2011-10-05-0826.58.pdiff [2824 B]
+Get:19 http://incoming.debian.org sid/non-free kfreebsd-i386 2011-10-05-0826.58.pdiff [1227 B]
+Get:20 http://incoming.debian.org Sources [36.7 kB]
+Get:21 http://incoming.debian.org Packages [271 kB]
+Get:22 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-05-0214.30.pdiff [54 B]
+Get:23 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 564 kB in 5s (98.9 kB/s)
+Get:24 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Get:25 http://incoming.debian.org sid/main kfreebsd-i386 2011-10-05-0826.58.pdiff [2824 B]
+Get:26 http://incoming.debian.org sid/non-free kfreebsd-i386 2011-10-05-0826.58.pdiff [1227 B]
+Fetched 504 kB in 8s (58.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -91,10 +107,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 2s (307 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 2s (258 kB/s)
Download complete and in download only mode
Check arch
@@ -108,18 +124,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.17-1)
+fakeroot: already installed (1.18.1-1)
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 6 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 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -131,20 +147,20 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.3)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
+dpkg: already installed (1.16.1)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.2+ds2-5)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -153,13 +169,13 @@ tar: already installed (1.25-3)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.7
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -182,47 +198,47 @@ The following NEW packages will be installed:
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/9047 kB of archives.
-After this operation, 25.6 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 12173 files and directories currently installed.)
+After this operation, 24.9 MB of additional disk space will be used.
+Selecting previously unselected package libpipeline1.
+(Reading database ... 12056 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-i386.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-i386.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../file_5.08-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package cdbs.
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+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 (1.2.0-3) ...
Setting up groff-base (1.21-6) ...
@@ -241,7 +257,7 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -249,11 +265,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 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_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.17-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-11 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-11 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-19 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111004-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libncursesw5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-13 libreadline6_6.2-6 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -264,12 +280,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -279,30 +295,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -315,21 +331,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3/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_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -347,7 +363,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -407,6 +423,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -576,7 +596,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -621,22 +641,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.13.2-1_kfreebsd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0346
+Build finished at 20111005-0941
-bedtools_2.13.2-1_kfreebsd-i386.changes:
+bedtools_2.13.3-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
@@ -644,34 +664,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- fb335e9c25af16780ffdf1ff276063bc0b7d648d 674716 bedtools_2.13.2-1_kfreebsd-i386.deb
+ e1571e7aee77c783b08e6e12e752b1bbb7a57d1e 676492 bedtools_2.13.3-1_kfreebsd-i386.deb
Checksums-Sha256:
- 8832ba4eefb27a6e2fafa7c1f1a18c4f6240e3669d6a1f1ca7fdfc4847fcda52 674716 bedtools_2.13.2-1_kfreebsd-i386.deb
+ 73cb86bd852b2932c943e78ec3c1c0fa33a245b4243db588c8adf388b78ae723 676492 bedtools_2.13.3-1_kfreebsd-i386.deb
Files:
- 54036367d246fa4e31933aef93a72954 674716 science optional bedtools_2.13.2-1_kfreebsd-i386.deb
+ 173d79bec66e0f6402792eac39a8fec2 676492 science optional bedtools_2.13.3-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_kfreebsd-i386.deb
+bedtools_2.13.3-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 674716 bytes: control archive= 1728 bytes.
+ size 676492 bytes: control archive= 1724 bytes.
845 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4872
- Depends: libc0.1 (>= 2.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4602
+ Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -685,49 +705,49 @@ bedtools_2.13.2-1_kfreebsd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 03:46 ./
-drwxr-xr-x root/root 0 2011-09-24 03:46 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 03:46 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 03:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 03:46 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-24 03:46 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-09-24 03:46 ./usr/bin/
--rwxr-xr-x root/root 102676 2011-09-24 03:46 ./usr/bin/annotateBed
--rwxr-xr-x root/root 220316 2011-09-24 03:46 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96352 2011-09-24 03:46 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227624 2011-09-24 03:46 ./usr/bin/bedToBam
--rwxr-xr-x root/root 120952 2011-09-24 03:46 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120912 2011-09-24 03:46 ./usr/bin/closestBed
--rwxr-xr-x root/root 104964 2011-09-24 03:46 ./usr/bin/complementBed
--rwxr-xr-x root/root 280916 2011-09-24 03:46 ./usr/bin/coverageBed
--rwxr-xr-x root/root 141748 2011-09-24 03:46 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 113728 2011-09-24 03:46 ./usr/bin/flankBed
--rwxr-xr-x root/root 297320 2011-09-24 03:46 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 347288 2011-09-24 03:46 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105044 2011-09-24 03:46 ./usr/bin/linksBed
--rwxr-xr-x root/root 108860 2011-09-24 03:46 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 106420 2011-09-24 03:46 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297308 2011-09-24 03:46 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 141796 2011-09-24 03:46 ./usr/bin/nucBed
--rwxr-xr-x root/root 88160 2011-09-24 03:46 ./usr/bin/overlap
--rwxr-xr-x root/root 366964 2011-09-24 03:46 ./usr/bin/pairToBed
--rwxr-xr-x root/root 176816 2011-09-24 03:46 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129156 2011-09-24 03:46 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 104836 2011-09-24 03:46 ./usr/bin/slopBed
--rwxr-xr-x root/root 142236 2011-09-24 03:46 ./usr/bin/sortBed
--rwxr-xr-x root/root 272740 2011-09-24 03:46 ./usr/bin/tagBam
--rwxr-xr-x root/root 112712 2011-09-24 03:46 ./usr/bin/subtractBed
--rwxr-xr-x root/root 59596 2011-09-24 03:46 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285020 2011-09-24 03:46 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/bin/
+-rwxr-xr-x root/root 103092 2011-10-05 09:41 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223440 2011-10-05 09:41 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96356 2011-10-05 09:41 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227628 2011-10-05 09:41 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121132 2011-10-05 09:41 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 120916 2011-10-05 09:41 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105212 2011-10-05 09:41 ./usr/bin/complementBed
+-rwxr-xr-x root/root 280920 2011-10-05 09:41 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142096 2011-10-05 09:41 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 114200 2011-10-05 09:41 ./usr/bin/flankBed
+-rwxr-xr-x root/root 297324 2011-10-05 09:41 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350572 2011-10-05 09:41 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105300 2011-10-05 09:41 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109244 2011-10-05 09:41 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 106804 2011-10-05 09:41 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297312 2011-10-05 09:41 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 142268 2011-10-05 09:41 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88164 2011-10-05 09:41 ./usr/bin/overlap
+-rwxr-xr-x root/root 366968 2011-10-05 09:41 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178284 2011-10-05 09:41 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129324 2011-10-05 09:41 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 105084 2011-10-05 09:41 ./usr/bin/slopBed
+-rwxr-xr-x root/root 143228 2011-10-05 09:41 ./usr/bin/sortBed
+-rwxr-xr-x root/root 272744 2011-10-05 09:41 ./usr/bin/tagBam
+-rwxr-xr-x root/root 112816 2011-10-05 09:41 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 59616 2011-10-05 09:41 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285024 2011-10-05 09:41 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -741,11 +761,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1316835693-12896/build/buildd-bedtools_2.13.2-1-kfreebsd-i386-9OGN7M
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1317807422-63202/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -753,9 +773,9 @@ The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 6 not upgraded.
-After this operation, 25.6 MB disk space will be freed.
-(Reading database ... 13522 files and directories currently installed.)
+0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
+After this operation, 24.9 MB disk space will be freed.
+(Reading database ... 13412 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -791,18 +811,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 94954
-Build-Time: 189
+Build-Space: 95358
+Build-Time: 193
Distribution: sid
-Install-Time: 80
-Job: bedtools_2.13.2-1
+Install-Time: 77
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 294
-Source-Version: 2.13.2-1
-Space: 94954
+Package-Time: 290
+Source-Version: 2.13.3-1
+Space: 95358
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0346
-Build needed 00:04:54, 94954k disc space
+Finished at 20111005-0941
+Build needed 00:04:50, 95358k disc space
Signature with key '6B8016EE' requested:
diff --git a/mips.log b/mips.log
index ecec8b1..2c41ba3 100644
--- a/mips.log
+++ b/mips.log
@@ -1,4 +1,4 @@
-From buildd2 at lucatelli.debian.org Sun Sep 25 16:50:57 2011
+From buildd2 at lucatelli.debian.org Wed Oct 05 10:13:34 2011
Return-path: <buildd2 at lucatelli.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,63 +6,63 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
- id 1R7rur-0005Wd-34
- for logs at buildd.debian.org; Sun, 25 Sep 2011 16:50:57 +0000
+ id 1RBOTm-0005Jc-E9
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:13:34 +0000
Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=lucatelli.debian.org,
EMAIL=hostmaster at lucatelli.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
- id 1R7rup-0007gC-Ss
- for logs at buildd.debian.org; Sun, 25 Sep 2011 16:50:56 +0000
+ id 1RBOTl-0003M0-5Y
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:13:33 +0000
Received: from buildd2 by lucatelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd2 at lucatelli.debian.org>) id 1R7pOj-00088g-Hw
- for logs at buildd.debian.org; Sun, 25 Sep 2011 14:09:37 +0000
+ (envelope-from <buildd2 at lucatelli.debian.org>) id 1RBOTj-0003bv-JI
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:13:31 +0000
From: buildd on lucatelli <buildd2 at lucatelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.2-1 on mips (dist=sid)
+Subject: Log for successful build of bedtools_2.13.3-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1R7pOj-00088g-Hw at lucatelli.debian.org>
-Date: Sun, 25 Sep 2011 14:09:37 +0000
+Message-Id: <E1RBOTj-0003bv-JI at lucatelli.debian.org>
+Date: Wed, 05 Oct 2011 10:13:31 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (mips) 25 Sep 2011 13:18 ║
+║ bedtools 2.13.3-1 (mips) 05 Oct 2011 09:35 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: mips
Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5792 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5816 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5792 kB]
-Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [56.8 kB]
-Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [102 kB]
-Get:9 http://mirror-ubc.debian.org unstable/main mips Packages [7530 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib mips Packages [55.4 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5816 kB]
+Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [57.1 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [103 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7555 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
+Get:10 http://mirror-ubc.debian.org unstable/contrib mips Packages [55.3 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [103 kB]
Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
+Get:12 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7555 kB]
Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [56.8 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [102 kB]
-Get:14 http://incoming.debian.org unstable/main mips Packages [7530 kB]
-Get:15 http://incoming.debian.org unstable/contrib mips Packages [55.4 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [55.3 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [36.3 kB]
-Get:18 http://incoming.debian.org Packages [508 kB]
-Ign http://incoming.debian.org Translation-en
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [36.7 kB]
+Get:18 http://incoming.debian.org Packages [271 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 27.9 MB in 1min 45s (265 kB/s)
+Ign http://incoming.debian.org Translation-en
+Fetched 27.8 MB in 1min 15s (369 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,10 +84,10 @@ 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 666 kB of source archives.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 0s (3708 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 1s (628 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +107,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -124,19 +124,19 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.13-1)
-dash: already installed (0.5.7-1)
+coreutils: already installed (8.13-2)
+dash: already installed (0.5.7-2)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
+dpkg: already installed (1.16.1)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -146,13 +146,13 @@ 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 (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.7
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -174,9 +174,9 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 7 not upgraded.
Need to get 9537 kB of archives.
-After this operation, 30.1 MB of additional disk space will be used.
+After this operation, 29.4 MB of additional disk space will be used.
Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-3 [35.6 kB]
Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
@@ -194,54 +194,54 @@ Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9
Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-4 [2025 kB]
Get:16 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:17 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
Get:20 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9537 kB in 1s (5151 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10546 files and directories currently installed.)
+Fetched 9537 kB in 1s (6136 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10545 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mips.deb) ...
-Selecting previously deselected package libpcre3.
+Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
-Selecting previously deselected package bsdmainutils.
+Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mips.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_mips.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_mips.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.08-1_mips.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mips.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mips.deb) ...
-Selecting previously deselected package cdbs.
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mips.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mips.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_mips.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mips.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
@@ -264,7 +264,7 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -272,11 +272,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 libc6-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-11 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011j-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +287,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -302,30 +302,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
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 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -338,21 +338,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3/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_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -370,7 +370,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -430,6 +430,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -599,7 +603,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -644,22 +648,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org> >../bedtools_2.13.2-1_mips.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110925-1409
+Build finished at 20111005-1013
-bedtools_2.13.2-1_mips.changes:
+bedtools_2.13.3-1_mips.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org>
@@ -667,34 +671,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- fccb540a7cb1bbf29fc62cd651d17b5a2a267b4a 596060 bedtools_2.13.2-1_mips.deb
+ 35a7cbc2dc148e2d205ed6360fdc59d4620d9c2b 596414 bedtools_2.13.3-1_mips.deb
Checksums-Sha256:
- 1f556218272a9879f901c7eb1d2bf3af3c5a4c4a25c191eeaf3baefe648ec415 596060 bedtools_2.13.2-1_mips.deb
+ a9ec77b26c39b83942ea1d7fde04876a3d35e92ca677a99864fbe1444ad14e04 596414 bedtools_2.13.3-1_mips.deb
Files:
- 70fcfea4c52588df83e24316e1cd3fb2 596060 science optional bedtools_2.13.2-1_mips.deb
+ c875ca9e8e4c4c8312981c08170c5494 596414 science optional bedtools_2.13.3-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_mips.deb
+bedtools_2.13.3-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 596060 bytes: control archive= 1720 bytes.
- 834 bytes, 18 lines control
+ size 596414 bytes: control archive= 1725 bytes.
+ 836 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5184
- Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 4999
+ Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -708,7 +712,7 @@ bedtools_2.13.2-1_mips.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-9eec9f59-3884-4d3e-b400-fcb6692b0005/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb/bedtools_2.13.2-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
+dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-778e4d3e-5ab4-4fae-b70e-0f59c0e4067a/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools_2.13.3-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -722,7 +726,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-9eec9f59-3884-4d3e-b400-fcb6692b0005/build/buildd2-bedtools_2.13.2-1-mips-gqBRBb
+Purging /var/lib/schroot/mount/sid-mips-sbuild-778e4d3e-5ab4-4fae-b70e-0f59c0e4067a/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd
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
@@ -732,78 +736,84 @@ Can't open average space db /var/lib/sbuild/avg-build-space
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 101716
-Build-Time: 2788
+Build-Space: 102152
+Build-Time: 2052
Distribution: sid
-Install-Time: 84
-Job: bedtools_2.13.2-1
+Install-Time: 74
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 3033
-Source-Version: 2.13.2-1
-Space: 101716
+Package-Time: 2248
+Source-Version: 2.13.3-1
+Space: 102152
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110925-1409
-Build needed 00:50:33, 101716k disc space
+Finished at 20111005-1013
+Build needed 00:37:28, 102152k disc space
Signature with key 'FDFDA76A' requested:
-From buildd at phrixos.ayous.org Sat Sep 24 04:29:14 2011
-Return-path: <buildd at phrixos.ayous.org>
-Received: from phrixos.ayous.org ([2001:a60:f006:deb:223:9eff:fe00:f7c]
- helo=alius.ayous.org)
+From buildd at mayer.debian.org Wed Oct 05 10:06:11 2011
+Return-path: <buildd at mayer.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 phrixos.ayous.org>)
- id 1R7JrU-0001Tl-UG
- for logs at buildd.debian.org; Sat, 24 Sep 2011 04:29:14 +0000
-Received: from buildd by phrixos.ayous.org with local (Exim 4.72)
- (envelope-from <buildd at phrixos.ayous.org>)
- id 1R7KLf-00063X-Sn; Sat, 24 Sep 2011 05:00:24 +0000
-Date: Sat, 24 Sep 2011 05:00:23 +0000
-Message-Id: <E1R7KLf-00063X-Sn at phrixos.ayous.org>
-From: buildd on phrixos <buildd at phrixos.ayous.org>
-To: aba+buildd_phrixos at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.2-1 on mipsel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RBOMd-0004JL-8U
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:11 +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 kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RBOMc-00034a-01
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:10 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>) id 1RBOMX-0004yO-0Q
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:05 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
+To: logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.3-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1RBOMX-0004yO-0Q at mayer.debian.org>
+Date: Wed, 05 Oct 2011 10:06:05 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on phrixos.ayous.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (mipsel) 24 Sep 2011 04:39 ║
+║ bedtools 2.13.3-1 (mipsel) 05 Oct 2011 09:44 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-5db71cd2-56ce-4b78-8919-738b65028116/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj
-Start Time: 20110924-0439
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://mirror.ayous.org unstable InRelease [146 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
-Get:4 http://mirror.ayous.org unstable/main Sources [7251 kB]
+Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
+Get:2 http://debian.oregonstate.edu sid/main Sources [5816 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:5 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://incoming.debian.org unstable/main Sources [7251 kB]
-Get:8 http://mirror.ayous.org unstable/contrib Sources [67.1 kB]
-Get:9 http://mirror.ayous.org unstable/non-free Sources [123 kB]
-Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9881 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [67.1 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [123 kB]
-Get:13 http://incoming.debian.org unstable/main mipsel Packages [9881 kB]
-Get:14 http://mirror.ayous.org unstable/contrib mipsel Packages [67.5 kB]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [67.5 kB]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [38.6 kB]
-Get:18 http://incoming.debian.org Packages [903 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Hit http://incoming.debian.org Release.gpg
+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
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
+Get:3 http://debian.oregonstate.edu sid/contrib Sources [57.1 kB]
+Get:4 http://debian.oregonstate.edu sid/main mipsel Packages [7572 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 36.0 MB in 27s (1296 kB/s)
+Get:5 http://debian.oregonstate.edu sid/contrib mipsel Packages [55.6 kB]
+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
+Fetched 13.6 MB in 27s (501 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -825,146 +835,108 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 2s (234 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 1s (663 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
-cdbs: missing
-debhelper: missing
-Using default version 8.9.7
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bedtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
+bash: already installed (4.1-3)
+coreutils: already installed (8.13-2)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.2)
+diffutils: already installed (1:3.0-1)
+dpkg: already installed (1.16.1)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+findutils: already installed (4.4.2-1+b1)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-4)
+sed: already installed (4.2.1-9)
+login: already installed (1:4.1.4.2+svn3283-3)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+cdbs: already installed (0.4.99)
+debhelper: already installed (8.9.8 >= 8 is satisfied)
quilt: missing
-zlib1g-dev: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+Checking for dependency conflicts...
+Installing positive dependencies: quilt
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ procmail graphviz
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 26 not upgraded.
-Need to get 9486 kB of archives.
-After this operation, 30.1 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.08-1 [248 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.08-1 [51.7 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-4 [133 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-4 [858 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-4 [2008 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+ diffstat quilt
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9486 kB in 1s (5578 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 11488 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_mipsel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.08-1_mipsel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mipsel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+0 upgraded, 2 newly installed, 0 to remove and 12 not upgraded.
+Need to get 0 B/385 kB of archives.
+After this operation, 835 kB of additional disk space will be used.
+Selecting previously unselected package diffstat.
+(Reading database ... 26387 files and directories currently installed.)
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
-Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Processing triggers for man-db ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 3.1.0-rc6+ mipsel (mips64)
-Toolchain package versions: libc6-dev_2.13-18 dpkg-dev_1.16.0.3 linux-libc-dev_3.0.0-3 gcc-4.6_4.6.1-9 g++-4.6_4.6.1-9 binutils_2.21.53.20110910-1 libstdc++6-4.6-dev_4.6.1-9 libstdc++6_4.6.1-9
-Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.4_4.4.6-10 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.4-dev_4.4.6-10 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 dh-buildinfo_0.9 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 docutils-common_0.8.1-3 doxygen_1.7.4-4 doxygen-latex_1.7.4-4 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 ed_1.5-3 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-3 gfortran-4.6_4.6.1-13 ghostscript_9.02~dfsg-3 gnupg_1.4.11-3 gperf_3.0.3-1+b1 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gs-cjk-resource_1.20100103-2 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 latex-xcolor_2.11-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libaudio2_1.9.2-9 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common3_0.6.30-5 libblas3gf_1.2.20110419-2 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 libcnf-dev_4.0-2 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libcups2_1.5.0-8 libcupsimage2_1.5.0-8 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-13 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgs9_9.02~dfsg-3 libgs9-common_9.02~dfsg-3 libgssapi-krb5-2_1.9.1+dfsg-3 libice6_2:1.0.7-2 libidn11_1.22-3 libijs-0.35_0.35-8 libjasper1_1.900.1-10 libjbig2dec0_0.11-1 libjpeg62_6b1-2 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkpathsea5_2009-11 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1+b1 libltdl-dev_2.4-4 libltdl7_2.4-4 liblua5.1-0_5.1.4-10 liblua5.1-0-dev_5.1.4-10 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-2 libodbc1_2.2.14p2-3 libodbcinstq1c2_2.2.14p2-3 libopenjpeg2_1.3+dfsg-4 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpoppler13_0.16.7-2+b1 libpopt-dev_1.16-1 libpopt0_1.16-1 libpython2.7_2.7.2-5 libqt3-mt_3:3.3.8b-11 libreadline-dev_6.2-4 libreadline6_6.2-4 libreadline6-dev_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm6_2:1.2.0-2 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-07-02-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtasn1-3_2.9-4 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libtut-dev_0.0.20070706-1 libudev0_172-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb1_1.7-3 libxcursor1_1:1.1.12-1 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxft2_2.2.0-3 libxi6_2:1.4.3-3 libxinerama1_2:1.1.1-3 libxml2_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxpm4_1:3.5.9-1 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.6-2 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 luatex_0.70.1-1+b1 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 odbcinst_2.2.14p2-3 odbcinst1debian2_2.2.14p2-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 preview-latex-style_11.86-4 procps_1:3.2.8-11 python_2.7.2-7 python-central_0.6.17 python-dev_2.7.2-7 python-docutils_0.8.1-3 python-minimal_2.7.2-7 python-numpy_1:1.5.1-2+b1 python-roman_0.8.1-3 python-support_1.0.14 python2.7_2.7.2-5 python2.7-dev_2.7.2-5 python2.7-minimal_2.7.2-5 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 swig_2.0.4-4 swig2.0_2.0.4-4 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tex-common_2.10 texlive-base_2009-14 texlive-binaries_2009-11 texlive-common_2009-14 texlive-doc-base_2009-2 texlive-extra-utils_2009-10 texlive-font-utils_2009-10 texlive-latex-base_2009-14 texlive-latex-extra_2009-10 texlive-latex-recommended_2009-14 texlive-pictures_2009-14 ttf-dejavu-core_2.33-2 tzdata_2011k-1 ucf_3.0025+nmu2 udev_172-1 unixodbc_2.2.14p2-3 unixodbc-dev_2.2.14p2-3 util-linux_2.19.1-5 x11-common_1:7.6+9 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -974,14 +946,13 @@ Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -991,30 +962,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1027,21 +998,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/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_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -1059,7 +1030,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -1119,6 +1090,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -1288,10 +1263,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -1321,6 +1296,7 @@ dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
dh_link -pbedtools
+dh_buildinfo -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
@@ -1333,57 +1309,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org> >../bedtools_2.13.2-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0500
+Build finished at 20111005-1005
-bedtools_2.13.2-1_mipsel.changes:
+bedtools_2.13.3-1_mipsel.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- 1d3ee7fad37ec420a7d4b1656f72d1556448c48a 626788 bedtools_2.13.2-1_mipsel.deb
+ 70a401adf167a606f58bc85ca0ea18b6b9363498 629960 bedtools_2.13.3-1_mipsel.deb
Checksums-Sha256:
- 427879ca44bf18f91af967d47332071b37096ba23f371c4f881e424c6cf903eb 626788 bedtools_2.13.2-1_mipsel.deb
+ d67904e6bc4035d5261c3dd4f42b6d92f00add1b96f581a8debbc20697ff8b7e 629960 bedtools_2.13.3-1_mipsel.deb
Files:
- dc43959f7bd8a1574bd49848f054183a 626788 science optional bedtools_2.13.2-1_mipsel.deb
+ 592b28403eb5b89cceb2eb041fb710e8 629960 science optional bedtools_2.13.3-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_mipsel.deb
+bedtools_2.13.3-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 626788 bytes: control archive= 1723 bytes.
- 836 bytes, 18 lines control
- 2025 bytes, 35 lines md5sums
+ size 629960 bytes: control archive= 1751 bytes.
+ 838 bytes, 18 lines control
+ 2095 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5184
- Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 5000
+ Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -1397,49 +1373,7 @@ bedtools_2.13.2-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 04:40 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/bin/
--rwxr-xr-x root/root 116408 2011-09-24 04:59 ./usr/bin/mergeBed
--rwxr-xr-x root/root 299084 2011-09-24 04:59 ./usr/bin/tagBam
--rwxr-xr-x root/root 378252 2011-09-24 04:59 ./usr/bin/intersectBed
--rwxr-xr-x root/root 93928 2011-09-24 04:59 ./usr/bin/overlap
--rwxr-xr-x root/root 128584 2011-09-24 04:59 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120088 2011-09-24 04:59 ./usr/bin/subtractBed
--rwxr-xr-x root/root 114776 2011-09-24 04:59 ./usr/bin/complementBed
--rwxr-xr-x root/root 248076 2011-09-24 04:59 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121256 2011-09-24 04:59 ./usr/bin/flankBed
--rwxr-xr-x root/root 118552 2011-09-24 04:59 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 139592 2011-09-24 04:59 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 127064 2011-09-24 04:59 ./usr/bin/closestBed
--rwxr-xr-x root/root 390940 2011-09-24 04:59 ./usr/bin/pairToBed
--rwxr-xr-x root/root 103768 2011-09-24 04:59 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 311532 2011-09-24 04:59 ./usr/bin/windowBed
--rwxr-xr-x root/root 186872 2011-09-24 04:59 ./usr/bin/pairToPair
--rwxr-xr-x root/root 326540 2011-09-24 04:59 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 111912 2011-09-24 04:59 ./usr/bin/annotateBed
--rwxr-xr-x root/root 63960 2011-09-24 04:59 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 152876 2011-09-24 04:59 ./usr/bin/nucBed
--rwxr-xr-x root/root 114664 2011-09-24 04:59 ./usr/bin/slopBed
--rwxr-xr-x root/root 303964 2011-09-24 04:59 ./usr/bin/coverageBed
--rwxr-xr-x root/root 152828 2011-09-24 04:59 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 152088 2011-09-24 04:59 ./usr/bin/sortBed
--rwxr-xr-x root/root 114184 2011-09-24 04:59 ./usr/bin/linksBed
--rwxr-xr-x root/root 320332 2011-09-24 04:59 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 241484 2011-09-24 04:59 ./usr/bin/bamToBed
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools_2.13.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1448,9 +1382,47 @@ drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-5db71cd2-56ce-4b78-8919-738b65028116/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ diffstat* quilt*
+0 upgraded, 0 newly installed, 2 to remove and 12 not upgraded.
+After this operation, 835 kB disk space will be freed.
+(Reading database ... 26467 files and directories currently installed.)
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Processing triggers for man-db ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 102184
+Build-Time: 1168
+Distribution: sid
+Install-Time: 33
+Job: bedtools_2.13.3-1
+Package: bedtools
+Package-Time: 1264
+Source-Version: 2.13.3-1
+Space: 102184
+Status: successful
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0500
-Build needed 00:21:13, 101752k disc space
+Finished at 20111005-1005
+Build needed 00:21:04, 102184k disc space
+Signature with key 'A5633F94' requested:
diff --git a/mipsel.log b/mipsel.log
index 3edfbac..e36fd63 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,59 +1,65 @@
-From buildd at phrixos.ayous.org Sat Sep 24 04:29:14 2011
-Return-path: <buildd at phrixos.ayous.org>
-Received: from phrixos.ayous.org ([2001:a60:f006:deb:223:9eff:fe00:f7c]
- helo=alius.ayous.org)
+From buildd at mayer.debian.org Wed Oct 05 10:06:11 2011
+Return-path: <buildd at mayer.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 phrixos.ayous.org>)
- id 1R7JrU-0001Tl-UG
- for logs at buildd.debian.org; Sat, 24 Sep 2011 04:29:14 +0000
-Received: from buildd by phrixos.ayous.org with local (Exim 4.72)
- (envelope-from <buildd at phrixos.ayous.org>)
- id 1R7KLf-00063X-Sn; Sat, 24 Sep 2011 05:00:24 +0000
-Date: Sat, 24 Sep 2011 05:00:23 +0000
-Message-Id: <E1R7KLf-00063X-Sn at phrixos.ayous.org>
-From: buildd on phrixos <buildd at phrixos.ayous.org>
-To: aba+buildd_phrixos at not.so.argh.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.2-1 on mipsel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RBOMd-0004JL-8U
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:11 +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 kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RBOMc-00034a-01
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:10 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>) id 1RBOMX-0004yO-0Q
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:05 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
+To: logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.3-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1RBOMX-0004yO-0Q at mayer.debian.org>
+Date: Wed, 05 Oct 2011 10:06:05 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on phrixos.ayous.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (mipsel) 24 Sep 2011 04:39 ║
+║ bedtools 2.13.3-1 (mipsel) 05 Oct 2011 09:44 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-5db71cd2-56ce-4b78-8919-738b65028116/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj
-Start Time: 20110924-0439
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://mirror.ayous.org unstable InRelease [146 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
-Get:4 http://mirror.ayous.org unstable/main Sources [7251 kB]
+Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
+Get:2 http://debian.oregonstate.edu sid/main Sources [5816 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:5 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://incoming.debian.org unstable/main Sources [7251 kB]
-Get:8 http://mirror.ayous.org unstable/contrib Sources [67.1 kB]
-Get:9 http://mirror.ayous.org unstable/non-free Sources [123 kB]
-Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9881 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [67.1 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [123 kB]
-Get:13 http://incoming.debian.org unstable/main mipsel Packages [9881 kB]
-Get:14 http://mirror.ayous.org unstable/contrib mipsel Packages [67.5 kB]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [67.5 kB]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [38.6 kB]
-Get:18 http://incoming.debian.org Packages [903 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Hit http://incoming.debian.org Release.gpg
+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
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
+Get:3 http://debian.oregonstate.edu sid/contrib Sources [57.1 kB]
+Get:4 http://debian.oregonstate.edu sid/main mipsel Packages [7572 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 36.0 MB in 27s (1296 kB/s)
+Get:5 http://debian.oregonstate.edu sid/contrib mipsel Packages [55.6 kB]
+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
+Fetched 13.6 MB in 27s (501 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -75,146 +81,108 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 2s (234 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 1s (663 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
-cdbs: missing
-debhelper: missing
-Using default version 8.9.7
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bedtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
+bash: already installed (4.1-3)
+coreutils: already installed (8.13-2)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.2)
+diffutils: already installed (1:3.0-1)
+dpkg: already installed (1.16.1)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+findutils: already installed (4.4.2-1+b1)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
+hostname: already installed (3.06)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-4)
+sed: already installed (4.2.1-9)
+login: already installed (1:4.1.4.2+svn3283-3)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+mount: already installed (2.19.1-5)
+util-linux: already installed (2.19.1-5)
+libc6-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+cdbs: already installed (0.4.99)
+debhelper: already installed (8.9.8 >= 8 is satisfied)
quilt: missing
-zlib1g-dev: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+Checking for dependency conflicts...
+Installing positive dependencies: quilt
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ procmail graphviz
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 26 not upgraded.
-Need to get 9486 kB of archives.
-After this operation, 30.1 MB of additional disk space will be used.
-Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
-Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.08-1 [248 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.08-1 [51.7 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-4 [133 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-4 [858 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-4 [2008 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
-Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
-Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+ diffstat quilt
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9486 kB in 1s (5578 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 11488 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_mipsel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.08-1_mipsel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mipsel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+0 upgraded, 2 newly installed, 0 to remove and 12 not upgraded.
+Need to get 0 B/385 kB of archives.
+After this operation, 835 kB of additional disk space will be used.
+Selecting previously unselected package diffstat.
+(Reading database ... 26387 files and directories currently installed.)
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
-Setting up cdbs (0.4.99) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Processing triggers for man-db ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 3.1.0-rc6+ mipsel (mips64)
-Toolchain package versions: libc6-dev_2.13-18 dpkg-dev_1.16.0.3 linux-libc-dev_3.0.0-3 gcc-4.6_4.6.1-9 g++-4.6_4.6.1-9 binutils_2.21.53.20110910-1 libstdc++6-4.6-dev_4.6.1-9 libstdc++6_4.6.1-9
-Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.4_4.4.6-10 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.4-dev_4.4.6-10 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 dh-buildinfo_0.9 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 docutils-common_0.8.1-3 doxygen_1.7.4-4 doxygen-latex_1.7.4-4 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 ed_1.5-3 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-3 gfortran-4.6_4.6.1-13 ghostscript_9.02~dfsg-3 gnupg_1.4.11-3 gperf_3.0.3-1+b1 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gs-cjk-resource_1.20100103-2 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 latex-xcolor_2.11-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libaudio2_1.9.2-9 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common3_0.6.30-5 libblas3gf_1.2.20110419-2 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 libcnf-dev_4.0-2 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libcups2_1.5.0-8 libcupsimage2_1.5.0-8 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-13 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgs9_9.02~dfsg-3 libgs9-common_9.02~dfsg-3 libgssapi-krb5-2_1.9.1+dfsg-3 libice6_2:1.0.7-2 libidn11_1.22-3 libijs-0.35_0.35-8 libjasper1_1.900.1-10 libjbig2dec0_0.11-1 libjpeg62_6b1-2 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkpathsea5_2009-11 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1+b1 libltdl-dev_2.4-4 libltdl7_2.4-4 liblua5.1-0_5.1.4-10 liblua5.1-0-dev_5.1.4-10 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-2 libodbc1_2.2.14p2-3 libodbcinstq1c2_2.2.14p2-3 libopenjpeg2_1.3+dfsg-4 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpoppler13_0.16.7-2+b1 libpopt-dev_1.16-1 libpopt0_1.16-1 libpython2.7_2.7.2-5 libqt3-mt_3:3.3.8b-11 libreadline-dev_6.2-4 libreadline6_6.2-4 libreadline6-dev_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm6_2:1.2.0-2 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-07-02-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtasn1-3_2.9-4 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libtut-dev_0.0.20070706-1 libudev0_172-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb1_1.7-3 libxcursor1_1:1.1.12-1 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxft2_2.2.0-3 libxi6_2:1.4.3-3 libxinerama1_2:1.1.1-3 libxml2_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxpm4_1:3.5.9-1 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.6-2 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 luatex_0.70.1-1+b1 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 odbcinst_2.2.14p2-3 odbcinst1debian2_2.2.14p2-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 preview-latex-style_11.86-4 procps_1:3.2.8-11 python_2.7.2-7 python-central_0.6.17 python-dev_2.7.2-7 python-docutils_0.8.1-3 python-minimal_2.7.2-7 python-numpy_1:1.5.1-2+b1 python-roman_0.8.1-3 python-support_1.0.14 python2.7_2.7.2-5 python2.7-dev_2.7.2-5 python2.7-minimal_2.7.2-5 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 swig_2.0.4-4 swig2.0_2.0.4-4 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tex-common_2.10 texlive-base_2009-14 texlive-binaries_2009-11 texlive-common_2009-14 texlive-doc-base_2009-2 texlive-extra-utils_2009-10 texlive-font-utils_2009-10 texlive-latex-base_2009-14 texlive-latex-extra_2009-10 texlive-latex-recommended_2009-14 texlive-pictures_2009-14 ttf-dejavu-core_2.33-2 tzdata_2011k-1 ucf_3.0025+nmu2 udev_172-1 unixodbc_2.2.14p2-3 unixodbc-dev_2.2.14p2-3 util-linux_2.19.1-5 x11-common_1:7.6+9 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -224,14 +192,13 @@ Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -241,30 +208,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -277,21 +244,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/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_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -309,7 +276,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -369,6 +336,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -538,10 +509,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -571,6 +542,7 @@ dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
dh_link -pbedtools
+dh_buildinfo -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
@@ -583,57 +555,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org> >../bedtools_2.13.2-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0500
+Build finished at 20111005-1005
-bedtools_2.13.2-1_mipsel.changes:
+bedtools_2.13.3-1_mipsel.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- 1d3ee7fad37ec420a7d4b1656f72d1556448c48a 626788 bedtools_2.13.2-1_mipsel.deb
+ 70a401adf167a606f58bc85ca0ea18b6b9363498 629960 bedtools_2.13.3-1_mipsel.deb
Checksums-Sha256:
- 427879ca44bf18f91af967d47332071b37096ba23f371c4f881e424c6cf903eb 626788 bedtools_2.13.2-1_mipsel.deb
+ d67904e6bc4035d5261c3dd4f42b6d92f00add1b96f581a8debbc20697ff8b7e 629960 bedtools_2.13.3-1_mipsel.deb
Files:
- dc43959f7bd8a1574bd49848f054183a 626788 science optional bedtools_2.13.2-1_mipsel.deb
+ 592b28403eb5b89cceb2eb041fb710e8 629960 science optional bedtools_2.13.3-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_mipsel.deb
+bedtools_2.13.3-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 626788 bytes: control archive= 1723 bytes.
- 836 bytes, 18 lines control
- 2025 bytes, 35 lines md5sums
+ size 629960 bytes: control archive= 1751 bytes.
+ 838 bytes, 18 lines control
+ 2095 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5184
- Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 5000
+ Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -647,49 +619,7 @@ bedtools_2.13.2-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 04:40 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/bin/
--rwxr-xr-x root/root 116408 2011-09-24 04:59 ./usr/bin/mergeBed
--rwxr-xr-x root/root 299084 2011-09-24 04:59 ./usr/bin/tagBam
--rwxr-xr-x root/root 378252 2011-09-24 04:59 ./usr/bin/intersectBed
--rwxr-xr-x root/root 93928 2011-09-24 04:59 ./usr/bin/overlap
--rwxr-xr-x root/root 128584 2011-09-24 04:59 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120088 2011-09-24 04:59 ./usr/bin/subtractBed
--rwxr-xr-x root/root 114776 2011-09-24 04:59 ./usr/bin/complementBed
--rwxr-xr-x root/root 248076 2011-09-24 04:59 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121256 2011-09-24 04:59 ./usr/bin/flankBed
--rwxr-xr-x root/root 118552 2011-09-24 04:59 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 139592 2011-09-24 04:59 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 127064 2011-09-24 04:59 ./usr/bin/closestBed
--rwxr-xr-x root/root 390940 2011-09-24 04:59 ./usr/bin/pairToBed
--rwxr-xr-x root/root 103768 2011-09-24 04:59 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 311532 2011-09-24 04:59 ./usr/bin/windowBed
--rwxr-xr-x root/root 186872 2011-09-24 04:59 ./usr/bin/pairToPair
--rwxr-xr-x root/root 326540 2011-09-24 04:59 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 111912 2011-09-24 04:59 ./usr/bin/annotateBed
--rwxr-xr-x root/root 63960 2011-09-24 04:59 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 152876 2011-09-24 04:59 ./usr/bin/nucBed
--rwxr-xr-x root/root 114664 2011-09-24 04:59 ./usr/bin/slopBed
--rwxr-xr-x root/root 303964 2011-09-24 04:59 ./usr/bin/coverageBed
--rwxr-xr-x root/root 152828 2011-09-24 04:59 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 152088 2011-09-24 04:59 ./usr/bin/sortBed
--rwxr-xr-x root/root 114184 2011-09-24 04:59 ./usr/bin/linksBed
--rwxr-xr-x root/root 320332 2011-09-24 04:59 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 241484 2011-09-24 04:59 ./usr/bin/bamToBed
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools_2.13.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -698,9 +628,47 @@ drwxr-xr-x root/root 0 2011-09-24 04:59 ./usr/bin/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-5db71cd2-56ce-4b78-8919-738b65028116/build/buildd-bedtools_2.13.2-1-mipsel-Aoe4Gj
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ diffstat* quilt*
+0 upgraded, 0 newly installed, 2 to remove and 12 not upgraded.
+After this operation, 835 kB disk space will be freed.
+(Reading database ... 26467 files and directories currently installed.)
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Processing triggers for man-db ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 102184
+Build-Time: 1168
+Distribution: sid
+Install-Time: 33
+Job: bedtools_2.13.3-1
+Package: bedtools
+Package-Time: 1264
+Source-Version: 2.13.3-1
+Space: 102184
+Status: successful
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0500
-Build needed 00:21:13, 101752k disc space
+Finished at 20111005-1005
+Build needed 00:21:04, 102184k disc space
+Signature with key 'A5633F94' requested:
diff --git a/powerpc.log b/powerpc.log
index 20fa6f6..5552de0 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,69 @@
-From buildd at poulenc.debian.org Sat Sep 24 03:28:45 2011
-Return-path: <buildd at poulenc.debian.org>
+From buildd at porpora.debian.org Wed Oct 05 09:41:50 2011
+Return-path: <buildd at porpora.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 poulenc.debian.org>)
- id 1R7Iuz-0001oV-Hc
- for logs at buildd.debian.org; Sat, 24 Sep 2011 03:28:45 +0000
-Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
- helo=poulenc.debian.org)
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1RBNz4-0007iQ-GN
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 09:41:50 +0000
+Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
+ helo=porpora.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=poulenc.debian.org, EMAIL=hostmaster at poulenc.debian.org (verified)
+ CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
- id 1R7Iuy-0002Qn-PK; Sat, 24 Sep 2011 03:28:44 +0000
-Received: from buildd by poulenc.debian.org with local (Exim 4.72)
- (envelope-from <buildd at poulenc.debian.org>)
- id 1R7Iux-0002ii-OX; Sat, 24 Sep 2011 03:28:43 +0000
-Message-Id: <E1R7Iux-0002ii-OX at poulenc.debian.org>
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1RBNz3-0001xK-Go; Wed, 05 Oct 2011 09:41:49 +0000
+Received: from buildd by porpora.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at porpora.debian.org>)
+ id 1RBNz1-00017M-G5; Wed, 05 Oct 2011 09:41:47 +0000
+Message-Id: <E1RBNz1-00017M-G5 at porpora.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 24 Sep 2011 03:28:43 +0000
-From: buildd on poulenc <buildd at poulenc.debian.org>
+Date: Wed, 5 Oct 2011 09:41:47 +0000
+From: buildd on porpora <buildd at porpora.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.2-1 on powerpc (dist=sid)
-Key-Id: 779E1DD6
+Subject: Log for successful build of bedtools_2.13.3-1 on powerpc (dist=sid)
+Key-Id: 6CB21D9F
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on poulenc.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (powerpc) 24 Sep 2011 03:22 ║
+║ bedtools 2.13.3-1 (powerpc) 05 Oct 2011 09:35 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: powerpc
Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5773 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5815 kB]
+Get:4 http://ftp.uk.debian.org unstable/contrib Sources [57.1 kB]
+Get:5 http://ftp.uk.debian.org unstable/non-free Sources [104 kB]
+Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [7638 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 [5783 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [56.5 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [102 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7627 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [54.9 kB]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org unstable/main Sources [5816 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.0 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7633 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [54.9 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7638 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [32.8 kB]
-Get:18 http://incoming.debian.org Packages [561 kB]
+Get:17 http://incoming.debian.org Sources [36.7 kB]
+Get:18 http://incoming.debian.org Packages [271 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.1 MB in 23s (1182 kB/s)
+Fetched 27.9 MB in 22s (1228 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,10 +85,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 1s (470 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 1s (536 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,18 +126,18 @@ base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
+dash: already installed (0.5.7-2)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+dpkg: already installed (1.16.1)
+e2fsprogs: already installed (1.42~WIP-2011-09-25-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -147,13 +147,13 @@ 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 (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.7
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -175,9 +175,9 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 12 not upgraded.
Need to get 9691 kB of archives.
-After this operation, 29.7 MB of additional disk space will be used.
+After this operation, 29.0 MB of additional disk space will be used.
Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-3 [37.2 kB]
Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
@@ -195,54 +195,54 @@ Get:14 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.
Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-4 [2032 kB]
Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9691 kB in 1s (5128 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10625 files and directories currently installed.)
+Fetched 9691 kB in 1s (6358 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10782 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_powerpc.deb) ...
-Selecting previously deselected package libpcre3.
+Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
-Selecting previously deselected package bsdmainutils.
+Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_powerpc.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_powerpc.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_powerpc.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../file_5.08-1_powerpc.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_powerpc.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_powerpc.deb) ...
-Selecting previously deselected package cdbs.
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_powerpc.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_powerpc.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_powerpc.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_powerpc.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
@@ -265,7 +265,7 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -273,11 +273,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 libc6-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-11 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011j-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-09-25-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-25-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +288,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -303,30 +303,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -339,21 +339,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3/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_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -371,7 +371,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -431,6 +431,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -600,7 +604,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -645,56 +649,56 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../bedtools_2.13.2-1_powerpc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0328
+Build finished at 20111005-0941
-bedtools_2.13.2-1_powerpc.changes:
+bedtools_2.13.3-1_powerpc.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
+Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- 3d1cb46a915d7058954652ebda2e0d0d4a4db91f 590392 bedtools_2.13.2-1_powerpc.deb
+ 4452933abda5cd318820804da673cbcb6ecac8ab 594494 bedtools_2.13.3-1_powerpc.deb
Checksums-Sha256:
- 775a831e804714c974a3f474fd870535ca6e106a7113035b7bec162bde82e5cb 590392 bedtools_2.13.2-1_powerpc.deb
+ e8999dfb8da086be7ea85c2a3f8d9dd365869dba7769e36f957e7fb8ca89b849 594494 bedtools_2.13.3-1_powerpc.deb
Files:
- 5d64ab381234ae8136107d2c92fa47de 590392 science optional bedtools_2.13.2-1_powerpc.deb
+ 589ac7c0e911a19e9d94e25885309acc 594494 science optional bedtools_2.13.3-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_powerpc.deb
+bedtools_2.13.3-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 590392 bytes: control archive= 1723 bytes.
+ size 594494 bytes: control archive= 1718 bytes.
837 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4976
+ Installed-Size: 4834
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
@@ -709,49 +713,49 @@ bedtools_2.13.2-1_powerpc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 03:28 ./
-drwxr-xr-x root/root 0 2011-09-24 03:28 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 03:28 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 03:28 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 03:24 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-09-24 03:28 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 03:28 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-24 03:28 ./usr/bin/
--rwxr-xr-x root/root 231864 2011-09-24 03:28 ./usr/bin/bamToBed
--rwxr-xr-x root/root 125196 2011-09-24 03:28 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 109300 2011-09-24 03:28 ./usr/bin/linksBed
--rwxr-xr-x root/root 289368 2011-09-24 03:28 ./usr/bin/tagBam
--rwxr-xr-x root/root 371864 2011-09-24 03:28 ./usr/bin/pairToBed
--rwxr-xr-x root/root 149852 2011-09-24 03:28 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 63764 2011-09-24 03:28 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 318040 2011-09-24 03:28 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 112884 2011-09-24 03:28 ./usr/bin/mergeBed
--rwxr-xr-x root/root 100652 2011-09-24 03:28 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 110516 2011-09-24 03:28 ./usr/bin/complementBed
--rwxr-xr-x root/root 174372 2011-09-24 03:28 ./usr/bin/pairToPair
--rwxr-xr-x root/root 109876 2011-09-24 03:28 ./usr/bin/slopBed
--rwxr-xr-x root/root 149868 2011-09-24 03:28 ./usr/bin/nucBed
--rwxr-xr-x root/root 133404 2011-09-24 03:28 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 121708 2011-09-24 03:28 ./usr/bin/closestBed
--rwxr-xr-x root/root 293448 2011-09-24 03:28 ./usr/bin/coverageBed
--rwxr-xr-x root/root 108772 2011-09-24 03:28 ./usr/bin/annotateBed
--rwxr-xr-x root/root 310360 2011-09-24 03:28 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 237276 2011-09-24 03:28 ./usr/bin/bedToBam
--rwxr-xr-x root/root 297776 2011-09-24 03:28 ./usr/bin/windowBed
--rwxr-xr-x root/root 113524 2011-09-24 03:28 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 92412 2011-09-24 03:28 ./usr/bin/overlap
--rwxr-xr-x root/root 116988 2011-09-24 03:28 ./usr/bin/flankBed
--rwxr-xr-x root/root 114700 2011-09-24 03:28 ./usr/bin/subtractBed
--rwxr-xr-x root/root 359008 2011-09-24 03:28 ./usr/bin/intersectBed
--rwxr-xr-x root/root 145628 2011-09-24 03:28 ./usr/bin/sortBed
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/bin/
+-rwxr-xr-x root/root 149868 2011-10-05 09:41 ./usr/bin/nucBed
+-rwxr-xr-x root/root 363104 2011-10-05 09:41 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 113332 2011-10-05 09:41 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 145636 2011-10-05 09:41 ./usr/bin/sortBed
+-rwxr-xr-x root/root 240116 2011-10-05 09:41 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 122484 2011-10-05 09:41 ./usr/bin/closestBed
+-rwxr-xr-x root/root 313952 2011-10-05 09:41 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 108772 2011-10-05 09:41 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 149860 2011-10-05 09:41 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 110972 2011-10-05 09:41 ./usr/bin/complementBed
+-rwxr-xr-x root/root 375408 2011-10-05 09:41 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 297552 2011-10-05 09:41 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 100652 2011-10-05 09:41 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 109684 2011-10-05 09:41 ./usr/bin/linksBed
+-rwxr-xr-x root/root 110324 2011-10-05 09:41 ./usr/bin/slopBed
+-rwxr-xr-x root/root 115364 2011-10-05 09:41 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 301656 2011-10-05 09:41 ./usr/bin/windowBed
+-rwxr-xr-x root/root 232804 2011-10-05 09:41 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 289608 2011-10-05 09:41 ./usr/bin/tagBam
+-rwxr-xr-x root/root 133724 2011-10-05 09:41 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 63772 2011-10-05 09:41 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 174836 2011-10-05 09:41 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 125204 2011-10-05 09:41 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 318048 2011-10-05 09:41 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 117412 2011-10-05 09:41 ./usr/bin/flankBed
+-rwxr-xr-x root/root 113948 2011-10-05 09:41 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 92620 2011-10-05 09:41 ./usr/bin/overlap
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 09:36 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -765,7 +769,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-3e930e01-48e6-4749-93bd-dc6d89fdd641/build/buildd-bedtools_2.13.2-1-powerpc-R4GStM
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-2854bbaa-0a5c-40ef-88cf-9869c9042605/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -773,18 +777,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 104436
-Build-Time: 263
+Build-Space: 105056
+Build-Time: 302
Distribution: sid
-Install-Time: 43
-Job: bedtools_2.13.2-1
+Install-Time: 42
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 346
-Source-Version: 2.13.2-1
-Space: 104436
+Package-Time: 383
+Source-Version: 2.13.3-1
+Space: 105056
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0328
-Build needed 00:05:46, 104436k disc space
-Signature with key '779E1DD6' requested:
+Finished at 20111005-0941
+Build needed 00:06:23, 105056k disc space
+Signature with key '6CB21D9F' requested:
diff --git a/s390.log b/s390.log
index 5ced078..4070110 100644
--- a/s390.log
+++ b/s390.log
@@ -1,69 +1,69 @@
-From buildd at zandonai.debian.org Sat Sep 24 03:43:22 2011
+From buildd at zandonai.debian.org Wed Oct 05 10:37:52 2011
Return-path: <buildd at zandonai.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1R7J98-0003it-Nm
- for logs at buildd.debian.org; Sat, 24 Sep 2011 03:43:22 +0000
+ id 1RBOrI-00026m-Rb
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:37:52 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1R7J98-0002zn-08; Sat, 24 Sep 2011 03:43:22 +0000
+ id 1RBOrI-0004F4-6l; Wed, 05 Oct 2011 10:37:52 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1R7J97-0003hw-MO; Sat, 24 Sep 2011 03:43:21 +0000
-Message-Id: <E1R7J97-0003hw-MO at zandonai.debian.org>
+ id 1RBOrH-0002Jl-Nr; Wed, 05 Oct 2011 10:37:51 +0000
+Message-Id: <E1RBOrH-0002Jl-Nr at zandonai.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 24 Sep 2011 03:43:21 +0000
+Date: Wed, 5 Oct 2011 10:37:51 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.2-1 on s390 (dist=sid)
+Subject: Log for successful build of bedtools_2.13.3-1 on s390 (dist=sid)
Key-Id: 2D941D26
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (s390) 24 Sep 2011 03:39 ║
+║ bedtools 2.13.3-1 (s390) 05 Oct 2011 10:33 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: s390
Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [5773 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5816 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 [5783 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.5 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [102 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7527 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5816 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [57.1 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [103 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7557 kB]
Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.0 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7537 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7557 kB]
Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [32.8 kB]
-Get:18 http://incoming.debian.org Packages [562 kB]
+Get:17 http://incoming.debian.org Sources [36.2 kB]
+Get:18 http://incoming.debian.org Packages [277 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 27.9 MB in 24s (1135 kB/s)
+Fetched 27.8 MB in 30s (908 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,10 +85,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 1s (426 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 1s (348 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,11 +126,11 @@ base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.13-2)
-dash: already installed (0.5.7-1)
+dash: already installed (0.5.7-2)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+dpkg: already installed (1.16.1)
+e2fsprogs: already installed (1.42~WIP-2011-09-25-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
@@ -147,13 +147,13 @@ 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 (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.7
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -175,9 +175,9 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 17 not upgraded.
Need to get 9823 kB of archives.
-After this operation, 29.6 MB of additional disk space will be used.
+After this operation, 28.8 MB of additional disk space will be used.
Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-3 [39.0 kB]
Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
@@ -195,54 +195,54 @@ Get:14 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-4
Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-4 [2073 kB]
Get:16 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:17 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.7 [552 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4 kB]
Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9823 kB in 2s (3385 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10632 files and directories currently installed.)
+Fetched 9823 kB in 6s (1414 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10624 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_s390.deb) ...
-Selecting previously deselected package libpcre3.
+Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
-Selecting previously deselected package bsdmainutils.
+Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_s390.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_s390.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.08-1_s390.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_s390.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_s390.deb) ...
-Selecting previously deselected package cdbs.
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_s390.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_s390.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_s390.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_s390.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
@@ -265,7 +265,7 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -273,11 +273,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 libc6-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-11 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011j-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-09-25-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-25-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +288,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -303,30 +303,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -339,21 +339,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3/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_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -371,7 +371,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -431,6 +431,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -600,7 +604,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-s390-Ao9dea/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -645,22 +649,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.13.2-1_s390.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0343
+Build finished at 20111005-1037
-bedtools_2.13.2-1_s390.changes:
+bedtools_2.13.3-1_s390.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -668,33 +672,33 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- e7a4e5318d7991308096426fc79e34c7e994bb0b 521918 bedtools_2.13.2-1_s390.deb
+ 75733846d436cd069c4f45c0bc3798046ff65052 523834 bedtools_2.13.3-1_s390.deb
Checksums-Sha256:
- f1908cf845b67c475baa72db519cafe31b4347991c6f4c79cb579d692f236fc7 521918 bedtools_2.13.2-1_s390.deb
+ 9e78f4027e5e57d87c901ddda8dc8777945d60e788ba990cf4a9c01a5db542a9 523834 bedtools_2.13.3-1_s390.deb
Files:
- b3f8fb410f50aad5b8260751c7d81da8 521918 science optional bedtools_2.13.2-1_s390.deb
+ 31c6269b3eb5b0d34373c12aa2bf4869 523834 science optional bedtools_2.13.3-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_s390.deb
+bedtools_2.13.3-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 521918 bytes: control archive= 1710 bytes.
+ size 523834 bytes: control archive= 1717 bytes.
834 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4884
+ Installed-Size: 4734
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
@@ -709,49 +713,49 @@ bedtools_2.13.2-1_s390.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./usr/bin/
--rwxr-xr-x root/root 284944 2011-09-24 03:43 ./usr/bin/coverageBed
--rwxr-xr-x root/root 105532 2011-09-24 03:43 ./usr/bin/linksBed
--rwxr-xr-x root/root 289552 2011-09-24 03:43 ./usr/bin/windowBed
--rwxr-xr-x root/root 113008 2011-09-24 03:43 ./usr/bin/subtractBed
--rwxr-xr-x root/root 280864 2011-09-24 03:43 ./usr/bin/tagBam
--rwxr-xr-x root/root 114472 2011-09-24 03:43 ./usr/bin/flankBed
--rwxr-xr-x root/root 88196 2011-09-24 03:43 ./usr/bin/overlap
--rwxr-xr-x root/root 228656 2011-09-24 03:43 ./usr/bin/bamToBed
--rwxr-xr-x root/root 109336 2011-09-24 03:43 ./usr/bin/complementBed
--rwxr-xr-x root/root 301784 2011-09-24 03:43 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 112720 2011-09-24 03:43 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 145544 2011-09-24 03:43 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 63620 2011-09-24 03:43 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 370992 2011-09-24 03:43 ./usr/bin/pairToBed
--rwxr-xr-x root/root 235748 2011-09-24 03:43 ./usr/bin/bedToBam
--rwxr-xr-x root/root 97192 2011-09-24 03:43 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 108792 2011-09-24 03:43 ./usr/bin/mergeBed
--rwxr-xr-x root/root 121736 2011-09-24 03:43 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 176088 2011-09-24 03:43 ./usr/bin/pairToPair
--rwxr-xr-x root/root 104460 2011-09-24 03:43 ./usr/bin/annotateBed
--rwxr-xr-x root/root 133192 2011-09-24 03:43 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 145556 2011-09-24 03:43 ./usr/bin/nucBed
--rwxr-xr-x root/root 120852 2011-09-24 03:43 ./usr/bin/closestBed
--rwxr-xr-x root/root 305768 2011-09-24 03:43 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 355256 2011-09-24 03:43 ./usr/bin/intersectBed
--rwxr-xr-x root/root 145416 2011-09-24 03:43 ./usr/bin/sortBed
--rwxr-xr-x root/root 106720 2011-09-24 03:43 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 03:40 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 03:43 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-10-05 10:37 ./
+drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/bin/
+-rwxr-xr-x root/root 285616 2011-10-05 10:37 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 105796 2011-10-05 10:37 ./usr/bin/linksBed
+-rwxr-xr-x root/root 293148 2011-10-05 10:37 ./usr/bin/windowBed
+-rwxr-xr-x root/root 113560 2011-10-05 10:37 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 280868 2011-10-05 10:37 ./usr/bin/tagBam
+-rwxr-xr-x root/root 114968 2011-10-05 10:37 ./usr/bin/flankBed
+-rwxr-xr-x root/root 88452 2011-10-05 10:37 ./usr/bin/overlap
+-rwxr-xr-x root/root 231568 2011-10-05 10:37 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 109648 2011-10-05 10:37 ./usr/bin/complementBed
+-rwxr-xr-x root/root 305448 2011-10-05 10:37 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 112724 2011-10-05 10:37 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 145548 2011-10-05 10:37 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 63832 2011-10-05 10:37 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 371160 2011-10-05 10:37 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 235752 2011-10-05 10:37 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 97464 2011-10-05 10:37 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 109200 2011-10-05 10:37 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 122076 2011-10-05 10:37 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 176448 2011-10-05 10:37 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 104464 2011-10-05 10:37 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 133196 2011-10-05 10:37 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 145560 2011-10-05 10:37 ./usr/bin/nucBed
+-rwxr-xr-x root/root 120916 2011-10-05 10:37 ./usr/bin/closestBed
+-rwxr-xr-x root/root 309532 2011-10-05 10:37 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 358696 2011-10-05 10:37 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 145728 2011-10-05 10:37 ./usr/bin/sortBed
+-rwxr-xr-x root/root 107056 2011-10-05 10:37 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 10:34 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -765,7 +769,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-e31d633e-7e1b-40d9-b9f1-36b200357d2c/build/buildd-bedtools_2.13.2-1-s390-Ao9dea
+Purging /var/lib/schroot/mount/sid-s390-sbuild-f49330f7-0046-47af-b265-29c81e0dd95e/build/buildd-bedtools_2.13.3-1-s390-oUtfeu
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -773,18 +777,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 108664
-Build-Time: 162
+Build-Space: 109228
+Build-Time: 191
Distribution: sid
-Install-Time: 10
-Job: bedtools_2.13.2-1
+Install-Time: 13
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 213
-Source-Version: 2.13.2-1
-Space: 108664
+Package-Time: 247
+Source-Version: 2.13.3-1
+Space: 109228
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0343
-Build needed 00:03:33, 108664k disc space
+Finished at 20111005-1037
+Build needed 00:04:07, 109228k disc space
Signature with key '2D941D26' requested:
diff --git a/sparc.log b/sparc.log
index e9791c7..fe8347d 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,69 @@
-From buildd at schroeder.debian.org Sat Sep 24 05:02:27 2011
-Return-path: <buildd at schroeder.debian.org>
+From buildd at lebrun.debian.org Wed Oct 05 10:14:25 2011
+Return-path: <buildd at lebrun.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1R7KNf-0006Tw-6B
- for logs at buildd.debian.org; Sat, 24 Sep 2011 05:02:27 +0000
-Received: from schroeder.debian.org ([193.198.184.11])
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1RBOUb-0005VT-1V
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:14:25 +0000
+Received: from lebrun.debian.org ([193.198.184.10])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=schroeder.debian.org,
- EMAIL=hostmaster at schroeder.debian.org (verified)
+ CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1R7KNe-0006Gq-DX
- for logs at buildd.debian.org; Sat, 24 Sep 2011 05:02:26 +0000
-Received: from buildd by schroeder.debian.org with local (Exim 4.72)
- (envelope-from <buildd at schroeder.debian.org>)
- id 1R7KNc-0005iG-F3; Sat, 24 Sep 2011 05:02:24 +0000
-Message-Id: <E1R7KNc-0005iG-F3 at schroeder.debian.org>
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1RBOUa-0003N0-4k
+ for logs at buildd.debian.org; Wed, 05 Oct 2011 10:14:24 +0000
+Received: from buildd by lebrun.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1RBOUY-0002Ie-7R; Wed, 05 Oct 2011 10:14:22 +0000
+Message-Id: <E1RBOUY-0002Ie-7R at lebrun.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 24 Sep 2011 05:02:24 +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_2.13.2-1 on sparc (dist=sid)
-Key-Id: 7C392B18
+Date: Wed, 5 Oct 2011 10:14:21 +0000
+From: buildd on lebrun <buildd at lebrun.debian.org>
+To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
+Subject: Log for successful build of bedtools_2.13.3-1 on sparc (dist=sid)
+Key-Id: 632E3DB6
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.2-1 (sparc) 24 Sep 2011 04:50 ║
+║ bedtools 2.13.3-1 (sparc) 05 Oct 2011 10:01 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.2-1
-Source Version: 2.13.2-1
+Version: 2.13.3-1
+Source Version: 2.13.3-1
Architecture: sparc
-Get:1 http://ftp.carnet.hr unstable InRelease [146 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.carnet.hr unstable/main Sources [5783 kB]
-Get:4 http://ftp.carnet.hr unstable/contrib Sources [56.5 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [5816 kB]
+Get:4 http://debian.carnet.hr unstable/contrib Sources [57.1 kB]
Ign http://incoming.debian.org InRelease
-Get:5 http://incoming.debian.org Release.gpg [836 B]
-Get:6 http://ftp.carnet.hr unstable/non-free Sources [102 kB]
-Get:7 http://incoming.debian.org unstable/main Sources [5783 kB]
-Get:8 http://ftp.carnet.hr unstable/main sparc Packages [7578 kB]
-Get:9 http://ftp.carnet.hr unstable/contrib sparc Packages [55.0 kB]
-Ign http://ftp.carnet.hr unstable/contrib TranslationIndex
-Get:10 http://ftp.carnet.hr unstable/main TranslationIndex [2045 B]
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [102 kB]
-Get:13 http://incoming.debian.org unstable/main sparc Packages [7578 kB]
-Ign http://ftp.carnet.hr unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib sparc Packages [55.0 kB]
+Get:5 http://debian.carnet.hr unstable/non-free Sources [103 kB]
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://debian.carnet.hr unstable/main sparc Packages [7604 kB]
+Get:9 http://incoming.debian.org unstable/main Sources [5816 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 [2045 B]
+Get:12 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7604 kB]
+Ign http://debian.carnet.hr unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [33.1 kB]
-Get:18 http://incoming.debian.org Packages [582 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [37.0 kB]
+Get:18 http://incoming.debian.org Packages [266 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 28.1 MB in 29s (966 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 27.9 MB in 29s (945 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,10 +85,10 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (tar) [659 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.2-1 (diff) [4285 B]
-Fetched 666 kB in 1s (379 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
+Fetched 666 kB in 1s (404 kB/s)
Download complete and in download only mode
Check arch
@@ -109,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,11 +125,11 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.13-1)
-dash: already installed (0.5.7-1)
+coreutils: already installed (8.13-2)
+dash: already installed (0.5.7-2)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
+dpkg: already installed (1.16.1)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b2)
grep: already installed (2.9-2)
@@ -149,13 +148,13 @@ mount: already installed (2.19.1-5)
util-linux: already installed (2.19.1-5)
libc6-dev: already installed (2.13-21)
libc6-dev-sparc64: already installed (2.13-21)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.7
+Using default version 8.9.8
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -177,74 +176,74 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 16 not upgraded.
Need to get 9519 kB of archives.
-After this operation, 29.1 MB of additional disk space will be used.
-Get:1 http://ftp.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
-Get:2 http://ftp.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:3 http://ftp.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:4 http://ftp.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:5 http://ftp.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
-Get:6 http://ftp.carnet.hr/debian/ unstable/main libmagic1 sparc 5.08-1 [246 kB]
-Get:7 http://ftp.carnet.hr/debian/ unstable/main file sparc 5.08-1 [51.0 kB]
-Get:8 http://ftp.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-4 [132 kB]
-Get:9 http://ftp.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-4 [816 kB]
-Get:10 http://ftp.carnet.hr/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://ftp.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:12 http://ftp.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
-Get:13 http://ftp.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:14 http://ftp.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
-Get:15 http://ftp.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-4 [1985 kB]
-Get:16 http://ftp.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.carnet.hr/debian/ unstable/main debhelper all 8.9.7 [552 kB]
-Get:19 http://ftp.carnet.hr/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
-Get:20 http://ftp.carnet.hr/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+After this operation, 28.4 MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.08-1 [246 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main file sparc 5.08-1 [51.0 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-4 [132 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-4 [816 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-4 [1985 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
+Get:20 http://debian.carnet.hr/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9519 kB in 8s (1168 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10910 files and directories currently installed.)
+Fetched 9519 kB in 8s (1121 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10902 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_sparc.deb) ...
-Selecting previously deselected package libpcre3.
+Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
-Selecting previously deselected package bsdmainutils.
+Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_sparc.deb) ...
-Selecting previously deselected package groff-base.
+Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
-Selecting previously deselected package man-db.
+Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_sparc.deb) ...
-Selecting previously deselected package libmagic1.
+Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.08-1_sparc.deb) ...
-Selecting previously deselected package file.
+Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.08-1_sparc.deb) ...
-Selecting previously deselected package gettext-base.
+Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_sparc.deb) ...
-Selecting previously deselected package libxml2.
+Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_sparc.deb) ...
-Selecting previously deselected package cdbs.
+Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package html2text.
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
-Selecting previously deselected package libglib2.0-0.
+Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_sparc.deb) ...
-Selecting previously deselected package libcroco3.
+Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
-Selecting previously deselected package libunistring0.
+Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_sparc.deb) ...
-Selecting previously deselected package gettext.
+Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-4_sparc.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
+Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.7_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_sparc.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
+Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
@@ -267,7 +266,7 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.7) ...
+Setting up debhelper (8.9.8) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -275,11 +274,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-11 gcc-4.6_4.6.1-11 libc6-dev_2.13-21 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110910-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-11 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.7 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b2 g++_4:4.6.1-2 g++-4.6_4.6.1-11 gcc_4:4.6.1-2 gcc-4.6_4.6.1-11 gcc-4.6-base_4.6.1-11 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-11 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-11 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-11 libstdc++6-4.6-dev_4.6.1-11 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15+b1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011j-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b2 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15+b1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -290,12 +289,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Sep 24 01:39:55 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.2
-dpkg-source: info: unpacking bedtools_2.13.2.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.3
+dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
+dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -305,30 +304,30 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
+dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.2-1
- dpkg-source --before-build bedtools-2.13.2
+dpkg-buildpackage: source version 2.13.3-1
+ dpkg-source --before-build bedtools-2.13.3
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -341,21 +340,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3/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_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -373,7 +372,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -g -O2 -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -433,6 +432,10 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
+Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
+Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
+Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -602,7 +605,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv/bedtools-2.13.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -647,56 +650,56 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.2-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org> >../bedtools_2.13.2-1_sparc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.13.3-1_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-2.13.2
+ dpkg-source --after-build bedtools-2.13.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110924-0502
+Build finished at 20111005-1014
-bedtools_2.13.2-1_sparc.changes:
+bedtools_2.13.3-1_sparc.changes:
Format: 1.8
-Date: Sat, 24 Sep 2011 09:34:29 +0900
+Date: Wed, 05 Oct 2011 17:18:15 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.13.2-1
+Version: 2.13.3-1
Distribution: sid
Urgency: low
-Maintainer: sparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org>
+Maintainer: sparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.2-1) unstable; urgency=low
+ bedtools (2.13.3-1) unstable; urgency=low
.
- [1930a26] New upstream release.
+ [ea1c596] New upstream release.
Checksums-Sha1:
- b3ad4b837e8575bb425e161992873f279e46ad33 564698 bedtools_2.13.2-1_sparc.deb
+ 6927d20756e9f5d81b86436d7eae3b0888737003 565030 bedtools_2.13.3-1_sparc.deb
Checksums-Sha256:
- bada4915cb9f25370e21de89d7daa1d35a16150206c3844be618f3e1653e3a15 564698 bedtools_2.13.2-1_sparc.deb
+ 55ba5ad7a2549281440a0856edf3255be799946ccc493208fc8630d61dd558ad 565030 bedtools_2.13.3-1_sparc.deb
Files:
- d95e2e1aef3475f6acd284231ebad240 564698 science optional bedtools_2.13.2-1_sparc.deb
+ 072e8e8f3aa5694db71114ca8731de99 565030 science optional bedtools_2.13.3-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.2-1_sparc.deb
+bedtools_2.13.3-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 564698 bytes: control archive= 1721 bytes.
+ size 565030 bytes: control archive= 1722 bytes.
835 bytes, 18 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.2-1
+ Version: 2.13.3-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4732
+ Installed-Size: 4590
Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
@@ -711,49 +714,49 @@ bedtools_2.13.2-1_sparc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-09-24 05:01 ./
-drwxr-xr-x root/root 0 2011-09-24 05:01 ./usr/
-drwxr-xr-x root/root 0 2011-09-24 05:01 ./usr/bin/
--rwxr-xr-x root/root 224264 2011-09-24 05:01 ./usr/bin/bamToBed
--rwxr-xr-x root/root 109468 2011-09-24 05:01 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 60224 2011-09-24 05:01 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 139100 2011-09-24 05:01 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 117480 2011-09-24 05:01 ./usr/bin/closestBed
--rwxr-xr-x root/root 103036 2011-09-24 05:01 ./usr/bin/complementBed
--rwxr-xr-x root/root 117588 2011-09-24 05:01 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 290220 2011-09-24 05:01 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 127160 2011-09-24 05:01 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110372 2011-09-24 05:01 ./usr/bin/flankBed
--rwxr-xr-x root/root 93800 2011-09-24 05:01 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 103928 2011-09-24 05:01 ./usr/bin/linksBed
--rwxr-xr-x root/root 293976 2011-09-24 05:01 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 274436 2011-09-24 05:01 ./usr/bin/coverageBed
--rwxr-xr-x root/root 224548 2011-09-24 05:01 ./usr/bin/bedToBam
--rwxr-xr-x root/root 84768 2011-09-24 05:01 ./usr/bin/overlap
--rwxr-xr-x root/root 281992 2011-09-24 05:01 ./usr/bin/windowBed
--rwxr-xr-x root/root 359456 2011-09-24 05:01 ./usr/bin/pairToBed
--rwxr-xr-x root/root 143824 2011-09-24 05:01 ./usr/bin/sortBed
--rwxr-xr-x root/root 269320 2011-09-24 05:01 ./usr/bin/tagBam
--rwxr-xr-x root/root 105884 2011-09-24 05:01 ./usr/bin/mergeBed
--rwxr-xr-x root/root 347548 2011-09-24 05:01 ./usr/bin/intersectBed
--rwxr-xr-x root/root 101400 2011-09-24 05:01 ./usr/bin/annotateBed
--rwxr-xr-x root/root 109732 2011-09-24 05:01 ./usr/bin/subtractBed
--rwxr-xr-x root/root 139640 2011-09-24 05:01 ./usr/bin/nucBed
--rwxr-xr-x root/root 174888 2011-09-24 05:01 ./usr/bin/pairToPair
--rwxr-xr-x root/root 102496 2011-09-24 05:01 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-09-24 05:01 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-24 05:01 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-24 05:01 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11135 2011-09-23 15:57 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-09-24 00:33 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 417 2011-09-24 00:36 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1442 2011-09-23 15:57 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2011-09-24 05:01 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-09-24 04:52 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-23 15:57 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 565 2011-09-23 15:57 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-10-05 10:13 ./
+drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/
+drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/bin/
+-rwxr-xr-x root/root 298604 2011-10-05 10:13 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 291176 2011-10-05 10:13 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 103476 2011-10-05 10:13 ./usr/bin/complementBed
+-rwxr-xr-x root/root 175004 2011-10-05 10:13 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 274036 2011-10-05 10:13 ./usr/bin/tagBam
+-rwxr-xr-x root/root 142564 2011-10-05 10:13 ./usr/bin/nucBed
+-rwxr-xr-x root/root 282188 2011-10-05 10:13 ./usr/bin/windowBed
+-rwxr-xr-x root/root 142528 2011-10-05 10:13 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 109568 2011-10-05 10:13 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 60340 2011-10-05 10:13 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 347776 2011-10-05 10:13 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 102904 2011-10-05 10:13 ./usr/bin/slopBed
+-rwxr-xr-x root/root 110472 2011-10-05 10:13 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 118112 2011-10-05 10:13 ./usr/bin/closestBed
+-rwxr-xr-x root/root 106176 2011-10-05 10:13 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 117984 2011-10-05 10:13 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 364188 2011-10-05 10:13 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 94224 2011-10-05 10:13 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 127696 2011-10-05 10:13 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 104252 2011-10-05 10:13 ./usr/bin/linksBed
+-rwxr-xr-x root/root 84868 2011-10-05 10:13 ./usr/bin/overlap
+-rwxr-xr-x root/root 276352 2011-10-05 10:13 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 144596 2011-10-05 10:13 ./usr/bin/sortBed
+-rwxr-xr-x root/root 224460 2011-10-05 10:13 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101772 2011-10-05 10:13 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 110908 2011-10-05 10:13 ./usr/bin/flankBed
+-rwxr-xr-x root/root 224712 2011-10-05 10:13 ./usr/bin/bedToBam
+drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-05 10:03 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -767,7 +770,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-2c15d191-6efb-4e44-9df4-c8282f44f07e/build/buildd-bedtools_2.13.2-1-sparc-9x_xrv
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-988ad83e-08e6-4653-9744-f669e0870e35/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -775,18 +778,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 101528
-Build-Time: 610
+Build-Space: 102048
+Build-Time: 622
Distribution: sid
-Install-Time: 55
-Job: bedtools_2.13.2-1
+Install-Time: 66
+Job: bedtools_2.13.3-1
Package: bedtools
-Package-Time: 716
-Source-Version: 2.13.2-1
-Space: 101528
+Package-Time: 740
+Source-Version: 2.13.3-1
+Space: 102048
Status: successful
-Version: 2.13.2-1
+Version: 2.13.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110924-0502
-Build needed 00:11:56, 101528k disc space
-Signature with key '7C392B18' requested:
+Finished at 20111005-1014
+Build needed 00:12:20, 102048k disc space
+Signature with key '632E3DB6' requested:
--
Suite of utilities for comparing genomic features.
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