[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.14.2-1-2-g9249757
Charles Plessy
plessy at debian.org
Thu Jan 5 01:44:30 UTC 2012
The following commit has been merged in the meta branch:
commit 92497579ad12b8889297ea2a6aa31244bc26721a
Author: Charles Plessy <plessy at debian.org>
Date: Thu Jan 5 10:44:19 2012 +0900
Build logs for 2.14.3-1.
diff --git a/armel.log b/armel.log
index 395e7a0..1636a80 100644
--- a/armel.log
+++ b/armel.log
@@ -1,66 +1,67 @@
-From buildd at ancina.debian.org Thu Nov 03 10:54:18 2011
-Return-path: <buildd at ancina.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at alwyn.debian.org Sat Nov 05 02:20:58 2011
+Return-path: <buildd at alwyn.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
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-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Thu, 3 Nov 2011 10:54:10 +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_2.14.2-1 on armel (dist=sid)
-Key-Id: 82E89EDA
-Message-Id: <E1RLuvz-0004kF-06 at ancina.debian.org>
+ CN=alwyn.debian.org, EMAIL=hostmaster at alwyn.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
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+Date: Sat, 05 Nov 2011 02:20:55 +0000
+Message-Id: <E1RMVsN-0000a1-DH at alwyn.debian.org>
+From: buildd on alwyn <buildd at alwyn.debian.org>
+To: buildd-porters at alwyn.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.3-1 on armel (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alwyn.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (armel) 03 Nov 2011 10:31 ║
+║ bedtools 2.14.3-1 (armel) 05 Nov 2011 01:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: armel
-Hit http://ftp.de.debian.org sid InRelease
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5890 kB]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
-Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Hit http://ftp.de.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib Translation-en
-Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org Release [1604 B]
+Get:6 http://incoming.debian.org unstable/main Sources [5890 kB]
+Get:7 http://ftp.uk.debian.org unstable/contrib Sources [56.9 kB]
+Get:8 http://ftp.uk.debian.org unstable/non-free Sources [103 kB]
+Get:9 http://ftp.uk.debian.org unstable/main armel Packages [7651 kB]
+Get:10 http://ftp.uk.debian.org unstable/contrib armel Packages [55.2 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:11 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:12 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:14 http://incoming.debian.org unstable/main armel Packages [7651 kB]
+Get:15 http://incoming.debian.org unstable/contrib armel Packages [55.2 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [25.7 kB]
+Get:18 http://incoming.debian.org Packages [300 kB]
Ign http://incoming.debian.org Translation-en
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 28.1 MB in 1min 4s (437 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,10 +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 928 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 0s (1202 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 1s (797 kB/s)
Download complete and in download only mode
Check arch
@@ -105,12 +106,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -149,45 +150,132 @@ g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
-debhelper: already installed (8.9.8 >= 8 is satisfied)
+debhelper: missing
+Using default version 8.9.9
quilt: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs quilt
+Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts procmail graphviz
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
+ www-browser libmail-box-perl procmail graphviz
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs diffstat quilt
-0 upgraded, 3 newly installed, 0 to remove and 14 not upgraded.
-Need to get 0 B/461 kB of archives.
-After this operation, 1215 kB of additional disk space will be used.
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 21 newly installed, 0 to remove and 25 not upgraded.
+Need to get 9379 kB of archives.
+After this operation, 26.3 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-4 [34.0 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.8-1 [1552 kB]
+Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-5 [815 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-2 [110 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-2 [990 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.09-2 [247 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.09-2 [51.8 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-5 [138 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-5 [1980 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.54-1 [27.7 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 9379 kB in 1s (8558 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10465 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_armel.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_armel.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_armel.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_armel.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armel.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-2_armel.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.09-2_armel.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.09-2_armel.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_armel.deb) ...
Selecting previously unselected package cdbs.
-(Reading database ... 23122 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_armel.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Processing triggers for man-db ...
+Selecting previously unselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
+Setting up libpipeline1 (1.2.0-4) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up libglib2.0-0 (2.28.8-1) ...
+No schema files found: doing nothing.
+Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libcroco3 (0.6.2-2) ...
+Setting up libunistring0 (0.9.3-5) ...
+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 (5.09-2) ...
+Setting up file (5.09-2) ...
+Setting up gettext-base (0.18.1.1-5) ...
Setting up cdbs (0.4.99) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up gettext (0.18.1.1-5) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-1 gcc-4.6_4.6.2-1 libc6-dev_2.13-21 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 linux-libc-dev_3.0.0-5
-Package versions: apex-nslu2_1.6.10 apt_0.8.15.9 apt-utils_0.8.15.9 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_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20111022 cdbs_0.4.99 cmake_2.8.5-1 cmake-data_2.8.5-1 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 cramfsprogs_1.1-6 dash_0.5.7-2 dctrl-tools_2.19 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_4.0.4 devio_1.2-1+b1 diffstat_1.54-1 diffutils_1:3.2-1 dmsetup_2:1.02.67-1 dns323-firmware-tools_0.3-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 emacsen-common_1.4.22 fakeroot_1.18.1-1 file_5.09-2 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_4.6.2-1 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_4.6.2-1 gcc-4.6-base_4.6.2-1 generatorrunner_0.6.14-2 genext2fs_1.4.1-3 genisoimage_9:1.1.11-2 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libapiextractor-dev_0.10.8-1 libapiextractor0.10_0.10.8-1 libarchive1_2.8.5-3+b1 libattr1_1:2.4.46-3 libaudio2_1.9.3-1 libblkid1_2.19.1-5 libbogl-dev_0.1.18-5 libbogl0_0.1.18-5 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-pic_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libcurl3_7.21.7-3 libcurl3-gnutls_7.21.7-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgcrypt11_1.5.0-3 libgd2-noxpm_2.0.36~rc1~dfsg-6 libgdbm3_1.8.3-10 libgenrunner-dev_0.6.14-2 libgenrunner0.6_0.6.14-2 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.11-1 libgomp1_4.6.2-1 libgpg-error0_1.10-1 libgpm2_1.20.4-4 libgssapi-krb5-2_1.9.1+dfsg-3 libhtml-parser-perl_3.69-1 libhtml-tagset-perl_3.20-2 libice6_2:1.0.7-2 libidn11_1.22-3 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 liblcms1_1.19.dfsg-1+b1 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libnewt-dev_0.52.11-2.1 libnewt-pic_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libp11-kit0_0.8-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpython2.6_2.6.7-4 libpython2.7_2.7.2-7 libqt4-dbus_4:4.7.3-8 libqt4-declarative_4:4.7.3-8 libqt4-designer_4:4.7.3-8 libqt4-dev_4:4.7.3-8 libqt4-help_4:4.7.3-8 libqt4-network_4:4.7.3-8 libqt4-qt3support_4:4.7.3-8 libqt4-script_4:4.7.3-8 libqt4-scripttools_4:4.7.3-8 libqt4-sql_4:4.7.3-8 libqt4-svg_4:4.7.3-8 libqt4-test_4:4.7.3-8 libqt4-xml_4:4.7.3-8 libqt4-xmlpatterns_4:4.7.3-8 libqtcore4_4:4.7.3-8 libqtgui4_4:4.7.3-8 libreadline5_5.2-11 libreadline6_6.2-7 libroman-perl_1.23-1 librtmp0_2.4~20110711.gitc28f1bab-1 libruby1.8_1.8.7.352-2 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libsgmls-perl_1.03ii-32 libsigsegv2_2.9-4 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libslang2-pic_2.2.4-3 libsm6_2:1.2.0-2 libsp1c2_1.3.4-1.2.1-47.1 libsparsehash-dev_1.10-1 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-10-16-1 libssh2-1_1.2.8-2 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtasn1-3_2.10-1 libtext-format-perl_0.53-1 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 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 libuuid1_2.19.1-5 libvolume-id1_0.141-2 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-3 libxcb1_1.7-3 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxml2_2.7.8.dfsg-5 libxmlrpc-core-c3_1.16.33-3.1 libxrender1_1:0.9.6-2 libxslt1.1_1.1.26-8 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 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_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 nullmailer_1:1.05-1 openssl_1.0.0e-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.14-1 python_2.7.2-9 python-all_2.7.2-9 python-all-dbg_2.7.2-9 python-all-dev_2.7.2-9 python-dbg_2.7.2-9 python-dev_2.7.2-9 python-minimal_2.7.2-9 python2.6_2.6.7-4 python2.6-dbg_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-7 python2.7-dbg_2.7.2-7 python2.7-dev_2.7.2-7 python2.7-minimal_2.7.2-7 qt4-linguist-tools_4:4.7.3-8 qt4-qmake_4:4.7.3-8 quilt_0.48-8 readline-common_6.2-7 ruby1.8_1.8.7.352-2 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sgmlspl_1.03ii-32 slugimage_1:0.0+r104-5 sp_1.3.4-1.2.1-47.1 sudo_1.8.3-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 ttf-dejavu-core_2.33-2 tzdata_2011n-1 u-boot-tools_2011.09-1 uboot-mkimage_2011.09-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 wget_1.13.4-1 x11-common_1:7.6+9 xml-core_0.13 xsltproc_1.1.26-8 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32 armel (armv5tel)
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-16 gcc-4.6_4.6.1-16 libc6-dev_2.13-21 libstdc++6_4.6.1-16 libstdc++6-4.6-dev_4.6.1-16 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-16 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-16 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-16 gcc-4.6-base_4.6.1-16 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-16 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.1-16 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.1-16 libstdc++6-4.6-dev_4.6.1-16 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,12 +286,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -214,24 +302,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -244,21 +332,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -433,9 +521,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -512,7 +602,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armel-yq6poG/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -557,13 +647,13 @@ dh_shlibdeps -pbedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/flankBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/unionBedGraphs contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/multiBamCov contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bed12ToBed6 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/pairToBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bed12ToBed6 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bamToBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/fastaFromBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/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/fastaFromBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/closestBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/overlap contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/maskFastaFromBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedToBam contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/genomeCoverageBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
@@ -581,59 +671,60 @@ dpkg-shlibdeps: warning: debian/bedtools/usr/bin/linksBed contains an unresolvab
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/slopBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/intersectBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/complementBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/multiIntersectBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.14.2-1_armel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org> >../bedtools_2.14.3-1_armel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-1053
+Build finished at 20111105-0220
-bedtools_2.14.2-1_armel.changes:
+bedtools_2.14.3-1_armel.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
-Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
+Maintainer: armel Build Daemon (alwyn) <buildd_armel-alwyn at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- cf11195f48310815e6789aa682caaf14b6a2dda8 539074 bedtools_2.14.2-1_armel.deb
+ 9ac81c842053d4d71d6a139b7d604afa8468e6d8 554080 bedtools_2.14.3-1_armel.deb
Checksums-Sha256:
- c8756bb902e813a1c124e9514ede1cbdc21dd7747c6bfd5b8f000474594c2628 539074 bedtools_2.14.2-1_armel.deb
+ b08774de3589fa3df41164ead694830e422f5b5cfe7e59c6aa9a12c71df6975b 554080 bedtools_2.14.3-1_armel.deb
Files:
- 33f2a427cfc41a17b6888b9ab33a8cf7 539074 science optional bedtools_2.14.2-1_armel.deb
+ ad26a27042d35a0adce1ab6db83580e4 554080 science optional bedtools_2.14.3-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_armel.deb
+bedtools_2.14.3-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 539074 bytes: control archive= 1725 bytes.
+ size 554080 bytes: control archive= 1759 bytes.
865 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3948
+ Installed-Size: 4067
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -649,7 +740,50 @@ bedtools_2.14.2-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-armel-sbuild-e3368794-2dfc-42e0-8818-e90a3e152634/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools_2.14.2-1_armel.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2011-11-05 02:19 ./
+drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 01:56 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2011-11-05 02:19 ./usr/bin/
+-rwxr-xr-x root/root 92284 2011-11-05 02:19 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 127640 2011-11-05 02:19 ./usr/bin/sortBed
+-rwxr-xr-x root/root 88208 2011-11-05 02:19 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 231848 2011-11-05 02:19 ./usr/bin/windowBed
+-rwxr-xr-x root/root 112836 2011-11-05 02:19 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 92316 2011-11-05 02:19 ./usr/bin/complementBed
+-rwxr-xr-x root/root 92300 2011-11-05 02:19 ./usr/bin/linksBed
+-rwxr-xr-x root/root 75920 2011-11-05 02:19 ./usr/bin/overlap
+-rwxr-xr-x root/root 305600 2011-11-05 02:19 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 122308 2011-11-05 02:19 ./usr/bin/nucBed
+-rwxr-xr-x root/root 121824 2011-11-05 02:19 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 102332 2011-11-05 02:19 ./usr/bin/flankBed
+-rwxr-xr-x root/root 108672 2011-11-05 02:19 ./usr/bin/closestBed
+-rwxr-xr-x root/root 93804 2011-11-05 02:19 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 289208 2011-11-05 02:19 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 240020 2011-11-05 02:19 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 104612 2011-11-05 02:19 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 223664 2011-11-05 02:19 ./usr/bin/tagBam
+-rwxr-xr-x root/root 159572 2011-11-05 02:19 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 186644 2011-11-05 02:19 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 122084 2011-11-05 02:19 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 231824 2011-11-05 02:19 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 240604 2011-11-05 02:19 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 104576 2011-11-05 02:19 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 186804 2011-11-05 02:19 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 55956 2011-11-05 02:19 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 94764 2011-11-05 02:19 ./usr/bin/slopBed
+-rwxr-xr-x root/root 96440 2011-11-05 02:19 ./usr/bin/maskFastaFromBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -663,42 +797,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-e3368794-2dfc-42e0-8818-e90a3e152634/build/buildd-bedtools_2.14.2-1-armel-rFTHtU
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 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 14 not upgraded.
-After this operation, 1215 kB disk space will be freed.
-(Reading database ... 23256 files and directories currently installed.)
-Removing cdbs ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-armel-sbuild-94c973b7-9831-421b-bfce-1b1012141207/build/buildd-bedtools_2.14.3-1-armel-yq6poG
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 98536
-Build-Time: 1288
+Build-Space: 100308
+Build-Time: 1451
Distribution: sid
-Install-Time: 26
-Job: bedtools_2.14.2-1
+Install-Time: 90
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 1344
-Source-Version: 2.14.2-1
-Space: 98536
+Package-Time: 1636
+Source-Version: 2.14.3-1
+Space: 100308
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-1053
-Build needed 00:22:24, 98536k disc space
-Signature with key '82E89EDA' requested:
+Finished at 20111105-0220
+Build needed 00:27:16, 100308k disc space
+Signature with key 'E832C355' requested:
+
diff --git a/armel.log b/armhf.log
similarity index 58%
copy from armel.log
copy to armhf.log
index 395e7a0..76f7413 100644
--- a/armel.log
+++ b/armhf.log
@@ -1,66 +1,67 @@
-From buildd at ancina.debian.org Thu Nov 03 10:54:18 2011
-Return-path: <buildd at ancina.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at hoiby.debian.org Mon Nov 28 19:37:56 2011
+Return-path: <buildd at hoiby.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from 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 ancina.debian.org>)
- id 1RLuw5-0001N1-Sc
- for logs at buildd.debian.org; Thu, 03 Nov 2011 10:54:17 +0000
-Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
+ (Exim 4.72) (envelope-from <buildd at hoiby.debian.org>)
+ id 1RV71Y-00014r-6X
+ for logs at buildd.debian.org; Mon, 28 Nov 2011 19:37:56 +0000
+Received: from [217.140.96.71] (helo=hoiby.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=ancina.debian.org, EMAIL=hostmaster at ancina.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
- id 1RLuw4-0005Xj-UY
- for logs at buildd.debian.org; Thu, 03 Nov 2011 10:54:17 +0000
-Received: from buildd by ancina.debian.org with local (Exim 4.69)
- (envelope-from <buildd at ancina.debian.org>)
- id 1RLuvz-0004kF-06; Thu, 03 Nov 2011 10:54:11 +0000
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Thu, 3 Nov 2011 10:54:10 +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_2.14.2-1 on armel (dist=sid)
-Key-Id: 82E89EDA
-Message-Id: <E1RLuvz-0004kF-06 at ancina.debian.org>
+ CN=hoiby.debian.org, EMAIL=hostmaster at hoiby.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at hoiby.debian.org>)
+ id 1RV71X-0006Vx-9w
+ for logs at buildd.debian.org; Mon, 28 Nov 2011 19:37:55 +0000
+Received: from buildd by hoiby.debian.org with local (Exim 4.77)
+ (envelope-from <buildd at hoiby.debian.org>)
+ id 1RV71V-0001GS-HJ; Mon, 28 Nov 2011 19:37:53 +0000
+From: buildd on hoiby <buildd at hoiby.debian.org>
+To: logs at buildd.debian.org,buildd-porters at hoiby.debian.org
+Subject: Log for successful build of bedtools_2.14.3-1 on armhf (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1RV71V-0001GS-HJ at hoiby.debian.org>
+Date: Mon, 28 Nov 2011 19:37:53 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hoiby.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (armel) 03 Nov 2011 10:31 ║
+║ bedtools 2.14.3-1 (armhf) 28 Nov 2011 19:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
-Architecture: armel
-Hit http://ftp.de.debian.org sid InRelease
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Version: 2.14.3-1
+Source Version: 2.14.3-1
+Architecture: armhf
+Get:1 http://ftp.debian.org unstable InRelease [181 kB]
+Get:2 http://incoming.debian.org unstable InRelease [181 kB]
+Get:3 http://ftp.debian.org unstable/main Sources [5911 kB]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
-Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Hit http://ftp.de.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib Translation-en
-Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [5911 kB]
+Get:6 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:7 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:8 http://incoming.debian.org unstable/main armhf Packages [4552 kB]
+Get:9 http://ftp.debian.org unstable/contrib Sources [56.5 kB]
+Get:10 http://ftp.debian.org unstable/non-free Sources [103 kB]
+Get:11 http://ftp.debian.org unstable/main armhf Packages [4552 kB]
+Get:12 http://incoming.debian.org unstable/contrib armhf Packages [33.7 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:13 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:14 http://incoming.debian.org Release [1616 B]
+Get:15 http://incoming.debian.org Sources [36.7 kB]
+Get:16 http://incoming.debian.org Packages [1092 kB]
+Get:17 http://ftp.debian.org unstable/contrib armhf Packages [33.7 kB]
+Ign http://ftp.debian.org unstable/contrib TranslationIndex
+Get:18 http://ftp.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
+Fetched 22.8 MB in 57s (397 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,10 +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 928 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://ftp.de.debian.org/debian/ sid/main bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 0s (1202 kB/s)
+Get:1 http://ftp.debian.org/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://ftp.debian.org/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://ftp.debian.org/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 0s (1514 kB/s)
Download complete and in download only mode
Check arch
@@ -105,89 +106,156 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Build-Depends: 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 (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-6)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
libc6-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
-debhelper: already installed (8.9.8 >= 8 is satisfied)
+debhelper: missing
+Using default version 8.9.11
quilt: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs quilt
+Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts procmail graphviz
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
+ www-browser libmail-box-perl procmail graphviz
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs diffstat quilt
-0 upgraded, 3 newly installed, 0 to remove and 14 not upgraded.
-Need to get 0 B/461 kB of archives.
-After this operation, 1215 kB of additional disk space will be used.
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 1 not upgraded.
+Need to get 9352 kB of archives.
+After this operation, 24.3 MB of additional disk space will be used.
+Get:1 http://ftp.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.0-5 [32.1 kB]
+Get:2 http://ftp.debian.org/debian/ unstable/main libpcre3 armhf 8.12-4 [222 kB]
+Get:3 http://ftp.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3 [22.2 kB]
+Get:4 http://ftp.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.30.2-4 [1672 kB]
+Get:5 http://ftp.debian.org/debian/ unstable/main libxml2 armhf 2.7.8.dfsg-5 [775 kB]
+Get:6 http://ftp.debian.org/debian/ unstable/main libcroco3 armhf 0.6.2-2 [104 kB]
+Get:7 http://ftp.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5 [404 kB]
+Get:8 http://ftp.debian.org/debian/ unstable/main bsdmainutils armhf 8.2.3 [201 kB]
+Get:9 http://ftp.debian.org/debian/ unstable/main groff-base armhf 1.21-6 [1029 kB]
+Get:10 http://ftp.debian.org/debian/ unstable/main man-db armhf 2.6.0.2-3 [976 kB]
+Get:11 http://ftp.debian.org/debian/ unstable/main libmagic1 armhf 5.09-2 [244 kB]
+Get:12 http://ftp.debian.org/debian/ unstable/main file armhf 5.09-2 [51.6 kB]
+Get:13 http://ftp.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-5 [131 kB]
+Get:14 http://ftp.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://ftp.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15 [97.2 kB]
+Get:16 http://ftp.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-5 [1925 kB]
+Get:17 http://ftp.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://ftp.debian.org/debian/ unstable/main debhelper all 8.9.11 [552 kB]
+Get:20 http://ftp.debian.org/debian/ unstable/main diffstat armhf 1.54-1 [26.4 kB]
+Get:21 http://ftp.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:22 http://ftp.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.3.4.dfsg-3 [200 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 9352 kB in 2s (4360 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10692 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_armhf.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_armhf.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_armhf.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_armhf.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_armhf.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_armhf.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armhf.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armhf.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_armhf.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-3_armhf.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.09-2_armhf.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.09-2_armhf.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_armhf.deb) ...
Selecting previously unselected package cdbs.
-(Reading database ... 23122 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_armhf.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
+Unpacking diffstat (from .../diffstat_1.54-1_armhf.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
-Processing triggers for man-db ...
+Selecting previously unselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armhf.deb) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
+No schema files found: doing nothing.
+Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libcroco3 (0.6.2-2) ...
+Setting up libunistring0 (0.9.3-5) ...
+Setting up bsdmainutils (8.2.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-3) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.09-2) ...
+Setting up file (5.09-2) ...
+Setting up gettext-base (0.18.1.1-5) ...
Setting up cdbs (0.4.99) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up gettext (0.18.1.1-5) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.11) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-1 gcc-4.6_4.6.2-1 libc6-dev_2.13-21 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 linux-libc-dev_3.0.0-5
-Package versions: apex-nslu2_1.6.10 apt_0.8.15.9 apt-utils_0.8.15.9 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_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20111022 cdbs_0.4.99 cmake_2.8.5-1 cmake-data_2.8.5-1 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 cramfsprogs_1.1-6 dash_0.5.7-2 dctrl-tools_2.19 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_4.0.4 devio_1.2-1+b1 diffstat_1.54-1 diffutils_1:3.2-1 dmsetup_2:1.02.67-1 dns323-firmware-tools_0.3-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 emacsen-common_1.4.22 fakeroot_1.18.1-1 file_5.09-2 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_4.6.2-1 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_4.6.2-1 gcc-4.6-base_4.6.2-1 generatorrunner_0.6.14-2 genext2fs_1.4.1-3 genisoimage_9:1.1.11-2 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libapiextractor-dev_0.10.8-1 libapiextractor0.10_0.10.8-1 libarchive1_2.8.5-3+b1 libattr1_1:2.4.46-3 libaudio2_1.9.3-1 libblkid1_2.19.1-5 libbogl-dev_0.1.18-5 libbogl0_0.1.18-5 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-pic_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libcurl3_7.21.7-3 libcurl3-gnutls_7.21.7-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgcrypt11_1.5.0-3 libgd2-noxpm_2.0.36~rc1~dfsg-6 libgdbm3_1.8.3-10 libgenrunner-dev_0.6.14-2 libgenrunner0.6_0.6.14-2 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.11-1 libgomp1_4.6.2-1 libgpg-error0_1.10-1 libgpm2_1.20.4-4 libgssapi-krb5-2_1.9.1+dfsg-3 libhtml-parser-perl_3.69-1 libhtml-tagset-perl_3.20-2 libice6_2:1.0.7-2 libidn11_1.22-3 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 liblcms1_1.19.dfsg-1+b1 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libnewt-dev_0.52.11-2.1 libnewt-pic_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libp11-kit0_0.8-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpython2.6_2.6.7-4 libpython2.7_2.7.2-7 libqt4-dbus_4:4.7.3-8 libqt4-declarative_4:4.7.3-8 libqt4-designer_4:4.7.3-8 libqt4-dev_4:4.7.3-8 libqt4-help_4:4.7.3-8 libqt4-network_4:4.7.3-8 libqt4-qt3support_4:4.7.3-8 libqt4-script_4:4.7.3-8 libqt4-scripttools_4:4.7.3-8 libqt4-sql_4:4.7.3-8 libqt4-svg_4:4.7.3-8 libqt4-test_4:4.7.3-8 libqt4-xml_4:4.7.3-8 libqt4-xmlpatterns_4:4.7.3-8 libqtcore4_4:4.7.3-8 libqtgui4_4:4.7.3-8 libreadline5_5.2-11 libreadline6_6.2-7 libroman-perl_1.23-1 librtmp0_2.4~20110711.gitc28f1bab-1 libruby1.8_1.8.7.352-2 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libsgmls-perl_1.03ii-32 libsigsegv2_2.9-4 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libslang2-pic_2.2.4-3 libsm6_2:1.2.0-2 libsp1c2_1.3.4-1.2.1-47.1 libsparsehash-dev_1.10-1 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-10-16-1 libssh2-1_1.2.8-2 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtasn1-3_2.10-1 libtext-format-perl_0.53-1 libtiff4_3.9.5-2 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python2.6_2.6.7-4 python2.6-dbg_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-7 python2.7-dbg_2.7.2-7 python2.7-dev_2.7.2-7 python2.7-minimal_2.7.2-7 qt4-linguist-tools_4:4.7.3-8 qt4-qmake_4:4.7.3-8 quilt_0.48-8 readline-common_6.2-7 ruby1.8_1.8.7.352-2 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sgmlspl_1.03ii-32 slugimage_1:0.0+r104-5 sp_1.3.4-1.2.1-47.1 sudo_1.8.3-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 ttf-dejavu-core_2.33-2 tzdata_2011n-1 u-boot-tools_2011.09-1 uboot-mkimage_2011.09-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 wget_1.13.4-1 x11-common_1:7.6+9 xml-core_0.13 xsltproc_1.1.26-8 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.35.3 armhf (armv7l)
+Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.2-1 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 g++_4:4.6.2-1 g++-4.6_4.6.2-4 gcc_4:4.6.2-1 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4.1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,12 +266,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -214,24 +282,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
-dpkg-buildpackage: host architecture armel
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -244,21 +312,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -433,9 +501,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -512,7 +582,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -555,19 +625,19 @@ dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/flankBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/unionBedGraphs contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/multiBamCov contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/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/unionBedGraphs contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/pairToBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bed12ToBed6 contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bamToBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/fastaFromBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/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/coverageBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/maskFastaFromBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/bedToBam contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
-dpkg-shlibdeps: warning: debian/bedtools/usr/bin/genomeCoverageBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/annotateBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/genomeCoverageBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/subtractBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/sortBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/pairToPair contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
@@ -581,59 +651,60 @@ dpkg-shlibdeps: warning: debian/bedtools/usr/bin/linksBed contains an unresolvab
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/slopBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/intersectBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dpkg-shlibdeps: warning: debian/bedtools/usr/bin/complementBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
+dpkg-shlibdeps: warning: debian/bedtools/usr/bin/multiIntersectBed contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1 at GCC_3.5: it's probably a plugin.
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.14.2-1_armel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (hoiby) <buildd_armhf-hoiby at buildd.debian.org> >../bedtools_2.14.3-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-1053
+Build finished at 20111128-1937
-bedtools_2.14.2-1_armel.changes:
+bedtools_2.14.3-1_armhf.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
-Architecture: armel
-Version: 2.14.2-1
+Architecture: armhf
+Version: 2.14.3-1
Distribution: sid
Urgency: low
-Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
+Maintainer: armhf Build Daemon (hoiby) <buildd_armhf-hoiby at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- cf11195f48310815e6789aa682caaf14b6a2dda8 539074 bedtools_2.14.2-1_armel.deb
+ 1f26b8312bb54a1a9895c6f948defaf425086de8 570276 bedtools_2.14.3-1_armhf.deb
Checksums-Sha256:
- c8756bb902e813a1c124e9514ede1cbdc21dd7747c6bfd5b8f000474594c2628 539074 bedtools_2.14.2-1_armel.deb
+ 24f1084eb220f71538a0b5d4ae21acb9eed29ec9402de0514a541b0d60f02a1b 570276 bedtools_2.14.3-1_armhf.deb
Files:
- 33f2a427cfc41a17b6888b9ab33a8cf7 539074 science optional bedtools_2.14.2-1_armel.deb
+ 7fcda3bf8e157d83110453bdb9dd6b81 570276 science optional bedtools_2.14.3-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_armel.deb
+bedtools_2.14.3-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
- size 539074 bytes: control archive= 1725 bytes.
+ size 570276 bytes: control archive= 1760 bytes.
865 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
- Architecture: armel
+ Version: 2.14.3-1
+ Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3948
+ Installed-Size: 2966
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -649,7 +720,50 @@ bedtools_2.14.2-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-armel-sbuild-e3368794-2dfc-42e0-8818-e90a3e152634/build/buildd-bedtools_2.14.2-1-armel-rFTHtU/bedtools_2.14.2-1_armel.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2011-11-28 19:37 ./
+drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/
+drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/bin/
+-rwxr-xr-x root/root 178576 2011-11-28 19:37 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 77380 2011-11-28 19:37 ./usr/bin/closestBed
+-rwxr-xr-x root/root 166664 2011-11-28 19:37 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 117460 2011-11-28 19:37 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 65428 2011-11-28 19:37 ./usr/bin/complementBed
+-rwxr-xr-x root/root 68044 2011-11-28 19:37 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 65272 2011-11-28 19:37 ./usr/bin/linksBed
+-rwxr-xr-x root/root 137552 2011-11-28 19:37 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 43308 2011-11-28 19:37 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 89672 2011-11-28 19:37 ./usr/bin/nucBed
+-rwxr-xr-x root/root 65132 2011-11-28 19:37 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 137508 2011-11-28 19:37 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 211344 2011-11-28 19:37 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 92260 2011-11-28 19:37 ./usr/bin/sortBed
+-rwxr-xr-x root/root 53396 2011-11-28 19:37 ./usr/bin/overlap
+-rwxr-xr-x root/root 75880 2011-11-28 19:37 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 67864 2011-11-28 19:37 ./usr/bin/slopBed
+-rwxr-xr-x root/root 62032 2011-11-28 19:37 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 73180 2011-11-28 19:37 ./usr/bin/flankBed
+-rwxr-xr-x root/root 88244 2011-11-28 19:37 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 167468 2011-11-28 19:37 ./usr/bin/windowBed
+-rwxr-xr-x root/root 89108 2011-11-28 19:37 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 174468 2011-11-28 19:37 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 162188 2011-11-28 19:37 ./usr/bin/tagBam
+-rwxr-xr-x root/root 223900 2011-11-28 19:37 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 75924 2011-11-28 19:37 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 67696 2011-11-28 19:37 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 80140 2011-11-28 19:37 ./usr/bin/shuffleBed
+drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-28 19:17 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-28 19:37 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -663,42 +777,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-e3368794-2dfc-42e0-8818-e90a3e152634/build/buildd-bedtools_2.14.2-1-armel-rFTHtU
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 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 14 not upgraded.
-After this operation, 1215 kB disk space will be freed.
-(Reading database ... 23256 files and directories currently installed.)
-Removing cdbs ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-9447f43e-bdd4-452f-b900-d5db504db0ef/build/buildd-bedtools_2.14.3-1-armhf-Rh0FWh
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Architecture: armel
-Build-Space: 98536
-Build-Time: 1288
+Architecture: armhf
+Build-Space: 98576
+Build-Time: 1201
Distribution: sid
-Install-Time: 26
-Job: bedtools_2.14.2-1
+Install-Time: 61
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 1344
-Source-Version: 2.14.2-1
-Space: 98536
+Package-Time: 1346
+Source-Version: 2.14.3-1
+Space: 98576
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-1053
-Build needed 00:22:24, 98536k disc space
-Signature with key '82E89EDA' requested:
+Finished at 20111128-1937
+Build needed 00:22:26, 98576k disc space
+Signature with key '49088707' requested:
+
diff --git a/hurd-i386.log b/hurd-i386.log
index 78fc3c8..d89c9cf 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,23 +1,23 @@
-From buildd at rossini.debian.net Thu Nov 03 04:07:06 2011
+From buildd at rossini.debian.net Sat Nov 05 11:59:02 2011
Return-path: <buildd at rossini.debian.net>
Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1RLoZy-0005x0-Og
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:07:06 +0000
+ id 1RMetp-0005vK-Dy
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 11:59:02 +0000
Received: from hurd.ethz.ch ([192.33.98.55] helo=rossini.debian.net)
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(Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1RLoZt-0002zC-UU; Thu, 03 Nov 2011 05:06:58 +0100
+ id 1RMetj-000JFM-Ty; Sat, 05 Nov 2011 12:58:56 +0100
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- id 1RLoZs-0000HZ-G6; Thu, 03 Nov 2011 04:06:56 +0000
-Date: Thu, 03 Nov 2011 04:06:56 +0000
-Message-Id: <E1RLoZs-0000HZ-G6 at rossini.debian.net>
+ id 1RMeti-0001HI-34; Sat, 05 Nov 2011 11:58:54 +0000
+Date: Sat, 05 Nov 2011 11:58:54 +0000
+Message-Id: <E1RMeti-0001HI-34 at rossini.debian.net>
From: Build Daemon <buildd at rossini.debian.net>
To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on hurd-i386 (dist=sid)
+Subject: Log for successful build of bedtools_2.14.3-1 on hurd-i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -25,12 +25,12 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rossini.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (hurd-i386) 03 Nov 2011 03:50 ║
+║ bedtools 2.14.3-1 (hurd-i386) 05 Nov 2011 11:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: hurd-i386
Ign file: ./ InRelease
Ign file: ./ Release.gpg
@@ -41,34 +41,34 @@ Hit http://ftp.ch.debian.org experimental InRelease
Hit http://ftp.fr.debian.org unstable InRelease
Hit http://ftp.fr.debian.org experimental InRelease
Ign http://incoming.debian.org InRelease
-Ign http://ftp.debian-ports.org unreleased InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
Hit http://ftp.ch.debian.org unstable/main Sources/DiffIndex
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Get:2 http://incoming.debian.org Release [1604 B]
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Ign http://ftp.debian-ports.org unreleased InRelease
Hit http://ftp.ch.debian.org unstable/contrib Sources/DiffIndex
Hit http://ftp.ch.debian.org unstable/non-free Sources/DiffIndex
Hit http://ftp.ch.debian.org unstable/main hurd-i386 Packages/DiffIndex
Hit http://ftp.ch.debian.org unstable/main TranslationIndex
-Hit http://ftp.debian-ports.org unreleased Release
+Hit http://incoming.debian.org Release
Hit http://ftp.ch.debian.org experimental/main Sources/DiffIndex
Hit http://ftp.ch.debian.org experimental/contrib Sources/DiffIndex
Hit http://ftp.ch.debian.org experimental/non-free Sources/DiffIndex
+Hit http://ftp.debian-ports.org unreleased Release.gpg
Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
-Get:3 http://incoming.debian.org Sources [40.9 kB]
+Hit http://ftp.debian-ports.org unreleased Release
Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
-Get:4 http://incoming.debian.org Packages [602 kB]
Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.fr.debian.org unstable/main TranslationIndex
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Hit http://incoming.debian.org Sources
+Hit http://ftp.fr.debian.org unstable/main TranslationIndex
Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
+Hit http://incoming.debian.org Packages
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
Ign http://incoming.debian.org Translation-en
Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Fetched 646 kB in 2min 35s (4163 B/s)
+Fetched 836 B in 2min 50s (5 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,10 +90,10 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 6s (152 kB/s)
+Get:1 http://ftp.ch.debian.org/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://ftp.ch.debian.org/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://ftp.ch.debian.org/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 0s (1742 kB/s)
Download complete and in download only mode
Check arch
@@ -116,7 +116,7 @@ Reading state information...
The following package was automatically installed and is no longer required:
libboost-iostreams1.42.0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -124,7 +124,7 @@ Reading state information...
The following package was automatically installed and is no longer required:
libboost-iostreams1.42.0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -141,14 +141,14 @@ dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
hurd: already installed (20110519-3)
ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
+ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -164,7 +164,7 @@ dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
hurd-dev: already installed (20110519-3)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -187,7 +187,7 @@ The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
libcroco3 libexpat1 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
quilt zlib1g-dev
-0 upgraded, 17 newly installed, 0 to remove and 22 not upgraded.
+0 upgraded, 17 newly installed, 0 to remove and 21 not upgraded.
Need to get 0 B/7203 kB of archives.
After this operation, 20.4 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
@@ -196,7 +196,7 @@ WARNING: The following packages cannot be authenticated!
diffstat quilt zlib1g-dev
Authentication warning overridden.
Selecting previously unselected package libglib2.0-0.
-(Reading database ... 12467 files and directories currently installed.)
+(Reading database ... 12466 files and directories currently installed.)
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_hurd-i386.deb) ...
Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_hurd-i386.deb) ...
@@ -223,7 +223,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
Selecting previously unselected package quilt.
@@ -246,7 +246,7 @@ Setting up html2text (1.3.2a-15+b1) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -257,11 +257,11 @@ Reading state information...
The following package was automatically installed and is no longer required:
libboost-iostreams1.42.0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 hurd-dev_20110519-3 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.4_4.4.6-11 cpp-4.5_4.5.3-9 cpp-4.6_4.6.1-9+hurd.1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.15.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-11 gcc-4.4-base_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.4_4.4.6-11 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-11 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.42.0_1.42.0-4+b3 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 libexpat1_2.0.1-7.2 libfribidi0_0.19.2-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgmpxx4ldbl_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libident_0.22-3 libidn11_1.22-3 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libnewt0.52_0.52.11-2.1 libobjc2_4.5.3-9 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-7 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-08-10-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 type-handling_0.2.23 tzdata_2011l-1 util-linux_2.19.1-5 wget_1.13-1 whiptail_0.52.11-2.1 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.4_4.4.6-11 cpp-4.5_4.5.3-9 cpp-4.6_4.6.1-9+hurd.1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.15.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-11 gcc-4.4-base_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.4_4.4.6-11 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-11 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.42.0_1.42.0-4+b3 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 libexpat1_2.0.1-7.2 libfribidi0_0.19.2-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgmpxx4ldbl_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libident_0.22-3 libidn11_1.22-3 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libnewt0.52_0.52.11-2.1 libobjc2_4.5.3-9 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-7 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-08-10-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 type-handling_0.2.23 tzdata_2011l-1 util-linux_2.19.1-5 wget_1.13-1 whiptail_0.52.11-2.1 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -272,12 +272,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -293,24 +293,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-p
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -323,21 +323,21 @@ rm -f debian/stamp-patch*
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -422,9 +422,9 @@ Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t,
* 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]
+ * compiling genomeFile.cpp
- Building in src/annotateBed
* compiling annotateMain.cpp
@@ -516,9 +516,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -583,11 +585,11 @@ tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunuse
- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
+ * compiling unionBedGraphsMain.cpp
unionBedGraphsMain.cpp: In function 'int main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
- * compiling unionBedGraphsMain.cpp
* linking unionBedGraphs
- Building in src/windowBed
@@ -595,7 +597,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR/bedtools-2.14.3'
touch debian/stamp-makefile-build
/usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
@@ -640,22 +642,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../bedtools_2.14.2-1_hurd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../bedtools_2.14.3-1_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0406
+Build finished at 20111105-1158
-bedtools_2.14.2-1_hurd-i386.changes:
+bedtools_2.14.3-1_hurd-i386.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
@@ -663,33 +665,33 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- dc6a53d72b587f81b0be5abcadecf3d826d25762 685282 bedtools_2.14.2-1_hurd-i386.deb
+ 78cec7a6dc1559b1477c22d1c3036be5c04d2b78 706072 bedtools_2.14.3-1_hurd-i386.deb
Checksums-Sha256:
- 5150c5992855eec99032e6f24e2d15f1f465b16e349784c56556a4af99c1c84c 685282 bedtools_2.14.2-1_hurd-i386.deb
+ 5d896b34dce2b5c8bba0c6683c96c43fee283b0ef4530ebffd4e3991d10ee531 706072 bedtools_2.14.3-1_hurd-i386.deb
Files:
- a9812484c705604e1d0e333bfb4af2b8 685282 science optional bedtools_2.14.2-1_hurd-i386.deb
+ d53831595be0a04ce1b9d29268576cb0 706072 science optional bedtools_2.14.3-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_hurd-i386.deb
+bedtools_2.14.3-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 685282 bytes: control archive= 1737 bytes.
+ size 706072 bytes: control archive= 1767 bytes.
869 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4655
+ Installed-Size: 4793
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.3 (>= 2.4), libgcc1 (>= 4.2.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -705,49 +707,50 @@ bedtools_2.14.2-1_hurd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 04:04 ./
-drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 03:54 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-03 04:04 ./usr/bin/
--rwxr-xr-x root/root 104532 2011-11-03 04:04 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223904 2011-11-03 04:04 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96364 2011-11-03 04:04 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 228132 2011-11-03 04:04 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121688 2011-11-03 04:04 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 122976 2011-11-03 04:04 ./usr/bin/closestBed
--rwxr-xr-x root/root 105832 2011-11-03 04:04 ./usr/bin/complementBed
--rwxr-xr-x root/root 285024 2011-11-03 04:04 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142684 2011-11-03 04:04 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 114788 2011-11-03 04:04 ./usr/bin/flankBed
--rwxr-xr-x root/root 301428 2011-11-03 04:04 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350580 2011-11-03 04:04 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105984 2011-11-03 04:04 ./usr/bin/linksBed
--rwxr-xr-x root/root 109928 2011-11-03 04:04 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 108636 2011-11-03 04:04 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297452 2011-11-03 04:04 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 142848 2011-11-03 04:04 ./usr/bin/nucBed
--rwxr-xr-x root/root 88172 2011-11-03 04:04 ./usr/bin/overlap
--rwxr-xr-x root/root 366976 2011-11-03 04:04 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178292 2011-11-03 04:04 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129976 2011-11-03 04:04 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105704 2011-11-03 04:04 ./usr/bin/slopBed
--rwxr-xr-x root/root 143848 2011-11-03 04:04 ./usr/bin/sortBed
--rwxr-xr-x root/root 113436 2011-11-03 04:04 ./usr/bin/subtractBed
--rwxr-xr-x root/root 272752 2011-11-03 04:04 ./usr/bin/tagBam
--rwxr-xr-x root/root 59976 2011-11-03 04:04 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285032 2011-11-03 04:04 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-11-05 11:55 ./
+drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 11:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 11:44 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-05 11:55 ./usr/bin/
+-rwxr-xr-x root/root 104532 2011-11-05 11:55 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223904 2011-11-05 11:55 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96364 2011-11-05 11:55 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 228132 2011-11-05 11:55 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121688 2011-11-05 11:55 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 122976 2011-11-05 11:55 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105832 2011-11-05 11:55 ./usr/bin/complementBed
+-rwxr-xr-x root/root 285024 2011-11-05 11:55 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142684 2011-11-05 11:55 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 114788 2011-11-05 11:55 ./usr/bin/flankBed
+-rwxr-xr-x root/root 301428 2011-11-05 11:55 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350580 2011-11-05 11:55 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105984 2011-11-05 11:55 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109928 2011-11-05 11:55 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 108636 2011-11-05 11:55 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297452 2011-11-05 11:55 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 141472 2011-11-05 11:55 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 142848 2011-11-05 11:55 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88172 2011-11-05 11:55 ./usr/bin/overlap
+-rwxr-xr-x root/root 366976 2011-11-05 11:55 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178292 2011-11-05 11:55 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129976 2011-11-05 11:55 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 105704 2011-11-05 11:55 ./usr/bin/slopBed
+-rwxr-xr-x root/root 143848 2011-11-05 11:55 ./usr/bin/sortBed
+-rwxr-xr-x root/root 113436 2011-11-05 11:55 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 272752 2011-11-05 11:55 ./usr/bin/tagBam
+-rwxr-xr-x root/root 59976 2011-11-05 11:55 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285032 2011-11-05 11:55 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -761,14 +764,14 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.14.2-1-hurd-i386-gOrR50
+Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.14.3-1-hurd-i386-yYHAkR
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
libboost-iostreams1.42.0
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -779,9 +782,9 @@ The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
intltool-debian* libcroco3* libexpat1* libglib2.0-0* libmagic1*
libunistring0* libxml2* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 17 to remove and 22 not upgraded.
+0 upgraded, 0 newly installed, 17 to remove and 21 not upgraded.
After this operation, 20.4 MB disk space will be freed.
-(Reading database ... 13441 files and directories currently installed.)
+(Reading database ... 13440 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -815,18 +818,18 @@ Processing triggers for install-info ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 95452
-Build-Time: 718
+Build-Space: 97260
+Build-Time: 846
Distribution: sid
-Install-Time: 58
-Job: bedtools_2.14.2-1
+Install-Time: 71
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 979
-Source-Version: 2.14.2-1
-Space: 95452
+Package-Time: 1125
+Source-Version: 2.14.3-1
+Space: 97260
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0406
-Build needed 00:16:19, 95452k disc space
+Finished at 20111105-1158
+Build needed 00:18:45, 97260k disc space
diff --git a/i386.log b/i386.log
index 41f2126..fcba8c2 100644
--- a/i386.log
+++ b/i386.log
@@ -1,68 +1,67 @@
-From buildd at biber.debian.org Thu Nov 03 03:44:34 2011
-Return-path: <buildd at biber.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at murphy.debian.org Sat Nov 05 02:00:38 2011
+Return-path: <buildd at murphy.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1RLoEE-0002fd-MP
- for logs at buildd.debian.org; Thu, 03 Nov 2011 03:44:34 +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 1RMVYj-0008Cu-S1
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:37 +0000
+Received: from murphy.debian.org ([70.103.162.31])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1RLoED-0002VL-Oe; Thu, 03 Nov 2011 03:44:33 +0000
-Received: from buildd by biber.debian.org with local (Exim 4.72)
- (envelope-from <buildd at biber.debian.org>)
- id 1RLoED-0006lz-5A; Thu, 03 Nov 2011 03:44:33 +0000
-Message-Id: <E1RLoED-0006lz-5A at biber.debian.org>
+ CN=murphy.debian.org, EMAIL=hostmaster at murphy.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
+ id 1RMVYi-0000ek-Qj
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:37 +0000
+Received: from buildd by murphy.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at murphy.debian.org>)
+ id 1RMVYg-0005pu-SP; Sat, 05 Nov 2011 02:00:34 +0000
+Message-Id: <E1RMVYg-0005pu-SP at murphy.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 3 Nov 2011 03:44:33 +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_2.14.2-1 on i386 (dist=sid)
-Key-Id: C83D412C
+Date: Sat, 5 Nov 2011 02:00:34 +0000
+From: buildd on murphy <buildd at murphy.debian.org>
+To: logs at buildd.debian.org,buildd-admin at murphy.debian.org
+Subject: Log for successful build of bedtools_2.14.3-1 on i386 (dist=sid)
+Key-Id: B074D6C9
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 2.14.2-1 (i386) 03 Nov 2011 03:40 ║
+║ bedtools 2.14.3-1 (i386) 05 Nov 2011 01:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5889 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [56.9 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [104 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7821 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.2 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
+Hit http://incoming.debian.org sid InRelease
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 [5896 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7820 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [68.2 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 [47.2 kB]
-Get:18 http://incoming.debian.org Packages [605 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Hit http://ftp.us.debian.org sid InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/main i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.us.debian.org sid/main i386 Packages/DiffIndex
+Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
+Ign http://ftp.us.debian.org sid/contrib TranslationIndex
+Hit http://ftp.us.debian.org sid/main TranslationIndex
+Get:3 http://incoming.debian.org Sources [25.7 kB]
+Get:4 http://incoming.debian.org Packages [300 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://ftp.us.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.8 MB in 31s (904 kB/s)
+Fetched 328 kB in 4s (73.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,10 +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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 2s (425 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 2s (330 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +106,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 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 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -135,7 +134,7 @@ 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)
+ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -152,7 +151,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -174,34 +173,12 @@ 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 16 not upgraded.
-Need to get 9694 kB of archives.
-After this operation, 27.3 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-4 [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 libglib2.0-0 i386 2.28.8-1 [1633 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-5 [882 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-2 [122 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.3 [203 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.2-2 [1013 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.09-2 [246 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.09-2 [51.5 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-5 [133 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-5 [2025 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 8.9.8 [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]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9694 kB in 0s (9802 kB/s)
+0 upgraded, 21 newly installed, 0 to remove and 7 not upgraded.
+Need to get 0 B/9694 kB of archives.
+After this operation, 27.3 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 10638 files and directories currently installed.)
+(Reading database ... 10684 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_i386.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
@@ -236,7 +213,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_i386.deb) ...
Selecting previously unselected package quilt.
@@ -264,7 +241,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -272,11 +249,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-2 gcc-4.6_4.6.2-2 libc6-dev_2.13-21 libstdc++6_4.6.2-2 libstdc++6-4.6-dev_4.6.2-2 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-2 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_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-2 gcc_4:4.6.1-3 gcc-4.6_4.6.2-2 gcc-4.6-base_4.6.2-2 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libquadmath0_4.6.2-2 libreadline6_6.2-7 libselinux1_2.1.0-3 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-2 libstdc++6-4.6-dev_4.6.2-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libquadmath0_4.6.2-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +264,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -303,24 +280,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -333,21 +310,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -522,9 +499,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -601,7 +580,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -646,56 +625,56 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.14.2-1_i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../bedtools_2.14.3-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0344
+Build finished at 20111105-0200
-bedtools_2.14.2-1_i386.changes:
+bedtools_2.14.3-1_i386.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.14.2-1
+Version: 2.14.3-1
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 (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- edd41d0a01700b5ff047a82dd5bf70650b346300 682334 bedtools_2.14.2-1_i386.deb
+ 5cb5267c0ba90f19deb8065c4dc6383f8e15050a 703702 bedtools_2.14.3-1_i386.deb
Checksums-Sha256:
- 89d0a8f40b651d682757545bf6ca5e9bf662cb83d5de705da997c907179d0307 682334 bedtools_2.14.2-1_i386.deb
+ 190d957c7b3fe6b270e9ecbc0baae04c370f18ec721f7876026f0c4faebe5d15 703702 bedtools_2.14.3-1_i386.deb
Files:
- 0aea0bd694c0be19d013c9997a322fd6 682334 science optional bedtools_2.14.2-1_i386.deb
+ 7834daa25db8853a9098b1a19d9441bf 703702 science optional bedtools_2.14.3-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_i386.deb
+bedtools_2.14.3-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 682334 bytes: control archive= 1733 bytes.
+ size 703702 bytes: control archive= 1757 bytes.
864 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4643
+ Installed-Size: 4782
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -711,49 +690,50 @@ bedtools_2.14.2-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/bin/
--rwxr-xr-x root/root 142420 2011-11-03 03:44 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 59648 2011-11-03 03:44 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 96356 2011-11-03 03:44 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227744 2011-11-03 03:44 ./usr/bin/bedToBam
--rwxr-xr-x root/root 114204 2011-11-03 03:44 ./usr/bin/flankBed
--rwxr-xr-x root/root 143008 2011-11-03 03:44 ./usr/bin/sortBed
--rwxr-xr-x root/root 297312 2011-11-03 03:44 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 105688 2011-11-03 03:44 ./usr/bin/linksBed
--rwxr-xr-x root/root 142360 2011-11-03 03:44 ./usr/bin/nucBed
--rwxr-xr-x root/root 350572 2011-11-03 03:44 ./usr/bin/intersectBed
--rwxr-xr-x root/root 112756 2011-11-03 03:44 ./usr/bin/subtractBed
--rwxr-xr-x root/root 285024 2011-11-03 03:44 ./usr/bin/windowBed
--rwxr-xr-x root/root 109600 2011-11-03 03:44 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 272744 2011-11-03 03:44 ./usr/bin/tagBam
--rwxr-xr-x root/root 129456 2011-11-03 03:44 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 281864 2011-11-03 03:44 ./usr/bin/coverageBed
--rwxr-xr-x root/root 107064 2011-11-03 03:44 ./usr/bin/mergeBed
--rwxr-xr-x root/root 104524 2011-11-03 03:44 ./usr/bin/annotateBed
--rwxr-xr-x root/root 88164 2011-11-03 03:44 ./usr/bin/overlap
--rwxr-xr-x root/root 122020 2011-11-03 03:44 ./usr/bin/closestBed
--rwxr-xr-x root/root 178284 2011-11-03 03:44 ./usr/bin/pairToPair
--rwxr-xr-x root/root 105472 2011-11-03 03:44 ./usr/bin/complementBed
--rwxr-xr-x root/root 223548 2011-11-03 03:44 ./usr/bin/bamToBed
--rwxr-xr-x root/root 301420 2011-11-03 03:44 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 366968 2011-11-03 03:44 ./usr/bin/pairToBed
--rwxr-xr-x root/root 121520 2011-11-03 03:44 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 105344 2011-11-03 03:44 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 03:41 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/bin/
+-rwxr-xr-x root/root 121520 2011-11-05 02:00 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 141464 2011-11-05 02:00 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 301420 2011-11-05 02:00 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 272744 2011-11-05 02:00 ./usr/bin/tagBam
+-rwxr-xr-x root/root 96356 2011-11-05 02:00 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 142360 2011-11-05 02:00 ./usr/bin/nucBed
+-rwxr-xr-x root/root 143008 2011-11-05 02:00 ./usr/bin/sortBed
+-rwxr-xr-x root/root 285024 2011-11-05 02:00 ./usr/bin/windowBed
+-rwxr-xr-x root/root 122020 2011-11-05 02:00 ./usr/bin/closestBed
+-rwxr-xr-x root/root 281864 2011-11-05 02:00 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 109600 2011-11-05 02:00 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 104524 2011-11-05 02:00 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 142420 2011-11-05 02:00 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 129456 2011-11-05 02:00 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 366968 2011-11-05 02:00 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 107064 2011-11-05 02:00 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 105472 2011-11-05 02:00 ./usr/bin/complementBed
+-rwxr-xr-x root/root 297312 2011-11-05 02:00 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 88164 2011-11-05 02:00 ./usr/bin/overlap
+-rwxr-xr-x root/root 178284 2011-11-05 02:00 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 105688 2011-11-05 02:00 ./usr/bin/linksBed
+-rwxr-xr-x root/root 112756 2011-11-05 02:00 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 227744 2011-11-05 02:00 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 59648 2011-11-05 02:00 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 223548 2011-11-05 02:00 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 114204 2011-11-05 02:00 ./usr/bin/flankBed
+-rwxr-xr-x root/root 350572 2011-11-05 02:00 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105344 2011-11-05 02:00 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 01:56 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -767,26 +747,73 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-c2668e15-cbf5-4daf-b806-fe3c94bb1ee8/build/buildd-bedtools_2.14.2-1-i386-u4h74k
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-i386-sbuild-9ac3eda1-5379-41f1-b5fc-933636f6c548/build/buildd-bedtools_2.14.3-1-i386-gPe2Lj
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base*
+ groff-base* html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
+ libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 21 to remove and 7 not upgraded.
+After this operation, 27.3 MB disk space will be freed.
+(Reading database ... 12161 files and directories currently installed.)
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing debhelper ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing cdbs ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 94984
-Build-Time: 173
+Build-Space: 96784
+Build-Time: 212
Distribution: sid
-Install-Time: 40
-Job: bedtools_2.14.2-1
+Install-Time: 10
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 258
-Source-Version: 2.14.2-1
-Space: 94984
+Package-Time: 236
+Source-Version: 2.14.3-1
+Space: 96784
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0344
-Build needed 00:04:18, 94984k disc space
-Signature with key 'C83D412C' requested:
+Finished at 20111105-0200
+Build needed 00:03:56, 96784k disc space
+Signature with key 'B074D6C9' requested:
diff --git a/ia64.log b/ia64.log
index fb4f5c7..eeeadfe 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,66 +1,67 @@
-From buildd at mundy.debian.org Thu Nov 03 06:50:36 2011
-Return-path: <buildd at mundy.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at alkman.debian.org Sat Nov 05 02:06:34 2011
+Return-path: <buildd at alkman.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=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 mundy.debian.org>)
- id 1RLr8G-0004d7-J3
- for logs at buildd.debian.org; Thu, 03 Nov 2011 06:50:36 +0000
-Received: from mundy.debian.org ([192.25.206.62])
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1RMVeT-0000ZB-MY
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:06:33 +0000
+Received: from alkman.debian.org ([192.25.206.63])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mundy.debian.org, EMAIL=hostmaster at mundy.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
- id 1RLr8F-0002SW-4b; Thu, 03 Nov 2011 06:50:35 +0000
-Received: from buildd by mundy.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mundy.debian.org>)
- id 1RLr8C-0005y1-EX; Thu, 03 Nov 2011 06:50:32 +0000
-Date: Thu, 03 Nov 2011 06:50:32 +0000
-Message-Id: <E1RLr8C-0005y1-EX at mundy.debian.org>
-From: buildd on mundy <buildd at mundy.debian.org>
-To: dannf at master.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on ia64 (dist=sid)
+ CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1RMVeR-0000vM-JX
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:06:32 +0000
+Received: from buildd by alkman.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at alkman.debian.org>)
+ id 1RMVeP-0002kB-2X; Sat, 05 Nov 2011 02:06:29 +0000
+Date: Sat, 05 Nov 2011 02:06:29 +0000
+Message-Id: <E1RMVeP-0002kB-2X at alkman.debian.org>
+From: buildd on alkman <buildd at alkman.debian.org>
+To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.3-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mundy.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (ia64) 03 Nov 2011 06:39 ║
+║ bedtools 2.14.3-1 (ia64) 05 Nov 2011 01:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: ia64
Get:1 http://spohr.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://spohr.debian.org unstable/main Sources [5896 kB]
-Ign http://incoming.debian.org InRelease
+Get:3 http://spohr.debian.org unstable/main Sources [5890 kB]
Get:4 http://spohr.debian.org unstable/contrib Sources [56.9 kB]
-Get:5 http://incoming.debian.org Release.gpg [836 B]
-Get:6 http://spohr.debian.org unstable/non-free Sources [104 kB]
-Get:7 http://spohr.debian.org unstable/main ia64 Packages [7525 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [103 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [7529 kB]
+Ign http://incoming.debian.org InRelease
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org unstable/main Sources [5890 kB]
Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [55.9 kB]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
Ign http://spohr.debian.org unstable/contrib Translation-en
Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [7525 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [7529 kB]
Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [55.9 kB]
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 [38.7 kB]
-Get:18 http://incoming.debian.org Packages [609 kB]
+Get:17 http://incoming.debian.org Sources [25.7 kB]
+Get:18 http://incoming.debian.org Packages [300 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.2 MB in 19s (1475 kB/s)
+Fetched 27.9 MB in 23s (1187 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,10 +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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 1s (919 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 1s (887 kB/s)
Download complete and in download only mode
Check arch
@@ -108,7 +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 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -116,7 +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 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -156,7 +157,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -181,32 +182,32 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 46 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 51 not upgraded.
Need to get 11.4 MB of archives.
After this operation, 38.5 MB of additional disk space will be used.
Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-4 [46.7 kB]
Get:2 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
Get:3 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.8-1 [1992 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-5 [1177 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-2 [147 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-5 [463 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-2 [1118 kB]
-Get:10 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.09-2 [271 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main file ia64 5.09-2 [54.4 kB]
-Get:12 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-5 [173 kB]
-Get:13 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-5 [2439 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 8.9.8 [552 kB]
+Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
+Get:5 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-5 [1177 kB]
+Get:6 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-2 [147 kB]
+Get:7 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-5 [463 kB]
+Get:8 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
+Get:9 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
+Get:10 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-2 [1118 kB]
+Get:11 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.09-2 [271 kB]
+Get:12 http://spohr.debian.org/debian/ unstable/main file ia64 5.09-2 [54.4 kB]
+Get:13 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-5 [173 kB]
+Get:14 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
+Get:16 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-5 [2439 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9 kB]
Get:20 http://spohr.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.4 MB in 1s (6219 kB/s)
+Fetched 11.4 MB in 1s (6326 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10538 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_ia64.deb) ...
@@ -243,7 +244,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_ia64.deb) ...
Selecting previously unselected package quilt.
@@ -271,7 +272,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -282,11 +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 46 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 51 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 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_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6.1_2.13-21 libc6.1-dev_2.13-21 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-5 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6.1_2.13-21 libc6.1-dev_2.13-21 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-5 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -297,12 +298,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -318,24 +319,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIF
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS =
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -348,21 +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_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -541,9 +542,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -620,7 +623,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -662,60 +665,60 @@ dh_makeshlibs -pbedtools
dh_installdeb -pbedtools
dh_perl -pbedtools
dh_shlibdeps -pbedtools
-dpkg-shlibdeps: warning: dependency on libm.so.6.1 could be avoided if "debian/bedtools/usr/bin/flankBed debian/bedtools/usr/bin/unionBedGraphs debian/bedtools/usr/bin/multiBamCov debian/bedtools/usr/bin/pairToBed debian/bedtools/usr/bin/bed12ToBed6 debian/bedtools/usr/bin/bamToBed debian/bedtools/usr/bin/coverageBed debian/bedtools/usr/bin/closestBed debian/bedtools/usr/bin/fastaFromBed debian/bedtools/usr/bin/overlap debian/bedtools/usr/bin/maskFastaFromBed debian/bedtools/usr/bin/bedToBam debian/bedtools/usr/bin/genomeCoverageBed debian/bedtools/usr/bin/annotateBed debian/bedtools/usr/bin/subtractBed debian/bedtools/usr/bin/sortBed debian/bedtools/usr/bin/pairToPair debian/bedtools/usr/bin/shuffleBed debian/bedtools/usr/bin/mergeBed debian/bedtools/usr/bin/nucBed debian/bedtools/usr/bin/bedToIgv debian/bedtools/usr/bin/windowBed debian/bedtools/usr/bin/linksBed debian/bedtools/usr/bin/tagBam debian/bedtools/usr/bin/slopBed debian/bedtools/usr/bin/intersectBed debian/bedtools/usr/bin/complementBed" were not uselessly linked against it (they use none of its symbols).
+dpkg-shlibdeps: warning: dependency on libm.so.6.1 could be avoided if "debian/bedtools/usr/bin/flankBed debian/bedtools/usr/bin/unionBedGraphs debian/bedtools/usr/bin/multiBamCov debian/bedtools/usr/bin/pairToBed debian/bedtools/usr/bin/bed12ToBed6 debian/bedtools/usr/bin/bamToBed debian/bedtools/usr/bin/overlap debian/bedtools/usr/bin/fastaFromBed debian/bedtools/usr/bin/closestBed debian/bedtools/usr/bin/coverageBed debian/bedtools/usr/bin/maskFastaFromBed debian/bedtools/usr/bin/bedToBam debian/bedtools/usr/bin/genomeCoverageBed debian/bedtools/usr/bin/annotateBed debian/bedtools/usr/bin/subtractBed debian/bedtools/usr/bin/sortBed debian/bedtools/usr/bin/pairToPair debian/bedtools/usr/bin/shuffleBed debian/bedtools/usr/bin/mergeBed debian/bedtools/usr/bin/nucBed debian/bedtools/usr/bin/bedToIgv debian/bedtools/usr/bin/windowBed debian/bedtools/usr/bin/tagBam debian/bedtools/usr/bin/linksBed debian/bedtools/usr/bin/slopBed debian/bedtools/usr/bin/intersectBed debian/bedtools/usr/bin/complementBed debian/bedtools/usr/bin/multiIntersectBed" were not uselessly linked against it (they use none of its symbols).
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../bedtools_2.14.2-1_ia64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bedtools_2.14.3-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0650
+Build finished at 20111105-0206
-bedtools_2.14.2-1_ia64.changes:
+bedtools_2.14.3-1_ia64.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
+Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- 8a121c79f061526410dba664211a0cf073923f7d 746882 bedtools_2.14.2-1_ia64.deb
+ 74974e8197a045607b945be9187fc45d42cb4eff 771472 bedtools_2.14.3-1_ia64.deb
Checksums-Sha256:
- 95d352509d50774920156e56071c2d402f8d94af280f201e2341a7c424011795 746882 bedtools_2.14.2-1_ia64.deb
+ 8e3bb00d4352a3083bb8f8ae61dcf8efae773d26e8f0c25f5c2d3fa684cdba46 771472 bedtools_2.14.3-1_ia64.deb
Files:
- 4be0fe6148184b114aeec9d2ed876ed1 746882 science optional bedtools_2.14.2-1_ia64.deb
+ 05d1f311850f304e6d8c650ec3896f5e 771472 science optional bedtools_2.14.3-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_ia64.deb
+bedtools_2.14.3-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 746882 bytes: control archive= 1745 bytes.
+ size 771472 bytes: control archive= 1775 bytes.
880 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 9566
+ Installed-Size: 9814
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6.1 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libunwind7, zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -731,49 +734,50 @@ bedtools_2.14.2-1_ia64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 06:49 ./
-drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 06:41 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-03 06:49 ./usr/bin/
--rwxr-xr-x root/root 463184 2011-11-03 06:49 ./usr/bin/bamToBed
--rwxr-xr-x root/root 178912 2011-11-03 06:49 ./usr/bin/overlap
--rwxr-xr-x root/root 270936 2011-11-03 06:49 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 472096 2011-11-03 06:49 ./usr/bin/bedToBam
--rwxr-xr-x root/root 220104 2011-11-03 06:49 ./usr/bin/complementBed
--rwxr-xr-x root/root 587992 2011-11-03 06:49 ./usr/bin/windowBed
--rwxr-xr-x root/root 217448 2011-11-03 06:49 ./usr/bin/slopBed
--rwxr-xr-x root/root 306000 2011-11-03 06:49 ./usr/bin/sortBed
--rwxr-xr-x root/root 226504 2011-11-03 06:49 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 297608 2011-11-03 06:49 ./usr/bin/nucBed
--rwxr-xr-x root/root 293872 2011-11-03 06:49 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 221304 2011-11-03 06:49 ./usr/bin/mergeBed
--rwxr-xr-x root/root 235192 2011-11-03 06:49 ./usr/bin/subtractBed
--rwxr-xr-x root/root 251936 2011-11-03 06:49 ./usr/bin/closestBed
--rwxr-xr-x root/root 728464 2011-11-03 06:49 ./usr/bin/intersectBed
--rwxr-xr-x root/root 199664 2011-11-03 06:49 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 565216 2011-11-03 06:49 ./usr/bin/tagBam
--rwxr-xr-x root/root 246984 2011-11-03 06:49 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 220504 2011-11-03 06:49 ./usr/bin/linksBed
--rwxr-xr-x root/root 216784 2011-11-03 06:49 ./usr/bin/annotateBed
--rwxr-xr-x root/root 580520 2011-11-03 06:49 ./usr/bin/coverageBed
--rwxr-xr-x root/root 378256 2011-11-03 06:49 ./usr/bin/pairToPair
--rwxr-xr-x root/root 612264 2011-11-03 06:49 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 620864 2011-11-03 06:49 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 120416 2011-11-03 06:49 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 767872 2011-11-03 06:49 ./usr/bin/pairToBed
--rwxr-xr-x root/root 234680 2011-11-03 06:49 ./usr/bin/flankBed
+drwxr-xr-x root/root 0 2011-11-05 02:05 ./
+drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/bin/
+-rwxr-xr-x root/root 216784 2011-11-05 02:05 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 463184 2011-11-05 02:05 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 199664 2011-11-05 02:05 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 472096 2011-11-05 02:05 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 246984 2011-11-05 02:05 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 251936 2011-11-05 02:05 ./usr/bin/closestBed
+-rwxr-xr-x root/root 220104 2011-11-05 02:05 ./usr/bin/complementBed
+-rwxr-xr-x root/root 580520 2011-11-05 02:05 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 293872 2011-11-05 02:05 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 234680 2011-11-05 02:05 ./usr/bin/flankBed
+-rwxr-xr-x root/root 612264 2011-11-05 02:05 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 728464 2011-11-05 02:05 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 220504 2011-11-05 02:05 ./usr/bin/linksBed
+-rwxr-xr-x root/root 226504 2011-11-05 02:05 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 221304 2011-11-05 02:05 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 620864 2011-11-05 02:05 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 290176 2011-11-05 02:05 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 297608 2011-11-05 02:05 ./usr/bin/nucBed
+-rwxr-xr-x root/root 178912 2011-11-05 02:05 ./usr/bin/overlap
+-rwxr-xr-x root/root 767872 2011-11-05 02:05 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 378256 2011-11-05 02:05 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 270936 2011-11-05 02:05 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 217448 2011-11-05 02:05 ./usr/bin/slopBed
+-rwxr-xr-x root/root 306000 2011-11-05 02:05 ./usr/bin/sortBed
+-rwxr-xr-x root/root 235192 2011-11-05 02:05 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 565216 2011-11-05 02:05 ./usr/bin/tagBam
+-rwxr-xr-x root/root 120416 2011-11-05 02:05 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 587992 2011-11-05 02:05 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 01:56 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 02:05 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -787,7 +791,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-99cf4c72-9adb-4338-9fcb-fd2e1867e020/build/buildd-bedtools_2.14.2-1-ia64-Xyhxph
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-0c108c67-886e-4139-903f-811a245b5655/build/buildd-bedtools_2.14.3-1-ia64-dYJHS5
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -795,19 +799,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 158140
-Build-Time: 559
+Build-Space: 166952
+Build-Time: 602
Distribution: sid
-Install-Time: 64
-Job: bedtools_2.14.2-1
+Install-Time: 65
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 677
-Source-Version: 2.14.2-1
-Space: 158140
+Package-Time: 725
+Source-Version: 2.14.3-1
+Space: 166952
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0650
-Build needed 00:11:17, 158140k disc space
-Signature with key '96FA48F4' requested:
+Finished at 20111105-0206
+Build needed 00:12:05, 166952k disc space
+Signature with key 'FC1E8668' requested:
diff --git a/info b/info
index 4f48ea4..042d53c 100644
--- a/info
+++ b/info
@@ -1,11 +1,13 @@
-i386~1320291875~sid~successful
-kfreebsd-i386~1320291957~sid~successful
-powerpc~1320292390~sid~successful
-hurd-i386~1320293227~sid~successful
-sparc~1320293519~sid~successful
-kfreebsd-amd64~1320293701~sid~successful
-mips~1320295049~sid~successful
-mipsel~1320295241~sid~successful
-s390~1320295596~sid~successful
-ia64~1320303037~sid~successful
-armel~1320317658~sid~successful
+s390~1320458404~sid~successful
+powerpc~1320458428~sid~successful
+i386~1320458438~sid~successful
+ia64~1320458794~sid~successful
+mipsel~1320459306~sid~successful
+armel~1320459658~sid~successful
+sparc~1320460114~sid~successful
+mips~1320460447~sid~successful
+kfreebsd-i386~1320463028~sid~successful
+kfreebsd-amd64~1320463952~sid~successful
+hurd-i386~1320494343~sid~successful
+s390x~1322367602~sid~successful
+armhf~1322509076~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 1e5650a..f086694 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,4 +1,4 @@
-From buildd at fano.debian.org Thu Nov 03 04:15:01 2011
+From buildd at fano.debian.org Sat Nov 05 03:32:31 2011
Return-path: <buildd at fano.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,
@@ -6,25 +6,25 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1RLohg-0006xW-VO
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:15:01 +0000
+ id 1RMWzf-0006Nk-Gj
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 03:32:31 +0000
Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1RLohf-0007dP-8H; Thu, 03 Nov 2011 04:15:00 +0000
+ id 1RMWze-00046C-A6; Sat, 05 Nov 2011 03:32:30 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1RLohc-0007bq-Cq; Thu, 03 Nov 2011 04:14:56 +0000
-Message-Id: <E1RLohc-0007bq-Cq at fano.debian.org>
+ id 1RMWzb-000Iui-Qp; Sat, 05 Nov 2011 03:32:27 +0000
+Message-Id: <E1RMWzb-000Iui-Qp at fano.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 3 Nov 2011 04:14:56 +0000
+Date: Sat, 5 Nov 2011 03:32:27 +0000
From: buildd on fano <buildd at fano.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on kfreebsd-amd64
+Subject: Log for successful build of bedtools_2.14.3-1 on kfreebsd-amd64
(dist=sid)
Key-Id: D33FE1D8
Delivered-To: logs at buildd.debian.org
@@ -32,45 +32,62 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (kfreebsd-amd64) 03 Nov 2011 04:09 ║
+║ bedtools 2.14.3-1 (kfreebsd-amd64) 05 Nov 2011 03:26 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: kfreebsd-amd64
-Hit http://mirror-ubc.debian.org sid InRelease
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org sid InRelease [146 kB]
Ign http://incoming.debian.org InRelease
-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
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:4 http://mirror-ubc.debian.org sid InRelease [146 kB]
+Get:5 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:6 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:7 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Get:8 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Ign http://incoming.debian.org sid/non-free TranslationIndex
+Get:9 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:10 http://incoming.debian.org Release [1604 B]
+Get:11 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
+Get:12 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:13 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:14 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
+Get:15 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [87.5 kB]
+Get:16 http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:17 http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:18 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main TranslationIndex
+Get:19 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages
+Get:20 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
+Get:21 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:22 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
+Get:23 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:24 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:25 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
+Get:26 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [87.5 kB]
+Get:27 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:28 http://incoming.debian.org Sources [26.0 kB]
+Get:29 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
Ign http://mirror-ubc.debian.org sid/contrib Translation-en
Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+Get:30 http://incoming.debian.org Packages [299 kB]
+Get:31 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
+Get:32 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:33 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:34 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-05-0215.30.pdiff [31.7 kB]
+Fetched 902 kB in 26s (34.3 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -92,10 +109,10 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 1s (544 kB/s)
+Get:1 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 0s (16.3 MB/s)
Download complete and in download only mode
Check arch
@@ -115,12 +132,12 @@ 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 8 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 8 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -144,7 +161,7 @@ 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)
+ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -160,7 +177,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -182,11 +199,11 @@ The following NEW packages will be installed:
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, 18 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 8 not upgraded.
Need to get 0 B/8237 kB of archives.
After this operation, 21.6 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 12290 files and directories currently installed.)
+(Reading database ... 12289 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_kfreebsd-amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-amd64.deb) ...
@@ -215,7 +232,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-amd64.deb) ...
Selecting previously unselected package quilt.
@@ -238,7 +255,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -246,11 +263,11 @@ 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 8 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 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_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.1-15 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.1-15 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 type-handling_0.2.23 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 type-handling_0.2.23 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -261,12 +278,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -277,24 +294,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -307,21 +324,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -496,9 +513,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -575,7 +594,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -620,22 +639,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.14.2-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.14.3-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0414
+Build finished at 20111105-0332
-bedtools_2.14.2-1_kfreebsd-amd64.changes:
+bedtools_2.14.3-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
@@ -643,33 +662,33 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- 2d0a50f22da7fa251de54ce643e56d183124a202 671650 bedtools_2.14.2-1_kfreebsd-amd64.deb
+ 672ddf8e5d47d16fc7ed858b108e604374d14334 692318 bedtools_2.14.3-1_kfreebsd-amd64.deb
Checksums-Sha256:
- e61b976c62901722a398acc0792398dbde0f41f234b1bce5be3ffd1717d8f3e7 671650 bedtools_2.14.2-1_kfreebsd-amd64.deb
+ 9342060799ef754f67dc2f26d3193b8e8c1f9d7cc80a7d128118d5f7fdd1799c 692318 bedtools_2.14.3-1_kfreebsd-amd64.deb
Files:
- 50b1b648289932f5cd976ce679dc5a68 671650 science optional bedtools_2.14.2-1_kfreebsd-amd64.deb
+ 651259a21f1a21ef63ee37d59de363c5 692318 science optional bedtools_2.14.3-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_kfreebsd-amd64.deb
+bedtools_2.14.3-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 671650 bytes: control archive= 1741 bytes.
+ size 692318 bytes: control archive= 1762 bytes.
876 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4665
+ Installed-Size: 4809
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -685,49 +704,50 @@ bedtools_2.14.2-1_kfreebsd-amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 04:13 ./
-drwxr-xr-x root/root 0 2011-11-03 04:13 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 04:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 04:09 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-03 04:14 ./usr/bin/
--rwxr-xr-x root/root 110000 2011-11-03 04:14 ./usr/bin/annotateBed
--rwxr-xr-x root/root 218376 2011-11-03 04:14 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101856 2011-11-03 04:14 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 229232 2011-11-03 04:14 ./usr/bin/bedToBam
--rwxr-xr-x root/root 126480 2011-11-03 04:14 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126656 2011-11-03 04:14 ./usr/bin/closestBed
--rwxr-xr-x root/root 114168 2011-11-03 04:14 ./usr/bin/complementBed
--rwxr-xr-x root/root 276592 2011-11-03 04:14 ./usr/bin/coverageBed
--rwxr-xr-x root/root 147112 2011-11-03 04:14 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 118920 2011-11-03 04:14 ./usr/bin/flankBed
--rwxr-xr-x root/root 294888 2011-11-03 04:14 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 345672 2011-11-03 04:14 ./usr/bin/intersectBed
--rwxr-xr-x root/root 110248 2011-11-03 04:14 ./usr/bin/linksBed
--rwxr-xr-x root/root 118328 2011-11-03 04:14 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 114112 2011-11-03 04:14 ./usr/bin/mergeBed
--rwxr-xr-x root/root 292912 2011-11-03 04:14 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 147136 2011-11-03 04:14 ./usr/bin/nucBed
--rwxr-xr-x root/root 93664 2011-11-03 04:14 ./usr/bin/overlap
--rwxr-xr-x root/root 356352 2011-11-03 04:14 ./usr/bin/pairToBed
--rwxr-xr-x root/root 180096 2011-11-03 04:14 ./usr/bin/pairToPair
--rwxr-xr-x root/root 135384 2011-11-03 04:14 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110200 2011-11-03 04:14 ./usr/bin/slopBed
--rwxr-xr-x root/root 150952 2011-11-03 04:14 ./usr/bin/sortBed
--rwxr-xr-x root/root 267792 2011-11-03 04:14 ./usr/bin/tagBam
--rwxr-xr-x root/root 118192 2011-11-03 04:14 ./usr/bin/subtractBed
--rwxr-xr-x root/root 65032 2011-11-03 04:14 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 278952 2011-11-03 04:14 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-11-05 03:31 ./
+drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 03:28 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-05 03:31 ./usr/bin/
+-rwxr-xr-x root/root 110000 2011-11-05 03:31 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 218376 2011-11-05 03:31 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101856 2011-11-05 03:31 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 229232 2011-11-05 03:31 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 126480 2011-11-05 03:31 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 126656 2011-11-05 03:31 ./usr/bin/closestBed
+-rwxr-xr-x root/root 114168 2011-11-05 03:31 ./usr/bin/complementBed
+-rwxr-xr-x root/root 276624 2011-11-05 03:31 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 147112 2011-11-05 03:31 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 118920 2011-11-05 03:31 ./usr/bin/flankBed
+-rwxr-xr-x root/root 294888 2011-11-05 03:31 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 345672 2011-11-05 03:31 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 110248 2011-11-05 03:31 ./usr/bin/linksBed
+-rwxr-xr-x root/root 118328 2011-11-05 03:31 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 114112 2011-11-05 03:31 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 292912 2011-11-05 03:31 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 147016 2011-11-05 03:31 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 147136 2011-11-05 03:31 ./usr/bin/nucBed
+-rwxr-xr-x root/root 93664 2011-11-05 03:31 ./usr/bin/overlap
+-rwxr-xr-x root/root 356352 2011-11-05 03:31 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 180096 2011-11-05 03:31 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 135416 2011-11-05 03:31 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 110232 2011-11-05 03:31 ./usr/bin/slopBed
+-rwxr-xr-x root/root 150952 2011-11-05 03:31 ./usr/bin/sortBed
+-rwxr-xr-x root/root 118192 2011-11-05 03:31 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 267792 2011-11-05 03:31 ./usr/bin/tagBam
+-rwxr-xr-x root/root 65032 2011-11-05 03:31 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 278952 2011-11-05 03:31 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -741,11 +761,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1320293343-26755/build/buildd-bedtools_2.14.2-1-kfreebsd-amd64-COfbU8
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1320463619-70245/build/buildd-bedtools_2.14.3-1-kfreebsd-amd64-7OZa9B
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 8 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* html2text*
intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 18 to remove and 8 not upgraded.
After this operation, 21.6 MB disk space will be freed.
-(Reading database ... 13466 files and directories currently installed.)
+(Reading database ... 13465 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -789,18 +809,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 137236
-Build-Time: 285
+Build-Space: 139476
+Build-Time: 225
Distribution: sid
-Install-Time: 34
-Job: bedtools_2.14.2-1
+Install-Time: 41
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 331
-Source-Version: 2.14.2-1
-Space: 137236
+Package-Time: 304
+Source-Version: 2.14.3-1
+Space: 139476
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0414
-Build needed 00:05:31, 137236k disc space
+Finished at 20111105-0332
+Build needed 00:05:04, 139476k disc space
Signature with key 'D33FE1D8' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 953072a..76c1772 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,4 +1,4 @@
-From buildd at finzi.debian.org Thu Nov 03 03:45:55 2011
+From buildd at finzi.debian.org Sat Nov 05 03:17:08 2011
Return-path: <buildd at finzi.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,25 +6,25 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1RLoFW-0002vE-Si
- for logs at buildd.debian.org; Thu, 03 Nov 2011 03:45:54 +0000
+ id 1RMWkm-0003Rm-77
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 03:17:08 +0000
Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1RLoFV-0006XB-O9; Thu, 03 Nov 2011 03:45:54 +0000
+ id 1RMWkk-0003XY-EX; Sat, 05 Nov 2011 03:17:07 +0000
Received: from buildd by finzi.debian.org with local (Exim 4.72)
(envelope-from <buildd at finzi.debian.org>)
- id 1RLoFQ-000GLL-Jh; Thu, 03 Nov 2011 03:45:48 +0000
-Message-Id: <E1RLoFQ-000GLL-Jh at finzi.debian.org>
+ id 1RMWkh-000GWL-Rp; Sat, 05 Nov 2011 03:17:03 +0000
+Message-Id: <E1RMWkh-000GWL-Rp at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 3 Nov 2011 03:45:48 +0000
+Date: Sat, 5 Nov 2011 03:17:03 +0000
From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on kfreebsd-i386
+Subject: Log for successful build of bedtools_2.14.3-1 on kfreebsd-i386
(dist=sid)
Key-Id: D859A500
Delivered-To: logs at buildd.debian.org
@@ -32,43 +32,60 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (kfreebsd-i386) 03 Nov 2011 03:40 ║
+║ bedtools 2.14.3-1 (kfreebsd-i386) 05 Nov 2011 03:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: kfreebsd-i386
-Hit http://mirror-ubc.debian.org sid InRelease
-Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org sid InRelease [146 kB]
Ign http://incoming.debian.org InRelease
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:4 http://mirror-ubc.debian.org sid InRelease [146 kB]
+Get:5 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:6 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:7 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Get:8 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Ign http://incoming.debian.org sid/non-free TranslationIndex
+Get:9 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:10 http://incoming.debian.org Release [1604 B]
+Get:11 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
+Get:12 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:13 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:14 http://incoming.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
+Get:15 http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:16 http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:17 http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main TranslationIndex
+Get:18 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org Release.gpg
+Get:19 http://incoming.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
+Get:20 http://incoming.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:21 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
+Get:22 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:23 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:24 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
+Get:25 http://incoming.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:26 http://incoming.debian.org Sources [26.4 kB]
+Get:27 http://incoming.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
Ign http://mirror-ubc.debian.org sid/contrib Translation-en
Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+Get:28 http://incoming.debian.org Packages [299 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
+Get:29 http://mirror-ubc.debian.org sid/main 2011-11-05-0215.30.pdiff [10.7 kB]
Ign http://incoming.debian.org Translation-en
+Get:30 http://mirror-ubc.debian.org sid/contrib 2011-11-05-0215.30.pdiff [373 B]
+Get:31 http://mirror-ubc.debian.org sid/non-free 2011-11-05-0215.30.pdiff [663 B]
+Get:32 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-11-05-0215.30.pdiff [29.4 kB]
+Fetched 722 kB in 17s (41.6 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,10 +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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 1s (601 kB/s)
+Get:1 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ sid/main bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 0s (17.2 MB/s)
Download complete and in download only mode
Check arch
@@ -113,12 +130,12 @@ 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 17 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 17 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -142,7 +159,7 @@ 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)
+ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -158,7 +175,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -180,11 +197,11 @@ The following NEW packages will be installed:
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, 18 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 17 not upgraded.
Need to get 0 B/8099 kB of archives.
After this operation, 21.1 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 14032 files and directories currently installed.)
+(Reading database ... 14030 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_kfreebsd-i386.deb) ...
Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-i386.deb) ...
@@ -213,7 +230,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-i386.deb) ...
Selecting previously unselected package quilt.
@@ -236,7 +253,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -244,11 +261,11 @@ 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 17 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3
-Package versions: apt_0.8.15.9 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.12-1 libgomp1_4.6.2-3 libgpg-error0_1.10-1 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libp11-kit0_0.7-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsasl2-2_2.1.25.dfsg1-2 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 tzdata_2011n-1 util-linux_2.19.1-5 vim_2:7.3.346-1 vim-common_2:7.3.346-1 vim-runtime_2:7.3.346-1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.9 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.12-1 libgomp1_4.6.2-3 libgpg-error0_1.10-1 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.7-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsasl2-2_2.1.25.dfsg1-2 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.25-3 tzdata_2011n-1 util-linux_2.19.1-5 vim_2:7.3.346-1 vim-common_2:7.3.346-1 vim-runtime_2:7.3.346-1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -259,12 +276,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -275,24 +292,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -305,21 +322,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -494,9 +511,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -573,7 +592,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -618,22 +637,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bedtools_2.14.2-1_kfreebsd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bedtools_2.14.3-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0345
+Build finished at 20111105-0316
-bedtools_2.14.2-1_kfreebsd-i386.changes:
+bedtools_2.14.3-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
@@ -641,33 +660,33 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- dcab0cf745f3d30ea9a98bf0df91de052f5ea5cf 682388 bedtools_2.14.2-1_kfreebsd-i386.deb
+ f3abe30f037aa655a0ae4e5d795109fabc65a549 702966 bedtools_2.14.3-1_kfreebsd-i386.deb
Checksums-Sha256:
- b4015ec543568cc051d184d2daab623f6b4961a1517cf156a89c1f5ffe5a453b 682388 bedtools_2.14.2-1_kfreebsd-i386.deb
+ 486c7bf303b6a707117ff061ba344cacf3d2472238184ddb4fb10cd3ecf85ccd 702966 bedtools_2.14.3-1_kfreebsd-i386.deb
Files:
- 9c755d1980e2143dfc29a31ae375d702 682388 science optional bedtools_2.14.2-1_kfreebsd-i386.deb
+ 5268f6a056f030ce7f202baccc482e30 702966 science optional bedtools_2.14.3-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_kfreebsd-i386.deb
+bedtools_2.14.3-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 682388 bytes: control archive= 1735 bytes.
+ size 702966 bytes: control archive= 1769 bytes.
875 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4611
+ Installed-Size: 4749
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc0.1 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -683,49 +702,50 @@ bedtools_2.14.2-1_kfreebsd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 03:42 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-03 03:45 ./usr/bin/
--rwxr-xr-x root/root 103224 2011-11-03 03:45 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223468 2011-11-03 03:45 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96356 2011-11-03 03:45 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227672 2011-11-03 03:45 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121488 2011-11-03 03:45 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 121988 2011-11-03 03:45 ./usr/bin/closestBed
--rwxr-xr-x root/root 105440 2011-11-03 03:45 ./usr/bin/complementBed
--rwxr-xr-x root/root 281784 2011-11-03 03:45 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142452 2011-11-03 03:45 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 114172 2011-11-03 03:45 ./usr/bin/flankBed
--rwxr-xr-x root/root 301420 2011-11-03 03:45 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350572 2011-11-03 03:45 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105656 2011-11-03 03:45 ./usr/bin/linksBed
--rwxr-xr-x root/root 109568 2011-11-03 03:45 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 107032 2011-11-03 03:45 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297312 2011-11-03 03:45 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 142392 2011-11-03 03:45 ./usr/bin/nucBed
--rwxr-xr-x root/root 88164 2011-11-03 03:45 ./usr/bin/overlap
--rwxr-xr-x root/root 366968 2011-11-03 03:45 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178284 2011-11-03 03:45 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129424 2011-11-03 03:45 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105312 2011-11-03 03:45 ./usr/bin/slopBed
--rwxr-xr-x root/root 142976 2011-11-03 03:45 ./usr/bin/sortBed
--rwxr-xr-x root/root 272744 2011-11-03 03:45 ./usr/bin/tagBam
--rwxr-xr-x root/root 112716 2011-11-03 03:45 ./usr/bin/subtractBed
--rwxr-xr-x root/root 59616 2011-11-03 03:45 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285024 2011-11-03 03:45 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-11-05 03:16 ./
+drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 03:13 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-05 03:16 ./usr/bin/
+-rwxr-xr-x root/root 103224 2011-11-05 03:16 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223468 2011-11-05 03:16 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96356 2011-11-05 03:16 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227672 2011-11-05 03:16 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121488 2011-11-05 03:16 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 121988 2011-11-05 03:16 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105440 2011-11-05 03:16 ./usr/bin/complementBed
+-rwxr-xr-x root/root 281784 2011-11-05 03:16 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142452 2011-11-05 03:16 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 114172 2011-11-05 03:16 ./usr/bin/flankBed
+-rwxr-xr-x root/root 301420 2011-11-05 03:16 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350572 2011-11-05 03:16 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105656 2011-11-05 03:16 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109568 2011-11-05 03:16 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 107032 2011-11-05 03:16 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297312 2011-11-05 03:16 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 141464 2011-11-05 03:16 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 142392 2011-11-05 03:16 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88164 2011-11-05 03:16 ./usr/bin/overlap
+-rwxr-xr-x root/root 366968 2011-11-05 03:16 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178284 2011-11-05 03:16 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129424 2011-11-05 03:16 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 105312 2011-11-05 03:16 ./usr/bin/slopBed
+-rwxr-xr-x root/root 142976 2011-11-05 03:16 ./usr/bin/sortBed
+-rwxr-xr-x root/root 112716 2011-11-05 03:16 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 272744 2011-11-05 03:16 ./usr/bin/tagBam
+-rwxr-xr-x root/root 59616 2011-11-05 03:16 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285024 2011-11-05 03:16 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -739,11 +759,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1320291640-59931/build/buildd-bedtools_2.14.2-1-kfreebsd-i386-4tt_Ii
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1320462740-60635/build/buildd-bedtools_2.14.3-1-kfreebsd-i386-OPzfGr
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 17 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -751,9 +771,9 @@ The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 18 to remove and 17 not upgraded.
After this operation, 21.1 MB disk space will be freed.
-(Reading database ... 15206 files and directories currently installed.)
+(Reading database ... 15204 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -787,18 +807,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 96054
-Build-Time: 204
+Build-Space: 97874
+Build-Time: 196
Distribution: sid
Install-Time: 36
-Job: bedtools_2.14.2-1
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 287
-Source-Version: 2.14.2-1
-Space: 96054
+Package-Time: 261
+Source-Version: 2.14.3-1
+Space: 97874
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0345
-Build needed 00:04:47, 96054k disc space
+Finished at 20111105-0316
+Build needed 00:04:21, 97874k disc space
Signature with key 'D859A500' requested:
diff --git a/mips.log b/mips.log
index 91f837a..16978a0 100644
--- a/mips.log
+++ b/mips.log
@@ -1,4 +1,4 @@
-From buildd at lucatelli.debian.org Thu Nov 03 04:37:28 2011
+From buildd at lucatelli.debian.org Sat Nov 05 02:34:06 2011
Return-path: <buildd at lucatelli.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,63 +6,63 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
- id 1RLp3Q-0002Bi-1L
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:37:28 +0000
+ id 1RMW4N-0004Hw-EW
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:33:51 +0000
Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=lucatelli.debian.org,
EMAIL=hostmaster at lucatelli.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
- id 1RLp3O-0004gH-BS
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:37:26 +0000
+ id 1RMW49-0005I0-5z
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:33:05 +0000
Received: from buildd by lucatelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd at lucatelli.debian.org>) id 1RLp3I-0006tu-Je
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:37:20 +0000
+ (envelope-from <buildd at lucatelli.debian.org>) id 1RMW47-0007z5-D1
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:33:03 +0000
From: buildd on lucatelli <buildd at lucatelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on mips (dist=sid)
+Subject: Log for successful build of bedtools_2.14.3-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RLp3I-0006tu-Je at lucatelli.debian.org>
-Date: Thu, 03 Nov 2011 04:37:20 +0000
+Message-Id: <E1RMW47-0007z5-D1 at lucatelli.debian.org>
+Date: Sat, 05 Nov 2011 02:33:03 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (mips) 03 Nov 2011 03:58 ║
+║ bedtools 2.14.3-1 (mips) 05 Nov 2011 01:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
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 [5889 kB]
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://mirror-ubc.debian.org unstable InRelease [146 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5890 kB]
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 [5896 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5890 kB]
Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [56.9 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [104 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7601 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [103 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7603 kB]
Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [55.8 kB]
Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7601 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7603 kB]
Get:14 http://incoming.debian.org unstable/contrib mips Packages [55.8 kB]
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 [40.9 kB]
-Get:18 http://incoming.debian.org Packages [602 kB]
+Get:17 http://incoming.debian.org Sources [25.7 kB]
+Get:18 http://incoming.debian.org Packages [300 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.4 MB in 1min 21s (348 kB/s)
+Fetched 28.0 MB in 1min 16s (366 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 1s (798 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 1s (703 kB/s)
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 33 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 33 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -152,7 +152,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -174,32 +174,32 @@ 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 33 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 38 not upgraded.
Need to get 9581 kB of archives.
After this operation, 28.2 MB of additional disk space will be used.
Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-4 [35.3 kB]
Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.8-1 [1565 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-5 [858 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-2 [104 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.09-2 [249 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.09-2 [51.8 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 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 8.9.8 [552 kB]
+Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-5 [858 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-2 [104 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.09-2 [249 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.09-2 [51.8 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
Get:20 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9581 kB in 1s (6016 kB/s)
+Fetched 9581 kB in 1s (6304 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10544 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_mips.deb) ...
@@ -236,7 +236,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mips.deb) ...
Selecting previously unselected package quilt.
@@ -264,7 +264,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -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 33 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +287,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -308,24 +308,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIF
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
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/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -531,9 +531,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -610,7 +612,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -655,22 +657,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../bedtools_2.14.2-1_mips.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../bedtools_2.14.3-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0437
+Build finished at 20111105-0232
-bedtools_2.14.2-1_mips.changes:
+bedtools_2.14.3-1_mips.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
@@ -678,33 +680,33 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- 96b3b284a9a56b05f39c176832ded7ba2c5650c4 599578 bedtools_2.14.2-1_mips.deb
+ 470d53e53208c78df490b9b29e1b12f51efcfdcc 617236 bedtools_2.14.3-1_mips.deb
Checksums-Sha256:
- 6cbd44fd6097408f6f9d7a4a22d1205f12d6eb7c526966f2564e0e6c19ce16cc 599578 bedtools_2.14.2-1_mips.deb
+ af2e136e7d389e5695cb3ccc6f7b282c288381cb40c24995cb7fd5d385e36e25 617236 bedtools_2.14.3-1_mips.deb
Files:
- 25a633d0694718d857c6278c510beb7d 599578 science optional bedtools_2.14.2-1_mips.deb
+ 622dd08fe7e3645aff5a03d0a16feef9 617236 science optional bedtools_2.14.3-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_mips.deb
+bedtools_2.14.3-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 599578 bytes: control archive= 1737 bytes.
+ size 617236 bytes: control archive= 1756 bytes.
866 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5015
+ Installed-Size: 5161
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -720,7 +722,7 @@ bedtools_2.14.2-1_mips.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-a2376810-8eb9-448a-b380-f078d7a1d694/build/buildd-bedtools_2.14.2-1-mips-oSMen2/bedtools_2.14.2-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
+dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-919d1dd9-220f-451b-9cdd-e921ba7947de/build/buildd-bedtools_2.14.3-1-mips-INFNuP/bedtools_2.14.3-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -734,7 +736,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-a2376810-8eb9-448a-b380-f078d7a1d694/build/buildd-bedtools_2.14.2-1-mips-oSMen2
+Purging /var/lib/schroot/mount/sid-mips-sbuild-919d1dd9-220f-451b-9cdd-e921ba7947de/build/buildd-bedtools_2.14.3-1-mips-INFNuP
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -742,86 +744,84 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 103176
-Build-Time: 2104
+Build-Space: 105080
+Build-Time: 2105
Distribution: sid
-Install-Time: 74
-Job: bedtools_2.14.2-1
+Install-Time: 72
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 2306
-Source-Version: 2.14.2-1
-Space: 103176
+Package-Time: 2299
+Source-Version: 2.14.3-1
+Space: 105080
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0437
-Build needed 00:38:26, 103176k disc space
-Signature with key 'FDFDA76A' requested:
+Finished at 20111105-0232
+Build needed 00:38:19, 105080k disc space
+Signature with key '7A0A8DA2' requested:
-From buildd at eysler.debian.org Thu Nov 03 04:40:33 2011
-Return-path: <buildd at eysler.debian.org>
+From buildd at mayer.debian.org Sat Nov 05 02:15:06 2011
+Return-path: <buildd at mayer.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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 eysler.debian.org>)
- id 1RLp6P-0002jm-HV
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:33 +0000
-Received: from eysler.debian.org ([2001:858:2:2:1a1a:0:563b:7698])
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RMVmk-0001lH-Az
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:06 +0000
+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=eysler.debian.org, EMAIL=hostmaster at eysler.debian.org (verified)
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at eysler.debian.org>)
- id 1RLp6O-0004sl-PU
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:32 +0000
-Received: from buildd by eysler.debian.org with local (Exim 4.72)
- (envelope-from <buildd at eysler.debian.org>) id 1RLp6U-00021C-4K
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:38 +0000
-Date: Thu, 03 Nov 2011 04:40:38 +0000
-Message-Id: <E1RLp6U-00021C-4K at eysler.debian.org>
-From: buildd on eysler <buildd at eysler.debian.org>
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RMVmj-0004an-9u
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:05 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>) id 1RMVmc-00027v-M2
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:14:58 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.14.3-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1RMVmc-00027v-M2 at mayer.debian.org>
+Date: Sat, 05 Nov 2011 02:14:58 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on eysler.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (mipsel) 03 Nov 2011 04:12 ║
+║ bedtools 2.14.3-1 (mipsel) 05 Nov 2011 01:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: mipsel
-Get:1 http://ftp.at.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://incoming.debian.org sid InRelease
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://ftp.at.debian.org unstable/main Sources [5889 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [5896 kB]
-Get:7 http://ftp.at.debian.org unstable/contrib Sources [56.9 kB]
-Get:8 http://ftp.at.debian.org unstable/non-free Sources [104 kB]
-Get:9 http://ftp.at.debian.org unstable/main mipsel Packages [7604 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:12 http://incoming.debian.org unstable/main mipsel Packages [7603 kB]
-Get:13 http://ftp.at.debian.org unstable/contrib mipsel Packages [56.1 kB]
-Ign http://ftp.at.debian.org unstable/contrib TranslationIndex
-Get:14 http://ftp.at.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.at.debian.org unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [56.1 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 [40.9 kB]
-Get:18 http://incoming.debian.org Packages [606 kB]
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [25.7 kB]
+Get:4 http://incoming.debian.org Packages [300 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 28.4 MB in 1min 38s (287 kB/s)
+Fetched 328 kB in 2s (156 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -843,10 +843,10 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 1s (619 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 1s (823 kB/s)
Download complete and in download only mode
Check arch
@@ -866,12 +866,18 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+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 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -888,13 +894,13 @@ dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
+ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -911,7 +917,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -919,52 +925,27 @@ Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libssl1.0.0
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat file gettext gettext-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ devscripts dh-make gettext-doc 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
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 28 not upgraded.
-Need to get 9531 kB of archives.
-After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://ftp.at.debian.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-4 [35.2 kB]
-Get:2 http://ftp.at.debian.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
-Get:3 http://ftp.at.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
-Get:4 http://ftp.at.debian.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
-Get:5 http://ftp.at.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
-Get:6 http://ftp.at.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
-Get:7 http://ftp.at.debian.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:8 http://ftp.at.debian.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:9 http://ftp.at.debian.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
-Get:10 http://ftp.at.debian.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
-Get:11 http://ftp.at.debian.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
-Get:12 http://ftp.at.debian.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
-Get:13 http://ftp.at.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.at.debian.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:15 http://ftp.at.debian.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
-Get:16 http://ftp.at.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.at.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.at.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://ftp.at.debian.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
-Get:20 http://ftp.at.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.at.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf quilt
+ zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9531 kB in 2s (3410 kB/s)
-Selecting previously unselected package libpipeline1.
-(Reading database ... 10699 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_mipsel.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
+0 upgraded, 16 newly installed, 0 to remove and 16 not upgraded.
+Need to get 0 B/6932 kB of archives.
+After this operation, 20.7 MB of additional disk space will be used.
Selecting previously unselected package libglib2.0-0.
+(Reading database ... 11452 files and directories currently installed.)
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mipsel.deb) ...
Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mipsel.deb) ...
@@ -972,12 +953,6 @@ Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_mipsel.deb) ...
Selecting previously unselected package file.
@@ -995,26 +970,19 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
-Setting up libpcre3 (8.12-4) ...
+Processing triggers for man-db ...
Setting up libglib2.0-0 (2.28.8-1) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
-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 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
@@ -1023,7 +991,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -1031,11 +999,14 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpopt0 libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.39-3-loongson-2e mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.67-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_172-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1046,12 +1017,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -1062,24 +1033,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -1092,21 +1063,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -1281,9 +1252,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -1360,7 +1333,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -1405,56 +1378,56 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (eysler) <buildd_mipsel-eysler at buildd.debian.org> >../bedtools_2.14.2-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.14.3-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0440
+Build finished at 20111105-0214
-bedtools_2.14.2-1_mipsel.changes:
+bedtools_2.14.3-1_mipsel.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (eysler) <buildd_mipsel-eysler 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 (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- e85647c71f0767f18a9dabe6367632fbb2ed4dac 630926 bedtools_2.14.2-1_mipsel.deb
+ f3f67766afd0c131c5259c19600b7f435888623d 651142 bedtools_2.14.3-1_mipsel.deb
Checksums-Sha256:
- 4dbbefe4686dece182ceaabc365c0e4c38def9d640a83ebfe5136349cc499f66 630926 bedtools_2.14.2-1_mipsel.deb
+ 083e81eaf94a1794d2110286acc43ef55d5ffe6ca2ba9920950c19d310220c35 651142 bedtools_2.14.3-1_mipsel.deb
Files:
- b5bf75997bd986267769ec4dcba8ca55 630926 science optional bedtools_2.14.2-1_mipsel.deb
+ 84c4679dc2ee0dc60cd2848da9956fbd 651142 science optional bedtools_2.14.3-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_mipsel.deb
+bedtools_2.14.3-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 630926 bytes: control archive= 1737 bytes.
+ size 651142 bytes: control archive= 1769 bytes.
866 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5010
+ Installed-Size: 5155
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -1470,49 +1443,7 @@ bedtools_2.14.2-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 04:18 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/bin/
--rwxr-xr-x root/root 114248 2011-11-03 04:39 ./usr/bin/linksBed
--rwxr-xr-x root/root 244460 2011-11-03 04:39 ./usr/bin/bamToBed
--rwxr-xr-x root/root 307036 2011-11-03 04:39 ./usr/bin/coverageBed
--rwxr-xr-x root/root 128968 2011-11-03 04:39 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 187256 2011-11-03 04:39 ./usr/bin/pairToPair
--rwxr-xr-x root/root 114840 2011-11-03 04:39 ./usr/bin/complementBed
--rwxr-xr-x root/root 116792 2011-11-03 04:39 ./usr/bin/mergeBed
--rwxr-xr-x root/root 120472 2011-11-03 04:39 ./usr/bin/subtractBed
--rwxr-xr-x root/root 118616 2011-11-03 04:39 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 104152 2011-11-03 04:39 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 324476 2011-11-03 04:39 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 139656 2011-11-03 04:39 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 114728 2011-11-03 04:39 ./usr/bin/slopBed
--rwxr-xr-x root/root 311596 2011-11-03 04:39 ./usr/bin/windowBed
--rwxr-xr-x root/root 94312 2011-11-03 04:39 ./usr/bin/overlap
--rwxr-xr-x root/root 378444 2011-11-03 04:39 ./usr/bin/intersectBed
--rwxr-xr-x root/root 112280 2011-11-03 04:39 ./usr/bin/annotateBed
--rwxr-xr-x root/root 153148 2011-11-03 04:39 ./usr/bin/nucBed
--rwxr-xr-x root/root 299148 2011-11-03 04:39 ./usr/bin/tagBam
--rwxr-xr-x root/root 391004 2011-11-03 04:39 ./usr/bin/pairToBed
--rwxr-xr-x root/root 121624 2011-11-03 04:39 ./usr/bin/flankBed
--rwxr-xr-x root/root 152972 2011-11-03 04:39 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 248140 2011-11-03 04:39 ./usr/bin/bedToBam
--rwxr-xr-x root/root 129208 2011-11-03 04:39 ./usr/bin/closestBed
--rwxr-xr-x root/root 63960 2011-11-03 04:39 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 152472 2011-11-03 04:39 ./usr/bin/sortBed
--rwxr-xr-x root/root 326604 2011-11-03 04:39 ./usr/bin/multiBamCov
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools_2.14.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1526,27 +1457,70 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-bbfa43d9-fdb6-4d10-9e30-1716fbb43730/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+The following packages will be REMOVED:
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libunistring0* libxml2*
+ po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 16 to remove and 16 not upgraded.
+After this operation, 20.7 MB disk space will be freed.
+(Reading database ... 12413 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 102756
-Build-Time: 1343
+Build-Space: 104656
+Build-Time: 1211
Distribution: sid
-Install-Time: 126
-Job: bedtools_2.14.2-1
+Install-Time: 44
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 1655
-Source-Version: 2.14.2-1
-Space: 102756
+Package-Time: 1304
+Source-Version: 2.14.3-1
+Space: 104656
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0440
-Build needed 00:27:35, 102756k disc space
-Signature with key '0D12A734' requested:
+Finished at 20111105-0214
+Build needed 00:21:44, 104656k disc space
+Signature with key 'B0903E66' requested:
diff --git a/mipsel.log b/mipsel.log
index c5b26bb..d3895a2 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,67 +1,65 @@
-From buildd at eysler.debian.org Thu Nov 03 04:40:33 2011
-Return-path: <buildd at eysler.debian.org>
+From buildd at mayer.debian.org Sat Nov 05 02:15:06 2011
+Return-path: <buildd at mayer.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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 eysler.debian.org>)
- id 1RLp6P-0002jm-HV
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:33 +0000
-Received: from eysler.debian.org ([2001:858:2:2:1a1a:0:563b:7698])
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RMVmk-0001lH-Az
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:06 +0000
+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=eysler.debian.org, EMAIL=hostmaster at eysler.debian.org (verified)
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at eysler.debian.org>)
- id 1RLp6O-0004sl-PU
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:32 +0000
-Received: from buildd by eysler.debian.org with local (Exim 4.72)
- (envelope-from <buildd at eysler.debian.org>) id 1RLp6U-00021C-4K
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:40:38 +0000
-Date: Thu, 03 Nov 2011 04:40:38 +0000
-Message-Id: <E1RLp6U-00021C-4K at eysler.debian.org>
-From: buildd on eysler <buildd at eysler.debian.org>
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1RMVmj-0004an-9u
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:15:05 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>) id 1RMVmc-00027v-M2
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:14:58 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on mipsel (dist=sid)
+Subject: Log for successful build of bedtools_2.14.3-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1RMVmc-00027v-M2 at mayer.debian.org>
+Date: Sat, 05 Nov 2011 02:14:58 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on eysler.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (mipsel) 03 Nov 2011 04:12 ║
+║ bedtools 2.14.3-1 (mipsel) 05 Nov 2011 01:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: mipsel
-Get:1 http://ftp.at.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://incoming.debian.org sid InRelease
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://ftp.at.debian.org unstable/main Sources [5889 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [5896 kB]
-Get:7 http://ftp.at.debian.org unstable/contrib Sources [56.9 kB]
-Get:8 http://ftp.at.debian.org unstable/non-free Sources [104 kB]
-Get:9 http://ftp.at.debian.org unstable/main mipsel Packages [7604 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:12 http://incoming.debian.org unstable/main mipsel Packages [7603 kB]
-Get:13 http://ftp.at.debian.org unstable/contrib mipsel Packages [56.1 kB]
-Ign http://ftp.at.debian.org unstable/contrib TranslationIndex
-Get:14 http://ftp.at.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.at.debian.org unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [56.1 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 [40.9 kB]
-Get:18 http://incoming.debian.org Packages [606 kB]
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [25.7 kB]
+Get:4 http://incoming.debian.org Packages [300 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 28.4 MB in 1min 38s (287 kB/s)
+Fetched 328 kB in 2s (156 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,10 +81,10 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 1s (619 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 1s (823 kB/s)
Download complete and in download only mode
Check arch
@@ -106,12 +104,18 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+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 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -128,13 +132,13 @@ dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
+ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -151,7 +155,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -159,52 +163,27 @@ Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libssl1.0.0
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat file gettext gettext-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
- www-browser libmail-box-perl procmail graphviz
+ devscripts dh-make gettext-doc 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
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 28 not upgraded.
-Need to get 9531 kB of archives.
-After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://ftp.at.debian.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-4 [35.2 kB]
-Get:2 http://ftp.at.debian.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
-Get:3 http://ftp.at.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
-Get:4 http://ftp.at.debian.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
-Get:5 http://ftp.at.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
-Get:6 http://ftp.at.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
-Get:7 http://ftp.at.debian.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
-Get:8 http://ftp.at.debian.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:9 http://ftp.at.debian.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
-Get:10 http://ftp.at.debian.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
-Get:11 http://ftp.at.debian.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
-Get:12 http://ftp.at.debian.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
-Get:13 http://ftp.at.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.at.debian.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:15 http://ftp.at.debian.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
-Get:16 http://ftp.at.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.at.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.at.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://ftp.at.debian.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
-Get:20 http://ftp.at.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.at.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf quilt
+ zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9531 kB in 2s (3410 kB/s)
-Selecting previously unselected package libpipeline1.
-(Reading database ... 10699 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_mipsel.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
+0 upgraded, 16 newly installed, 0 to remove and 16 not upgraded.
+Need to get 0 B/6932 kB of archives.
+After this operation, 20.7 MB of additional disk space will be used.
Selecting previously unselected package libglib2.0-0.
+(Reading database ... 11452 files and directories currently installed.)
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mipsel.deb) ...
Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mipsel.deb) ...
@@ -212,12 +191,6 @@ Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_mipsel.deb) ...
Selecting previously unselected package file.
@@ -235,26 +208,19 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
-Setting up libpcre3 (8.12-4) ...
+Processing triggers for man-db ...
Setting up libglib2.0-0 (2.28.8-1) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
-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 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
@@ -263,7 +229,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -271,11 +237,14 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libpopt0 libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.39-3-loongson-2e mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.67-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_172-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -286,12 +255,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -302,24 +271,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -332,21 +301,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -521,9 +490,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -600,7 +571,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -645,56 +616,56 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (eysler) <buildd_mipsel-eysler at buildd.debian.org> >../bedtools_2.14.2-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.14.3-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0440
+Build finished at 20111105-0214
-bedtools_2.14.2-1_mipsel.changes:
+bedtools_2.14.3-1_mipsel.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (eysler) <buildd_mipsel-eysler 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 (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- e85647c71f0767f18a9dabe6367632fbb2ed4dac 630926 bedtools_2.14.2-1_mipsel.deb
+ f3f67766afd0c131c5259c19600b7f435888623d 651142 bedtools_2.14.3-1_mipsel.deb
Checksums-Sha256:
- 4dbbefe4686dece182ceaabc365c0e4c38def9d640a83ebfe5136349cc499f66 630926 bedtools_2.14.2-1_mipsel.deb
+ 083e81eaf94a1794d2110286acc43ef55d5ffe6ca2ba9920950c19d310220c35 651142 bedtools_2.14.3-1_mipsel.deb
Files:
- b5bf75997bd986267769ec4dcba8ca55 630926 science optional bedtools_2.14.2-1_mipsel.deb
+ 84c4679dc2ee0dc60cd2848da9956fbd 651142 science optional bedtools_2.14.3-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_mipsel.deb
+bedtools_2.14.3-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 630926 bytes: control archive= 1737 bytes.
+ size 651142 bytes: control archive= 1769 bytes.
866 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5010
+ Installed-Size: 5155
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.2), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -710,49 +681,7 @@ bedtools_2.14.2-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 04:18 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
-drwxr-xr-x root/root 0 2011-11-03 04:39 ./usr/bin/
--rwxr-xr-x root/root 114248 2011-11-03 04:39 ./usr/bin/linksBed
--rwxr-xr-x root/root 244460 2011-11-03 04:39 ./usr/bin/bamToBed
--rwxr-xr-x root/root 307036 2011-11-03 04:39 ./usr/bin/coverageBed
--rwxr-xr-x root/root 128968 2011-11-03 04:39 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 187256 2011-11-03 04:39 ./usr/bin/pairToPair
--rwxr-xr-x root/root 114840 2011-11-03 04:39 ./usr/bin/complementBed
--rwxr-xr-x root/root 116792 2011-11-03 04:39 ./usr/bin/mergeBed
--rwxr-xr-x root/root 120472 2011-11-03 04:39 ./usr/bin/subtractBed
--rwxr-xr-x root/root 118616 2011-11-03 04:39 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 104152 2011-11-03 04:39 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 324476 2011-11-03 04:39 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 139656 2011-11-03 04:39 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 114728 2011-11-03 04:39 ./usr/bin/slopBed
--rwxr-xr-x root/root 311596 2011-11-03 04:39 ./usr/bin/windowBed
--rwxr-xr-x root/root 94312 2011-11-03 04:39 ./usr/bin/overlap
--rwxr-xr-x root/root 378444 2011-11-03 04:39 ./usr/bin/intersectBed
--rwxr-xr-x root/root 112280 2011-11-03 04:39 ./usr/bin/annotateBed
--rwxr-xr-x root/root 153148 2011-11-03 04:39 ./usr/bin/nucBed
--rwxr-xr-x root/root 299148 2011-11-03 04:39 ./usr/bin/tagBam
--rwxr-xr-x root/root 391004 2011-11-03 04:39 ./usr/bin/pairToBed
--rwxr-xr-x root/root 121624 2011-11-03 04:39 ./usr/bin/flankBed
--rwxr-xr-x root/root 152972 2011-11-03 04:39 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 248140 2011-11-03 04:39 ./usr/bin/bedToBam
--rwxr-xr-x root/root 129208 2011-11-03 04:39 ./usr/bin/closestBed
--rwxr-xr-x root/root 63960 2011-11-03 04:39 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 152472 2011-11-03 04:39 ./usr/bin/sortBed
--rwxr-xr-x root/root 326604 2011-11-03 04:39 ./usr/bin/multiBamCov
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15/bedtools_2.14.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -766,27 +695,70 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-bbfa43d9-fdb6-4d10-9e30-1716fbb43730/build/buildd-bedtools_2.14.2-1-mipsel-LWzfMb
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-33e93dd5-4413-432a-ab36-87d9c1e5c80f/build/buildd-bedtools_2.14.3-1-mipsel-k0rf15
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 groff-base libpipeline1 man-db libssl1.0.0
+Use 'apt-get autoremove' to remove them.
+The following packages will be REMOVED:
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libunistring0* libxml2*
+ po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 16 to remove and 16 not upgraded.
+After this operation, 20.7 MB disk space will be freed.
+(Reading database ... 12413 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 102756
-Build-Time: 1343
+Build-Space: 104656
+Build-Time: 1211
Distribution: sid
-Install-Time: 126
-Job: bedtools_2.14.2-1
+Install-Time: 44
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 1655
-Source-Version: 2.14.2-1
-Space: 102756
+Package-Time: 1304
+Source-Version: 2.14.3-1
+Space: 104656
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0440
-Build needed 00:27:35, 102756k disc space
-Signature with key '0D12A734' requested:
+Finished at 20111105-0214
+Build needed 00:21:44, 104656k disc space
+Signature with key 'B0903E66' requested:
diff --git a/powerpc.log b/powerpc.log
index 6d5f2a8..96f7fc3 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,69 @@
-From buildd at porpora.debian.org Thu Nov 03 03:53:09 2011
+From buildd at porpora.debian.org Sat Nov 05 02:00:27 2011
Return-path: <buildd at porpora.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 porpora.debian.org>)
- id 1RLoMX-0003oo-N8
- for logs at buildd.debian.org; Thu, 03 Nov 2011 03:53:09 +0000
+ id 1RMVYZ-000891-Pr
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:27 +0000
Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
helo=porpora.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1RLoMW-0002sH-Q4; Thu, 03 Nov 2011 03:53:08 +0000
+ id 1RMVYZ-0000c5-05; Sat, 05 Nov 2011 02:00:27 +0000
Received: from buildd by porpora.debian.org with local (Exim 4.72)
(envelope-from <buildd at porpora.debian.org>)
- id 1RLoMW-0003Aq-5F; Thu, 03 Nov 2011 03:53:08 +0000
-Message-Id: <E1RLoMW-0003Aq-5F at porpora.debian.org>
+ id 1RMVYY-00056G-9c; Sat, 05 Nov 2011 02:00:26 +0000
+Message-Id: <E1RMVYY-00056G-9c at porpora.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 3 Nov 2011 03:53:08 +0000
+Date: Sat, 5 Nov 2011 02:00:26 +0000
From: buildd on porpora <buildd at porpora.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.14.2-1 on powerpc (dist=sid)
-Key-Id: 6CB21D9F
+Subject: Log for successful build of bedtools_2.14.3-1 on powerpc (dist=sid)
+Key-Id: 8CE75D05
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (powerpc) 03 Nov 2011 03:46 ║
+║ bedtools 2.14.3-1 (powerpc) 05 Nov 2011 01:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: powerpc
Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.uk.debian.org unstable/main Sources [5889 kB]
+Get:2 http://ftp.uk.debian.org unstable/main Sources [5890 kB]
Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:4 http://ftp.uk.debian.org unstable/contrib Sources [56.9 kB]
+Get:5 http://ftp.uk.debian.org unstable/non-free Sources [103 kB]
+Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [7704 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://ftp.uk.debian.org unstable/contrib Sources [56.9 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [5896 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [104 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7702 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.5 kB]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.5 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Get:9 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Get:10 http://incoming.debian.org unstable/main Sources [5890 kB]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7702 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7704 kB]
Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.5 kB]
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 [47.2 kB]
-Get:18 http://incoming.debian.org Packages [605 kB]
+Get:17 http://incoming.debian.org Sources [25.7 kB]
+Get:18 http://incoming.debian.org Packages [300 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.6 MB in 28s (1014 kB/s)
+Fetched 28.2 MB in 24s (1176 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,9 +85,9 @@ Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
Need to get 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
Fetched 928 kB in 2s (454 kB/s)
Download complete and in download only mode
@@ -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 4 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 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -153,7 +153,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -175,32 +175,32 @@ 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.
+0 upgraded, 21 newly installed, 0 to remove and 17 not upgraded.
Need to get 9676 kB of archives.
After this operation, 27.8 MB of additional disk space will be used.
Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-4 [37.2 kB]
Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 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 8.9.8 [552 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9676 kB in 1s (8339 kB/s)
+Fetched 9676 kB in 1s (5904 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10725 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_powerpc.deb) ...
@@ -237,7 +237,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_powerpc.deb) ...
Selecting previously unselected package quilt.
@@ -265,7 +265,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -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 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 libc6-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +288,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -304,24 +304,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -334,21 +334,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -523,9 +523,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -602,7 +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_2.14.2-1-powerpc-mz0_bT/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -647,22 +649,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bedtools_2.14.2-1_powerpc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bedtools_2.14.3-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0353
+Build finished at 20111105-0200
-bedtools_2.14.2-1_powerpc.changes:
+bedtools_2.14.3-1_powerpc.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
@@ -670,33 +672,33 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- 4a3f297f39976240e89d11e60ba6701ec48aa6c0 597052 bedtools_2.14.2-1_powerpc.deb
+ 2566af9b100d3ce57600d80a171e4086c9121370 615234 bedtools_2.14.3-1_powerpc.deb
Checksums-Sha256:
- 537a161c6461430e3545194e903c49744d6f7b129dd3067dea1c16b7422d77fa 597052 bedtools_2.14.2-1_powerpc.deb
+ 9a63ca3bbad8479b781ab8b69169be3d7446b857860671b6ec3f31eed58171cf 615234 bedtools_2.14.3-1_powerpc.deb
Files:
- 319f9c3767930db8fdb8469c824e60a6 597052 science optional bedtools_2.14.2-1_powerpc.deb
+ e81ecddc44fffd56bdff51b2b214077d 615234 science optional bedtools_2.14.3-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_powerpc.deb
+bedtools_2.14.3-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 597052 bytes: control archive= 1736 bytes.
+ size 615234 bytes: control archive= 1765 bytes.
867 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4845
+ Installed-Size: 4988
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -712,49 +714,50 @@ bedtools_2.14.2-1_powerpc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 03:52 ./
-drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/bin/
--rwxr-xr-x root/root 149868 2011-11-03 03:52 ./usr/bin/nucBed
--rwxr-xr-x root/root 363104 2011-11-03 03:52 ./usr/bin/intersectBed
--rwxr-xr-x root/root 113620 2011-11-03 03:52 ./usr/bin/mergeBed
--rwxr-xr-x root/root 145636 2011-11-03 03:52 ./usr/bin/sortBed
--rwxr-xr-x root/root 240116 2011-11-03 03:52 ./usr/bin/bedToBam
--rwxr-xr-x root/root 125164 2011-11-03 03:52 ./usr/bin/closestBed
--rwxr-xr-x root/root 314976 2011-11-03 03:52 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 109028 2011-11-03 03:52 ./usr/bin/annotateBed
--rwxr-xr-x root/root 149860 2011-11-03 03:52 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 111260 2011-11-03 03:52 ./usr/bin/complementBed
--rwxr-xr-x root/root 375408 2011-11-03 03:52 ./usr/bin/pairToBed
--rwxr-xr-x root/root 297552 2011-11-03 03:52 ./usr/bin/coverageBed
--rwxr-xr-x root/root 101012 2011-11-03 03:52 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 110100 2011-11-03 03:52 ./usr/bin/linksBed
--rwxr-xr-x root/root 110692 2011-11-03 03:52 ./usr/bin/slopBed
--rwxr-xr-x root/root 115588 2011-11-03 03:52 ./usr/bin/subtractBed
--rwxr-xr-x root/root 301656 2011-11-03 03:52 ./usr/bin/windowBed
--rwxr-xr-x root/root 235964 2011-11-03 03:52 ./usr/bin/bamToBed
--rwxr-xr-x root/root 289808 2011-11-03 03:52 ./usr/bin/tagBam
--rwxr-xr-x root/root 133996 2011-11-03 03:52 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 63772 2011-11-03 03:52 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 175244 2011-11-03 03:52 ./usr/bin/pairToPair
--rwxr-xr-x root/root 125204 2011-11-03 03:52 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 318048 2011-11-03 03:52 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 117732 2011-11-03 03:52 ./usr/bin/flankBed
--rwxr-xr-x root/root 114284 2011-11-03 03:52 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 92940 2011-11-03 03:52 ./usr/bin/overlap
-drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 03:47 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 03:52 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/bin/
+-rwxr-xr-x root/root 149868 2011-11-05 02:00 ./usr/bin/nucBed
+-rwxr-xr-x root/root 363104 2011-11-05 02:00 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 113620 2011-11-05 02:00 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 145636 2011-11-05 02:00 ./usr/bin/sortBed
+-rwxr-xr-x root/root 240116 2011-11-05 02:00 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 125164 2011-11-05 02:00 ./usr/bin/closestBed
+-rwxr-xr-x root/root 314976 2011-11-05 02:00 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 109028 2011-11-05 02:00 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 149860 2011-11-05 02:00 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 111260 2011-11-05 02:00 ./usr/bin/complementBed
+-rwxr-xr-x root/root 375408 2011-11-05 02:00 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 297552 2011-11-05 02:00 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 101012 2011-11-05 02:00 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 110100 2011-11-05 02:00 ./usr/bin/linksBed
+-rwxr-xr-x root/root 110692 2011-11-05 02:00 ./usr/bin/slopBed
+-rwxr-xr-x root/root 115588 2011-11-05 02:00 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 301656 2011-11-05 02:00 ./usr/bin/windowBed
+-rwxr-xr-x root/root 235964 2011-11-05 02:00 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 289808 2011-11-05 02:00 ./usr/bin/tagBam
+-rwxr-xr-x root/root 133996 2011-11-05 02:00 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 63772 2011-11-05 02:00 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 175244 2011-11-05 02:00 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 125204 2011-11-05 02:00 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 318048 2011-11-05 02:00 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 117732 2011-11-05 02:00 ./usr/bin/flankBed
+-rwxr-xr-x root/root 146492 2011-11-05 02:00 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 114284 2011-11-05 02:00 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 92940 2011-11-05 02:00 ./usr/bin/overlap
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 01:55 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 02:00 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -768,7 +771,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-81e24f53-3bc3-46da-80f1-9a79708e877d/build/buildd-bedtools_2.14.2-1-powerpc-mz0_bT
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-b6490ec3-a9d4-40ac-b508-aeb1b41839c2/build/buildd-bedtools_2.14.3-1-powerpc-KZUEAD
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -776,18 +779,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 105644
-Build-Time: 306
+Build-Space: 107548
+Build-Time: 311
Distribution: sid
-Install-Time: 40
-Job: bedtools_2.14.2-1
+Install-Time: 44
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 390
-Source-Version: 2.14.2-1
-Space: 105644
+Package-Time: 396
+Source-Version: 2.14.3-1
+Space: 107548
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0353
-Build needed 00:06:30, 105644k disc space
-Signature with key '6CB21D9F' requested:
+Finished at 20111105-0200
+Build needed 00:06:36, 107548k disc space
+Signature with key '8CE75D05' requested:
diff --git a/s390.log b/s390.log
index 32cba12..1494c28 100644
--- a/s390.log
+++ b/s390.log
@@ -1,4 +1,4 @@
-From buildd at zandonai.debian.org Thu Nov 03 04:46:36 2011
+From buildd at zandonai.debian.org Sat Nov 05 02:00:03 2011
Return-path: <buildd at zandonai.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,64 +6,64 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RLpCG-0003dn-9q
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:46:36 +0000
+ id 1RMVYB-00085h-PO
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:00:03 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RLpCF-0000Yf-Fo; Thu, 03 Nov 2011 04:46:35 +0000
+ id 1RMVYA-0000bb-Ku; Sat, 05 Nov 2011 02:00:02 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1RLpCE-0005Iq-6z; Thu, 03 Nov 2011 04:46:34 +0000
-Message-Id: <E1RLpCE-0005Iq-6z at zandonai.debian.org>
+ id 1RMVY9-00015R-GA; Sat, 05 Nov 2011 02:00:01 +0000
+Message-Id: <E1RMVY9-00015R-GA at zandonai.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 3 Nov 2011 04:46:34 +0000
+Date: Sat, 5 Nov 2011 02:00:01 +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_2.14.2-1 on s390 (dist=sid)
-Key-Id: 2D941D26
+Subject: Log for successful build of bedtools_2.14.3-1 on s390 (dist=sid)
+Key-Id: 772711F7
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (s390) 03 Nov 2011 04:42 ║
+║ bedtools 2.14.3-1 (s390) 05 Nov 2011 01:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
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 [5889 kB]
+Get:2 http://ftp.de.debian.org unstable/main Sources [5890 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5896 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5890 kB]
Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.9 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [104 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7612 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [103 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7615 kB]
Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.5 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7612 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7615 kB]
Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.5 kB]
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 [40.2 kB]
-Get:18 http://incoming.debian.org Packages [601 kB]
+Get:17 http://incoming.debian.org Sources [25.7 kB]
+Get:18 http://incoming.debian.org Packages [300 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.4 MB in 24s (1173 kB/s)
+Fetched 28.1 MB in 29s (962 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 1s (487 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 2s (432 kB/s)
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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -153,7 +153,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -175,32 +175,32 @@ 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 41 not upgraded.
-Need to get 9864 kB of archives.
+0 upgraded, 21 newly installed, 0 to remove and 46 not upgraded.
+Need to get 9863 kB of archives.
After this operation, 28.0 MB of additional disk space will be used.
Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-4 [38.9 kB]
Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
Get:3 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.8-1 [1681 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-5 [879 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-2 [122 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-2 [1029 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.09-2 [257 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main file s390 5.09-2 [52.6 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-5 [143 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-5 [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 8.9.8 [552 kB]
+Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-5 [879 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-2 [122 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-2 [1029 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.09-2 [257 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main file s390 5.09-2 [52.6 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-5 [143 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-5 [2073 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4 kB]
Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9864 kB in 2s (3419 kB/s)
+Fetched 9863 kB in 2s (3829 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10631 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_s390.deb) ...
@@ -237,7 +237,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_s390.deb) ...
Selecting previously unselected package quilt.
@@ -265,7 +265,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
Toolchain package versions: binutils_2.21.90.20111004-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 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-2011-10-05-2 e2fsprogs_1.42~WIP-2011-10-05-2 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-05-2 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-6 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-05-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-05-2 e2fsprogs_1.42~WIP-2011-10-05-2 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-05-2 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-6 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-05-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +288,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -309,24 +309,24 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-p
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
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_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -532,9 +532,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -611,7 +613,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-s390-iHFiKc/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390-fsMyKX/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -656,22 +658,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.14.2-1_s390.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.14.3-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0446
+Build finished at 20111105-0159
-bedtools_2.14.2-1_s390.changes:
+bedtools_2.14.3-1_s390.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -679,33 +681,33 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- 0c593168e425781e7e31f78234990ffb23ee10c4 526928 bedtools_2.14.2-1_s390.deb
+ 9d67dfd763f71205f941761a89627915ab993a48 543134 bedtools_2.14.3-1_s390.deb
Checksums-Sha256:
- 0d243a497531f0b00198351760cebfd017a113b194d92dcd980316f026c9be79 526928 bedtools_2.14.2-1_s390.deb
+ 5114b326bb1cbb5a946292f98051d59e86a74a427a628af61ac9e3c09f6b735b 543134 bedtools_2.14.3-1_s390.deb
Files:
- 5fdfeffb5d04e621414f595a4ca30852 526928 science optional bedtools_2.14.2-1_s390.deb
+ 3ae61fbf34fcdddb48566b809ac5cebb 543134 science optional bedtools_2.14.3-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_s390.deb
+bedtools_2.14.3-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 526928 bytes: control archive= 1739 bytes.
+ size 543134 bytes: control archive= 1758 bytes.
864 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4749
+ Installed-Size: 4891
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -721,49 +723,50 @@ bedtools_2.14.2-1_s390.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 04:46 ./
-drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/bin/
--rwxr-xr-x root/root 289044 2011-11-03 04:46 ./usr/bin/coverageBed
--rwxr-xr-x root/root 106140 2011-11-03 04:46 ./usr/bin/linksBed
--rwxr-xr-x root/root 293148 2011-11-03 04:46 ./usr/bin/windowBed
--rwxr-xr-x root/root 114056 2011-11-03 04:46 ./usr/bin/subtractBed
--rwxr-xr-x root/root 280868 2011-11-03 04:46 ./usr/bin/tagBam
--rwxr-xr-x root/root 116780 2011-11-03 04:46 ./usr/bin/flankBed
--rwxr-xr-x root/root 88724 2011-11-03 04:46 ./usr/bin/overlap
--rwxr-xr-x root/root 232524 2011-11-03 04:46 ./usr/bin/bamToBed
--rwxr-xr-x root/root 109912 2011-11-03 04:46 ./usr/bin/complementBed
--rwxr-xr-x root/root 305840 2011-11-03 04:46 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 112724 2011-11-03 04:46 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 145548 2011-11-03 04:46 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 63832 2011-11-03 04:46 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 371648 2011-11-03 04:46 ./usr/bin/pairToBed
--rwxr-xr-x root/root 235752 2011-11-03 04:46 ./usr/bin/bedToBam
--rwxr-xr-x root/root 97800 2011-11-03 04:46 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 109472 2011-11-03 04:46 ./usr/bin/mergeBed
--rwxr-xr-x root/root 122412 2011-11-03 04:46 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 178220 2011-11-03 04:46 ./usr/bin/pairToPair
--rwxr-xr-x root/root 104652 2011-11-03 04:46 ./usr/bin/annotateBed
--rwxr-xr-x root/root 133196 2011-11-03 04:46 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 145560 2011-11-03 04:46 ./usr/bin/nucBed
--rwxr-xr-x root/root 122760 2011-11-03 04:46 ./usr/bin/closestBed
--rwxr-xr-x root/root 309532 2011-11-03 04:46 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 358696 2011-11-03 04:46 ./usr/bin/intersectBed
--rwxr-xr-x root/root 146224 2011-11-03 04:46 ./usr/bin/sortBed
--rwxr-xr-x root/root 108588 2011-11-03 04:46 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 04:43 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 04:46 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-11-05 01:59 ./
+drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/bin/
+-rwxr-xr-x root/root 289044 2011-11-05 01:59 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 106140 2011-11-05 01:59 ./usr/bin/linksBed
+-rwxr-xr-x root/root 293148 2011-11-05 01:59 ./usr/bin/windowBed
+-rwxr-xr-x root/root 114056 2011-11-05 01:59 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 280868 2011-11-05 01:59 ./usr/bin/tagBam
+-rwxr-xr-x root/root 116780 2011-11-05 01:59 ./usr/bin/flankBed
+-rwxr-xr-x root/root 88724 2011-11-05 01:59 ./usr/bin/overlap
+-rwxr-xr-x root/root 232524 2011-11-05 01:59 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 109912 2011-11-05 01:59 ./usr/bin/complementBed
+-rwxr-xr-x root/root 305840 2011-11-05 01:59 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 112724 2011-11-05 01:59 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 145548 2011-11-05 01:59 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 63832 2011-11-05 01:59 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 371648 2011-11-05 01:59 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 235752 2011-11-05 01:59 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 97800 2011-11-05 01:59 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 109472 2011-11-05 01:59 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 122412 2011-11-05 01:59 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 178220 2011-11-05 01:59 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 145500 2011-11-05 01:59 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 104652 2011-11-05 01:59 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 133196 2011-11-05 01:59 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 145560 2011-11-05 01:59 ./usr/bin/nucBed
+-rwxr-xr-x root/root 122760 2011-11-05 01:59 ./usr/bin/closestBed
+-rwxr-xr-x root/root 309532 2011-11-05 01:59 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 358696 2011-11-05 01:59 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 146224 2011-11-05 01:59 ./usr/bin/sortBed
+-rwxr-xr-x root/root 108588 2011-11-05 01:59 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 01:57 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 01:59 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -777,7 +780,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-d3df2d3d-da7c-4ff3-a2d6-632bc0b5be2b/build/buildd-bedtools_2.14.2-1-s390-iHFiKc
+Purging /var/lib/schroot/mount/sid-s390-sbuild-4c46a11e-6346-4db3-b381-caefe0d5dd1c/build/buildd-bedtools_2.14.3-1-s390-fsMyKX
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -785,18 +788,790 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 110352
-Build-Time: 172
+Build-Space: 112288
+Build-Time: 169
Distribution: sid
-Install-Time: 9
-Job: bedtools_2.14.2-1
+Install-Time: 8
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 218
-Source-Version: 2.14.2-1
-Space: 110352
+Package-Time: 227
+Source-Version: 2.14.3-1
+Space: 112288
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0446
-Build needed 00:03:38, 110352k disc space
-Signature with key '2D941D26' requested:
+Finished at 20111105-0159
+Build needed 00:03:47, 112288k disc space
+Signature with key '772711F7' requested:
+From buildd at zemlinsky.debian.org Sun Nov 27 04:20:02 2011
+Return-path: <buildd at zemlinsky.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1RUWDi-0002Aw-8p
+ for logs at buildd.debian.org; Sun, 27 Nov 2011 04:20:02 +0000
+Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1RUWDh-0007uz-IR; Sun, 27 Nov 2011 04:20:01 +0000
+Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1RUWDh-0007Jd-33; Sun, 27 Nov 2011 04:20:01 +0000
+Message-Id: <E1RUWDh-0007Jd-33 at zemlinsky.debian.org>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Sun, 27 Nov 2011 04:20:01 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
+To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.3-1 on s390x (dist=sid)
+Key-Id: B5D24954
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ bedtools 2.14.3-1 (s390x) 27 Nov 2011 04:16 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: bedtools
+Version: 2.14.3-1
+Source Version: 2.14.3-1
+Architecture: s390x
+Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [181 kB]
+Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [5921 kB]
+Get:3 http://incoming.debian.org unstable InRelease [181 kB]
+Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [56.5 kB]
+Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [103 kB]
+Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390x Packages [3917 kB]
+Get:7 http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages [33.4 kB]
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
+Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2045 B]
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
+Ign http://incoming.debian.org InRelease
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [5924 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main s390x Packages [4100 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390x Packages [33.4 kB]
+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 [1616 B]
+Get:17 http://incoming.debian.org Sources [32.6 kB]
+Get:18 http://incoming.debian.org Packages [1102 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 21.8 MB in 6s (3290 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/git/debian-med/bedtools.git
+Need to get 928 kB of source archives.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 0s (6910 kB/s)
+Download complete and in download only mode
+
+Check arch
+──────────
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18.1-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install bedtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Checking for already installed dependencies...
+libc6-dev: already installed (2.13-21)
+gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
+cdbs: missing
+debhelper: missing
+Using default version 8.9.11
+quilt: missing
+zlib1g-dev: missing
+Checking for dependency conflicts...
+Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
+Reading package lists...
+Building dependency tree...
+The following extra packages will be installed:
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf
+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
+The following NEW packages will be installed:
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 3 not upgraded.
+Need to get 10.2 MB of archives.
+After this operation, 29.1 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.0-5 [39.4 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4 [234 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3 [26.1 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-4 [1866 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-5 [890 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.2-2 [123 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5 [438 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 8.2.3 [213 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6 [1181 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.0.2-3 [1021 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.09-2 [253 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.09-2 [52.7 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5 [155 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15 [111 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5 [2157 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 8.9.11 [552 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.54-1 [29.2 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.3.4.dfsg-3 [199 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 10.2 MB in 0s (26.7 MB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10717 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_s390x.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_s390x.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_s390x.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_s390x.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_s390x.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_s390x.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_s390x.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390x.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_s390x.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-3_s390x.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.09-2_s390x.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.09-2_s390x.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_s390x.deb) ...
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_s390x.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_s390x.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_s390x.deb) ...
+Selecting previously unselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
+Selecting previously unselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390x.deb) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
+No schema files found: doing nothing.
+Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libcroco3 (0.6.2-2) ...
+Setting up libunistring0 (0.9.3-5) ...
+Setting up bsdmainutils (8.2.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-3) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.09-2) ...
+Setting up file (5.09-2) ...
+Setting up gettext-base (0.18.1.1-5) ...
+Setting up cdbs (0.4.99) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up gettext (0.18.1.1-5) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.11) ...
+Setting up diffstat (1.54-1) ...
+Setting up quilt (0.48-8) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-s390x s390x (s390x)
+Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-5 gcc-4.6_4.6.2-5 libc6-dev_2.13-21 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-5 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 g++_4:4.6.1-3 g++-4.6_4.6.2-5 gcc_4:4.6.1-3 gcc-4.6_4.6.2-5 gcc-4.6-base_4.6.2-5 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-5 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4.1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Sat Nov 5 01:38:08 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
+dpkg-source: info: applying gzstream.h.patch
+
+Check disc space
+────────────────
+
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package bedtools
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: host architecture s390x
+ fakeroot debian/rules clean
+test -x debian/rules
+dh_testroot
+rm -f debian/stamp-makefile-build debian/stamp-makefile-install
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+Cleaning up.
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch gzstream.h.patch
+Restoring src/utils/gzstream/gzstream.C
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
+ debian/rules build
+test -x debian/rules
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch gzstream.h.patch
+patching file src/utils/gzstream/gzstream.C
+
+Now at patch gzstream.h.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+[ -d obj ] || mkdir -p obj
+[ -d bin ] || mkdir -p bin
+Building BEDTools:
+=========================================================
+- Building in src/utils/lineFileUtilities
+ * compiling lineFileUtilities.cpp
+
+- Building in src/utils/bedFile
+ * compiling bedFile.cpp
+
+- Building in src/utils/bedGraphFile
+ * compiling bedGraphFile.cpp
+
+- Building in src/utils/chromsweep
+ * compiling chromsweep.cpp
+
+- Building in src/utils/gzstream
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+
+- Building in src/utils/fileType
+ * compiling fileType.cpp
+
+- Building in src/utils/bedFilePE
+ * compiling bedFilePE.cpp
+
+- Building in src/utils/sequenceUtilities
+ * compiling sequenceUtils.cpp
+
+- Building in src/utils/tabFile
+ * compiling tabFile.cpp
+
+- Building in src/utils/BamTools
+ * compiling BamAlignment.cpp
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<unsigned int>&) const':
+src/api/BamAlignment.cpp:1769:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<int>&) const':
+src/api/BamAlignment.cpp:1856:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+src/api/BamAlignment.cpp: In member function 'bool BamTools::BamAlignment::GetTag(const string&, std::vector<float>&) const':
+src/api/BamAlignment.cpp:1944:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
+ * compiling BamMultiReader.cpp
+ * compiling BamReader.cpp
+ * compiling BamWriter.cpp
+ * compiling SamHeader.cpp
+ * compiling SamProgram.cpp
+ * compiling SamProgramChain.cpp
+ * compiling SamReadGroup.cpp
+ * compiling SamReadGroupDictionary.cpp
+ * compiling SamSequence.cpp
+ * compiling SamSequenceDictionary.cpp
+ * compiling BamHeader_p.cpp
+ * compiling BamIndexFactory_p.cpp
+ * compiling BamMultiReader_p.cpp
+ * compiling BamRandomAccessController_p.cpp
+ * compiling BamReader_p.cpp
+ * compiling BamStandardIndex_p.cpp
+ * compiling BamToolsIndex_p.cpp
+ * compiling BamWriter_p.cpp
+ * compiling BgzfStream_p.cpp
+ * compiling SamFormatParser_p.cpp
+ * compiling SamFormatPrinter_p.cpp
+ * compiling SamHeaderValidator_p.cpp
+[ -d lib ] || mkdir -p lib
+[ -d include ] || mkdir -p include
+[ -d include/api ] || mkdir -p include/api
+[ -d include/shared ] || mkdir -p include/shared
+ * linking libbamtools.a
+ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/BamHeader_p.o src/api/internal/BamIndexFactory_p.o src/api/internal/BamMultiReader_p.o src/api/internal/BamRandomAccessController_p.o src/api/internal/BamReader_p.o src/api/internal/BamStandardIndex_p.o src/api/internal/BamToolsIndex_p.o src/api/internal/BamWriter_p.o src/api/internal/BgzfStream_p.o src/api/internal/SamFormatParser_p.o src/api/internal/SamFormatPrinter_p.o src/api/internal/SamHeaderValidator_p.o
+
+- Building in src/utils/BamTools-Ancillary
+ * compiling BamAncillary.cpp
+
+- Building in src/utils/Fasta
+ * compiling Fasta.cpp
+Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
+Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
+ * compiling split.cpp
+
+- Building in src/utils/genomeFile
+ * compiling genomeFile.cpp
+genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
+genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
+
+- Building in src/annotateBed
+ * compiling annotateMain.cpp
+annotateMain.cpp: In function 'int main(int, char**)':
+annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
+ * compiling annotateBed.cpp
+ * linking annotateBed
+
+- Building in src/bamToBed
+ * compiling bamToBed.cpp
+bamToBed.cpp: In function 'int main(int, char**)':
+bamToBed.cpp:70:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
+ * linking bamToBed
+
+- Building in src/bedToBam
+ * compiling bedToBam.cpp
+bedToBam.cpp: In function 'int main(int, char**)':
+bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
+ * linking bedToBam
+
+- Building in src/bedToIgv
+ * compiling bedToIgv.cpp
+ * linking bedToIgv
+
+- Building in src/bed12ToBed6
+ * compiling bed12ToBed6.cpp
+ * linking bed12ToBed6
+
+- Building in src/closestBed
+ * compiling closestMain.cpp
+ * compiling closestBed.cpp
+ * linking closestBed
+
+- Building in src/complementBed
+ * compiling complementMain.cpp
+ * compiling complementBed.cpp
+ * linking complementBed
+
+- Building in src/coverageBed
+ * compiling coverageMain.cpp
+ * compiling coverageBed.cpp
+ * linking coverageBed
+
+- Building in src/fastaFromBed
+ * compiling fastaFromBedMain.cpp
+ * compiling fastaFromBed.cpp
+ * linking fastaFromBed
+
+- Building in src/flankBed
+ * compiling flankBedMain.cpp
+ * compiling flankBed.cpp
+ * linking flankBed
+
+- Building in src/genomeCoverageBed
+ * compiling genomeCoverageMain.cpp
+ * compiling genomeCoverageBed.cpp
+ * linking genomeCoverageBed
+
+- Building in src/intersectBed
+ * compiling intersectMain.cpp
+ * compiling intersectBed.cpp
+ * linking intersectBed
+
+- Building in src/linksBed
+ * compiling linksMain.cpp
+ * compiling linksBed.cpp
+ * linking linksBed
+
+- Building in src/maskFastaFromBed
+ * compiling maskFastaFromBedMain.cpp
+ * compiling maskFastaFromBed.cpp
+ * linking maskFastaFromBed
+
+- Building in src/mergeBed
+ * compiling mergeMain.cpp
+mergeMain.cpp: In function 'int main(int, char**)':
+mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
+ * compiling mergeBed.cpp
+ * linking mergeBed
+
+- Building in src/multiBamCov
+ * compiling multiBamCovMain.cpp
+multiBamCovMain.cpp: In function 'int main(int, char**)':
+multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
+multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
+ * compiling multiBamCov.cpp
+ * linking multiBamCov
+
+- Building in src/multiIntersectBed
+ * compiling multiIntersectBed.cpp
+ * compiling multiIntersectBedMain.cpp
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
+
+- Building in src/nucBed
+ * compiling nucBedMain.cpp
+ * compiling nucBed.cpp
+ * linking nucBed
+
+- Building in src/overlap
+ * compiling overlap.cpp
+overlap.cpp: In function 'int main(int, char**)':
+overlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
+ * linking overlap
+
+- Building in src/pairToBed
+ * compiling pairToBedMain.cpp
+pairToBedMain.cpp: In function 'int main(int, char**)':
+pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling pairToBed.cpp
+pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
+pairToBed.cpp:255:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
+pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
+ * linking pairToBed
+
+- Building in src/pairToPair
+ * compiling pairToPairMain.cpp
+pairToPairMain.cpp: In function 'int main(int, char**)':
+pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling pairToPair.cpp
+pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
+pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
+pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
+ * linking pairToPair
+
+- Building in src/shuffleBed
+ * compiling shuffleBedMain.cpp
+ * compiling shuffleBed.cpp
+ * linking shuffleBed
+
+- Building in src/slopBed
+ * compiling slopBedMain.cpp
+ * compiling slopBed.cpp
+ * linking slopBed
+
+- Building in src/sortBed
+ * compiling sortMain.cpp
+ * compiling sortBed.cpp
+ * linking sortBed
+
+- Building in src/subtractBed
+ * compiling subtractMain.cpp
+subtractMain.cpp: In function 'int main(int, char**)':
+subtractMain.cpp:41:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling subtractBed.cpp
+ * linking subtractBed
+
+- Building in src/tagBam
+ * compiling tagBamMain.cpp
+tagBamMain.cpp: In function 'int main(int, char**)':
+tagBamMain.cpp:38:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
+ * compiling tagBam.cpp
+ * linking tagBam
+
+- Building in src/unionBedGraphs
+ * compiling unionBedGraphs.cpp
+ * compiling unionBedGraphsMain.cpp
+unionBedGraphsMain.cpp: In function 'int main(int, char**)':
+unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking unionBedGraphs
+
+- Building in src/windowBed
+ * compiling windowMain.cpp
+ * compiling windowBed.cpp
+ * linking windowBed
+
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+touch debian/stamp-makefile-build
+DEB_MAKE_CHECK_TARGET unset, not running checks
+ fakeroot debian/rules binary-arch
+test -x debian/rules
+dh_testroot
+dh_prep
+dh_installdirs -A
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+DEB_MAKE_CHECK_TARGET unset, not running checks
+DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
+Adding cdbs dependencies to debian/bedtools.substvars
+dh_installdirs -pbedtools
+dh_installdocs -pbedtools
+dh_installexamples -pbedtools
+dh_installman -pbedtools
+dh_installinfo -pbedtools
+dh_installmenu -pbedtools
+dh_installcron -pbedtools
+dh_installinit -pbedtools
+dh_installdebconf -pbedtools
+dh_installemacsen -pbedtools
+dh_installcatalogs -pbedtools
+dh_installpam -pbedtools
+dh_installlogrotate -pbedtools
+dh_installlogcheck -pbedtools
+dh_installchangelogs -pbedtools RELEASE_HISTORY
+dh_installudev -pbedtools
+dh_lintian -pbedtools
+dh_bugfiles -pbedtools
+dh_install -pbedtools
+dh_link -pbedtools
+dh_installmime -pbedtools
+dh_installgsettings -pbedtools
+dh_strip -pbedtools
+dh_compress -pbedtools
+dh_fixperms -pbedtools
+dh_makeshlibs -pbedtools
+dh_installdeb -pbedtools
+dh_perl -pbedtools
+dh_shlibdeps -pbedtools
+dh_gencontrol -pbedtools
+dh_md5sums -pbedtools
+dh_builddeb -pbedtools -- -Z xz
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.14.3-1_s390x.changes
+dpkg-genchanges: arch-specific upload - not including arch-independent packages
+dpkg-genchanges: binary-only upload - not including any source code
+ dpkg-source --after-build bedtools-2.14.3
+dpkg-buildpackage: binary only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20111127-0419
+
+bedtools_2.14.3-1_s390x.changes:
+Format: 1.8
+Date: Fri, 04 Nov 2011 09:25:38 +0900
+Source: bedtools
+Binary: bedtools
+Architecture: s390x
+Version: 2.14.3-1
+Distribution: sid
+Urgency: low
+Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description:
+ bedtools - suite of utilities for comparing genomic features
+Changes:
+ bedtools (2.14.3-1) unstable; urgency=low
+ .
+ [04f6aa3] Bugfix release.
+Checksums-Sha1:
+ 25c2141d4ca508d380a476cfa004a06adb1a820e 694528 bedtools_2.14.3-1_s390x.deb
+Checksums-Sha256:
+ b7097ca02edd72237d807cb86b673a0591b690212ccc797974004758ba705ff6 694528 bedtools_2.14.3-1_s390x.deb
+Files:
+ 3f8a10e9c92162e105019acb895e5441 694528 science optional bedtools_2.14.3-1_s390x.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+bedtools_2.14.3-1_s390x.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 694528 bytes: control archive= 1759 bytes.
+ 866 bytes, 19 lines control
+ 2085 bytes, 36 lines md5sums
+ Package: bedtools
+ Version: 2.14.3-1
+ Architecture: s390x
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 5629
+ Pre-Depends: dpkg (>= 1.15.6)
+ Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Suggests: filo
+ Section: science
+ Priority: optional
+ Homepage: http://code.google.com/p/bedtools/
+ Description: suite of utilities for comparing genomic features
+ The BEDTools utilities allow one to address common genomics tasks such as
+ finding feature overlaps and computing coverage. The utilities are largely
+ based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
+ BEDTools, one can develop sophisticated pipelines that answer complicated
+ research questions by streaming several BEDTools together.
+ .
+ The groupBy utility is distribued in the filo package.
+
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-27 04:16 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/bin/
+-rwxr-xr-x root/root 105864 2011-11-27 04:19 ./usr/bin/overlap
+-rwxr-xr-x root/root 422632 2011-11-27 04:19 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 261888 2011-11-27 04:19 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 126352 2011-11-27 04:19 ./usr/bin/slopBed
+-rwxr-xr-x root/root 134488 2011-11-27 04:19 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 171344 2011-11-27 04:19 ./usr/bin/sortBed
+-rwxr-xr-x root/root 348032 2011-11-27 04:19 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 135248 2011-11-27 04:19 ./usr/bin/flankBed
+-rwxr-xr-x root/root 122920 2011-11-27 04:19 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 143048 2011-11-27 04:19 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 329400 2011-11-27 04:19 ./usr/bin/windowBed
+-rwxr-xr-x root/root 168184 2011-11-27 04:19 ./usr/bin/nucBed
+-rwxr-xr-x root/root 271480 2011-11-27 04:19 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 171600 2011-11-27 04:19 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 130408 2011-11-27 04:19 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 349576 2011-11-27 04:19 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 114880 2011-11-27 04:19 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 143256 2011-11-27 04:19 ./usr/bin/closestBed
+-rwxr-xr-x root/root 130464 2011-11-27 04:19 ./usr/bin/complementBed
+-rwxr-xr-x root/root 126336 2011-11-27 04:19 ./usr/bin/linksBed
+-rwxr-xr-x root/root 134624 2011-11-27 04:19 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 208272 2011-11-27 04:19 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 155328 2011-11-27 04:19 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 317304 2011-11-27 04:19 ./usr/bin/tagBam
+-rwxr-xr-x root/root 171504 2011-11-27 04:19 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 327512 2011-11-27 04:19 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 405624 2011-11-27 04:19 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 77224 2011-11-27 04:19 ./usr/bin/unionBedGraphs
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Finished │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Built successfully
+────────────────────────────────────────────────────────────────────────────────
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-77d51d80-d702-41d3-80db-5a13a750c941/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: s390x
+Build-Space: 146144
+Build-Time: 201
+Distribution: sid
+Install-Time: 11
+Job: bedtools_2.14.3-1
+Package: bedtools
+Package-Time: 221
+Source-Version: 2.14.3-1
+Space: 146144
+Status: successful
+Version: 2.14.3-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20111127-0419
+Build needed 00:03:41, 146144k disc space
+Signature with key 'B5D24954' requested:
diff --git a/i386.log b/s390x.log
similarity index 61%
copy from i386.log
copy to s390x.log
index 41f2126..e46773d 100644
--- a/i386.log
+++ b/s390x.log
@@ -1,68 +1,69 @@
-From buildd at biber.debian.org Thu Nov 03 03:44:34 2011
-Return-path: <buildd at biber.debian.org>
+From buildd at zemlinsky.debian.org Sun Nov 27 04:20:02 2011
+Return-path: <buildd at zemlinsky.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
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- for logs at buildd.debian.org; Thu, 03 Nov 2011 03:44:34 +0000
-Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
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+ for logs at buildd.debian.org; Sun, 27 Nov 2011 04:20:02 +0000
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- CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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-Message-Id: <E1RLoED-0006lz-5A at biber.debian.org>
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+ id 1RUWDh-0007Jd-33; Sun, 27 Nov 2011 04:20:01 +0000
+Message-Id: <E1RUWDh-0007Jd-33 at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 3 Nov 2011 03:44:33 +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_2.14.2-1 on i386 (dist=sid)
-Key-Id: C83D412C
+Date: Sun, 27 Nov 2011 04:20:01 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
+To: aurelien at aurel32.net,phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.14.3-1 on s390x (dist=sid)
+Key-Id: B5D24954
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 zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (i386) 03 Nov 2011 03:40 ║
+║ bedtools 2.14.3-1 (s390x) 27 Nov 2011 04:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
-Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5889 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [56.9 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [104 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7821 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.2 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
+Version: 2.14.3-1
+Source Version: 2.14.3-1
+Architecture: s390x
+Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [181 kB]
+Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [5921 kB]
+Get:3 http://incoming.debian.org unstable InRelease [181 kB]
+Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [56.5 kB]
+Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [103 kB]
+Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390x Packages [3917 kB]
+Get:7 http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages [33.4 kB]
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib TranslationIndex
+Get:8 http://ftp-stud.hs-esslingen.de unstable/main TranslationIndex [2045 B]
+Ign http://ftp-stud.hs-esslingen.de unstable/contrib Translation-en
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 [5896 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7820 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [68.2 kB]
+Get:10 http://incoming.debian.org unstable/main Sources [5924 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main s390x Packages [4100 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390x Packages [33.4 kB]
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 [47.2 kB]
-Get:18 http://incoming.debian.org Packages [605 kB]
+Get:16 http://incoming.debian.org Release [1616 B]
+Get:17 http://incoming.debian.org Sources [32.6 kB]
+Get:18 http://incoming.debian.org Packages [1102 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.8 MB in 31s (904 kB/s)
+Fetched 21.8 MB in 6s (3290 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,14 +81,13 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
Need to get 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 2s (425 kB/s)
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 0s (6910 kB/s)
Download complete and in download only mode
Check arch
@@ -106,45 +106,19 @@ 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 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bedtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
+Build-Depends: 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 (8.13-3)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.2-1)
-dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-6)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
libc6-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
@@ -152,18 +126,17 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.11
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
Installing positive dependencies: cdbs debhelper quilt zlib1g-dev
Reading package lists...
Building dependency tree...
-Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff less
www-browser libmail-box-perl procmail graphviz
@@ -172,80 +145,84 @@ Recommended packages:
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
+ html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 16 not upgraded.
-Need to get 9694 kB of archives.
-After this operation, 27.3 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-4 [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 libglib2.0-0 i386 2.28.8-1 [1633 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-5 [882 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-2 [122 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.3 [203 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.2-2 [1013 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.09-2 [246 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.09-2 [51.5 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-5 [133 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-5 [2025 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 8.9.8 [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]
+0 upgraded, 22 newly installed, 0 to remove and 3 not upgraded.
+Need to get 10.2 MB of archives.
+After this operation, 29.1 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.0-5 [39.4 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 8.12-4 [234 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3 [26.1 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.30.2-4 [1866 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.7.8.dfsg-5 [890 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.2-2 [123 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5 [438 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 8.2.3 [213 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-6 [1181 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.0.2-3 [1021 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.09-2 [253 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.09-2 [52.7 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-5 [155 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15 [111 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-5 [2157 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 8.9.11 [552 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.54-1 [29.2 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.3.4.dfsg-3 [199 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9694 kB in 0s (9802 kB/s)
+Fetched 10.2 MB in 0s (26.7 MB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10638 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_i386.deb) ...
+(Reading database ... 10717 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_s390x.deb) ...
Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-4_s390x.deb) ...
+Selecting previously unselected package libffi5.
+Unpacking libffi5 (from .../libffi5_3.0.10-3_s390x.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_s390x.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_s390x.deb) ...
Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_i386.deb) ...
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_s390x.deb) ...
Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_i386.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_s390x.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390x.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6_s390x.deb) ...
Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-3_s390x.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_i386.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_i386.deb) ...
+Unpacking file (from .../archives/file_5.09-2_s390x.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_s390x.deb) ...
Selecting previously unselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
+Unpacking html2text (from .../html2text_1.3.2a-15_s390x.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_s390x.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_i386.deb) ...
+Unpacking diffstat (from .../diffstat_1.54-1_s390x.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
-Setting up libpipeline1 (1.2.0-4) ...
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390x.deb) ...
+Setting up libpipeline1 (1.2.0-5) ...
Setting up libpcre3 (8.12-4) ...
-Setting up libglib2.0-0 (2.28.8-1) ...
+Setting up libffi5 (3.0.10-3) ...
+Setting up libglib2.0-0 (2.30.2-4) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
@@ -254,7 +231,7 @@ Setting up bsdmainutils (8.2.3) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
@@ -264,7 +241,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.11) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -272,11 +249,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-2 gcc-4.6_4.6.2-2 libc6-dev_2.13-21 libstdc++6_4.6.2-2 libstdc++6-4.6-dev_4.6.2-2 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-2 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_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-2 gcc_4:4.6.1-3 gcc-4.6_4.6.2-2 gcc-4.6-base_4.6.2-2 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libquadmath0_4.6.2-2 libreadline6_6.2-7 libselinux1_2.1.0-3 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-2 libstdc++6-4.6-dev_4.6.2-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-s390x s390x (s390x)
+Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-5 gcc-4.6_4.6.2-5 libc6-dev_2.13-21 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 linux-libc-dev_3.1.1-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-5 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 g++_4:4.6.1-3 g++-4.6_4.6.2-5 gcc_4:4.6.1-3 gcc-4.6_4.6.2-5 gcc-4.6-base_4.6.2-5 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-3 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-5 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-4.1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-8 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,12 +264,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -303,24 +280,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
-dpkg-buildpackage: host architecture i386
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
+dpkg-buildpackage: host architecture s390x
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -333,21 +310,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -522,9 +499,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -601,7 +580,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-i386-u4h74k/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -646,58 +625,58 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.14.2-1_i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../bedtools_2.14.3-1_s390x.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0344
+Build finished at 20111127-0419
-bedtools_2.14.2-1_i386.changes:
+bedtools_2.14.3-1_s390x.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
-Architecture: i386
-Version: 2.14.2-1
+Architecture: s390x
+Version: 2.14.3-1
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
+Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- edd41d0a01700b5ff047a82dd5bf70650b346300 682334 bedtools_2.14.2-1_i386.deb
+ 25c2141d4ca508d380a476cfa004a06adb1a820e 694528 bedtools_2.14.3-1_s390x.deb
Checksums-Sha256:
- 89d0a8f40b651d682757545bf6ca5e9bf662cb83d5de705da997c907179d0307 682334 bedtools_2.14.2-1_i386.deb
+ b7097ca02edd72237d807cb86b673a0591b690212ccc797974004758ba705ff6 694528 bedtools_2.14.3-1_s390x.deb
Files:
- 0aea0bd694c0be19d013c9997a322fd6 682334 science optional bedtools_2.14.2-1_i386.deb
+ 3f8a10e9c92162e105019acb895e5441 694528 science optional bedtools_2.14.3-1_s390x.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_i386.deb
-──────────────────────────
+bedtools_2.14.3-1_s390x.deb
+───────────────────────────
new debian package, version 2.0.
- size 682334 bytes: control archive= 1733 bytes.
- 864 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ size 694528 bytes: control archive= 1759 bytes.
+ 866 bytes, 19 lines control
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
- Architecture: i386
+ Version: 2.14.3-1
+ Architecture: s390x
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4643
+ Installed-Size: 5629
Pre-Depends: dpkg (>= 1.15.6)
- Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Depends: libc6 (>= 2.13), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
Section: science
Priority: optional
@@ -711,49 +690,50 @@ bedtools_2.14.2-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/bin/
--rwxr-xr-x root/root 142420 2011-11-03 03:44 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 59648 2011-11-03 03:44 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 96356 2011-11-03 03:44 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227744 2011-11-03 03:44 ./usr/bin/bedToBam
--rwxr-xr-x root/root 114204 2011-11-03 03:44 ./usr/bin/flankBed
--rwxr-xr-x root/root 143008 2011-11-03 03:44 ./usr/bin/sortBed
--rwxr-xr-x root/root 297312 2011-11-03 03:44 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 105688 2011-11-03 03:44 ./usr/bin/linksBed
--rwxr-xr-x root/root 142360 2011-11-03 03:44 ./usr/bin/nucBed
--rwxr-xr-x root/root 350572 2011-11-03 03:44 ./usr/bin/intersectBed
--rwxr-xr-x root/root 112756 2011-11-03 03:44 ./usr/bin/subtractBed
--rwxr-xr-x root/root 285024 2011-11-03 03:44 ./usr/bin/windowBed
--rwxr-xr-x root/root 109600 2011-11-03 03:44 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 272744 2011-11-03 03:44 ./usr/bin/tagBam
--rwxr-xr-x root/root 129456 2011-11-03 03:44 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 281864 2011-11-03 03:44 ./usr/bin/coverageBed
--rwxr-xr-x root/root 107064 2011-11-03 03:44 ./usr/bin/mergeBed
--rwxr-xr-x root/root 104524 2011-11-03 03:44 ./usr/bin/annotateBed
--rwxr-xr-x root/root 88164 2011-11-03 03:44 ./usr/bin/overlap
--rwxr-xr-x root/root 122020 2011-11-03 03:44 ./usr/bin/closestBed
--rwxr-xr-x root/root 178284 2011-11-03 03:44 ./usr/bin/pairToPair
--rwxr-xr-x root/root 105472 2011-11-03 03:44 ./usr/bin/complementBed
--rwxr-xr-x root/root 223548 2011-11-03 03:44 ./usr/bin/bamToBed
--rwxr-xr-x root/root 301420 2011-11-03 03:44 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 366968 2011-11-03 03:44 ./usr/bin/pairToBed
--rwxr-xr-x root/root 121520 2011-11-03 03:44 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 105344 2011-11-03 03:44 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
-drwxr-xr-x root/root 0 2011-11-03 03:44 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 03:41 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-27 04:16 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-11-27 04:19 ./usr/bin/
+-rwxr-xr-x root/root 105864 2011-11-27 04:19 ./usr/bin/overlap
+-rwxr-xr-x root/root 422632 2011-11-27 04:19 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 261888 2011-11-27 04:19 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 126352 2011-11-27 04:19 ./usr/bin/slopBed
+-rwxr-xr-x root/root 134488 2011-11-27 04:19 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 171344 2011-11-27 04:19 ./usr/bin/sortBed
+-rwxr-xr-x root/root 348032 2011-11-27 04:19 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 135248 2011-11-27 04:19 ./usr/bin/flankBed
+-rwxr-xr-x root/root 122920 2011-11-27 04:19 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 143048 2011-11-27 04:19 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 329400 2011-11-27 04:19 ./usr/bin/windowBed
+-rwxr-xr-x root/root 168184 2011-11-27 04:19 ./usr/bin/nucBed
+-rwxr-xr-x root/root 271480 2011-11-27 04:19 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 171600 2011-11-27 04:19 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 130408 2011-11-27 04:19 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 349576 2011-11-27 04:19 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 114880 2011-11-27 04:19 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 143256 2011-11-27 04:19 ./usr/bin/closestBed
+-rwxr-xr-x root/root 130464 2011-11-27 04:19 ./usr/bin/complementBed
+-rwxr-xr-x root/root 126336 2011-11-27 04:19 ./usr/bin/linksBed
+-rwxr-xr-x root/root 134624 2011-11-27 04:19 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 208272 2011-11-27 04:19 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 155328 2011-11-27 04:19 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 317304 2011-11-27 04:19 ./usr/bin/tagBam
+-rwxr-xr-x root/root 171504 2011-11-27 04:19 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 327512 2011-11-27 04:19 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 405624 2011-11-27 04:19 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 77224 2011-11-27 04:19 ./usr/bin/unionBedGraphs
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -767,26 +747,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-c2668e15-cbf5-4daf-b806-fe3c94bb1ee8/build/buildd-bedtools_2.14.2-1-i386-u4h74k
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-77d51d80-d702-41d3-80db-5a13a750c941/build/buildd-bedtools_2.14.3-1-s390x-4BxNE7
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Architecture: i386
-Build-Space: 94984
-Build-Time: 173
+Architecture: s390x
+Build-Space: 146144
+Build-Time: 201
Distribution: sid
-Install-Time: 40
-Job: bedtools_2.14.2-1
+Install-Time: 11
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 258
-Source-Version: 2.14.2-1
-Space: 94984
+Package-Time: 221
+Source-Version: 2.14.3-1
+Space: 146144
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0344
-Build needed 00:04:18, 94984k disc space
-Signature with key 'C83D412C' requested:
+Finished at 20111127-0419
+Build needed 00:03:41, 146144k disc space
+Signature with key 'B5D24954' requested:
diff --git a/sparc.log b/sparc.log
index cbe1c26..0413067 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,70 @@
-From buildd at schroeder.debian.org Thu Nov 03 04:11:58 2011
-Return-path: <buildd at schroeder.debian.org>
+From buildd at spontini.debian.org Sat Nov 05 02:28:34 2011
+Return-path: <buildd at spontini.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1RLoek-0006q6-Oz
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:11:58 +0000
-Received: from schroeder.debian.org ([193.198.184.11])
+ (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
+ id 1RMVzE-0003ZS-Hf
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:28:03 +0000
+Received: from spontini.debian.org ([2607:f8f0:610:4000:a00:20ff:fea0:918b])
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=spontini.debian.org,
+ EMAIL=hostmaster at spontini.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1RLoek-0003dU-47
- for logs at buildd.debian.org; Thu, 03 Nov 2011 04:11:58 +0000
-Received: from buildd by schroeder.debian.org with local (Exim 4.72)
- (envelope-from <buildd at schroeder.debian.org>)
- id 1RLoei-0004Be-Hs; Thu, 03 Nov 2011 04:11:56 +0000
-Message-Id: <E1RLoei-0004Be-Hs at schroeder.debian.org>
+ (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
+ id 1RMVzD-0005Aw-FC
+ for logs at buildd.debian.org; Sat, 05 Nov 2011 02:27:59 +0000
+Received: from buildd by spontini.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at spontini.debian.org>)
+ id 1RMVz8-0001wt-TX; Sat, 05 Nov 2011 02:27:55 +0000
+Message-Id: <E1RMVz8-0001wt-TX at spontini.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 3 Nov 2011 04:11:56 +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_2.14.2-1 on sparc (dist=sid)
-Key-Id: 7C392B18
+Date: Sat, 5 Nov 2011 02:27:54 +0000
+From: buildd on spontini <buildd at spontini.debian.org>
+To: logs at buildd.debian.org,buildd-admin at spontini.debian.org
+Subject: Log for successful build of bedtools_2.14.3-1 on sparc (dist=sid)
+Key-Id: 0D4C040C
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 spontini.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.14.2-1 (sparc) 03 Nov 2011 03:59 ║
+║ bedtools 2.14.3-1 (sparc) 05 Nov 2011 01:57 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.14.2-1
-Source Version: 2.14.2-1
+Version: 2.14.3-1
+Source Version: 2.14.3-1
Architecture: sparc
-Get:1 http://ftp.hr.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.hr.debian.org unstable/main Sources [5889 kB]
-Get:4 http://ftp.hr.debian.org unstable/contrib Sources [56.9 kB]
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://mirror-ubc.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
-Get:5 http://incoming.debian.org Release.gpg [836 B]
-Get:6 http://ftp.hr.debian.org unstable/non-free Sources [104 kB]
-Get:7 http://incoming.debian.org Release [1604 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5896 kB]
-Get:9 http://ftp.hr.debian.org unstable/main sparc Packages [7651 kB]
-Get:10 http://ftp.hr.debian.org unstable/contrib sparc Packages [55.5 kB]
-Ign http://ftp.hr.debian.org unstable/contrib TranslationIndex
-Get:11 http://ftp.hr.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.hr.debian.org unstable/contrib Translation-en
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1604 B]
+Get:5 http://mirror-ubc.debian.org unstable/main Sources [5890 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [5890 kB]
+Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [56.9 kB]
+Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [103 kB]
+Get:9 http://mirror-ubc.debian.org unstable/main sparc Packages [7653 kB]
+Get:10 http://mirror-ubc.debian.org unstable/contrib sparc Packages [55.4 kB]
+Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
+Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
Get:12 http://incoming.debian.org unstable/contrib Sources [56.9 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [104 kB]
-Get:14 http://incoming.debian.org unstable/main sparc Packages [7652 kB]
-Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.5 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7653 kB]
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.4 kB]
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 [40.9 kB]
-Get:18 http://incoming.debian.org Packages [602 kB]
+Get:17 http://incoming.debian.org Sources [25.7 kB]
+Get:18 http://incoming.debian.org Packages [300 kB]
Ign http://incoming.debian.org Translation-en
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 28.5 MB in 33s (846 kB/s)
+Fetched 28.1 MB in 1min 4s (436 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,10 +86,10 @@ 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 928 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (tar) [922 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.2-1 (diff) [4317 B]
-Fetched 928 kB in 2s (397 kB/s)
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (tar) [922 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.14.3-1 (diff) [4338 B]
+Fetched 928 kB in 1s (543 kB/s)
Download complete and in download only mode
Check arch
@@ -109,12 +109,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -155,7 +155,7 @@ make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
-Using default version 8.9.8
+Using default version 8.9.9
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -177,32 +177,32 @@ 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 20 not upgraded.
Need to get 9454 kB of archives.
After this operation, 27.2 MB of additional disk space will be used.
-Get:1 http://ftp.hr.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-4 [34.9 kB]
-Get:2 http://ftp.hr.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:3 http://ftp.hr.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
-Get:4 http://ftp.hr.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
-Get:5 http://ftp.hr.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
-Get:6 http://ftp.hr.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:7 http://ftp.hr.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:8 http://ftp.hr.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:9 http://ftp.hr.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
-Get:10 http://ftp.hr.debian.org/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
-Get:11 http://ftp.hr.debian.org/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
-Get:12 http://ftp.hr.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
-Get:13 http://ftp.hr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:14 http://ftp.hr.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:15 http://ftp.hr.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
-Get:16 http://ftp.hr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.hr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.hr.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://ftp.hr.debian.org/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
-Get:20 http://ftp.hr.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.hr.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-4 [34.9 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
+Get:4 http://incoming.debian.org/buildd-unstable/ debhelper 8.9.9 [552 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9454 kB in 8s (1162 kB/s)
+Fetched 9454 kB in 2s (3528 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10913 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-4_sparc.deb) ...
@@ -239,7 +239,7 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_sparc.deb) ...
Selecting previously unselected package quilt.
@@ -267,7 +267,7 @@ Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-5) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.8) ...
+Setting up debhelper (8.9.9) ...
Setting up diffstat (1.54-1) ...
Setting up quilt (0.48-8) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
@@ -275,11 +275,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-1 gcc-4.6_4.6.2-1 libc6-dev_2.13-21 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b2 g++_4:4.6.1-3 g++-4.6_4.6.2-1 gcc_4:4.6.1-3 gcc-4.6_4.6.2-1 gcc-4.6-base_4.6.2-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-3 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-1 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffstat_1.54-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b2 g++_4:4.6.1-3 g++-4.6_4.6.2-1 gcc_4:4.6.1-3 gcc-4.6_4.6.2-1 gcc-4.6-base_4.6.2-1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-1 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-4 libreadline6_6.2-7 libselinux1_2.1.0-3 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011m-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -290,12 +290,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Nov 3 03:21:00 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Nov 5 01:38:08 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_2.14.2-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.14.2
-dpkg-source: info: unpacking bedtools_2.14.2.orig.tar.gz
-dpkg-source: info: unpacking bedtools_2.14.2-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.14.3-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.14.3
+dpkg-source: info: unpacking bedtools_2.14.3.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.14.3-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -306,24 +306,24 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.14.2-1
- dpkg-source --before-build bedtools-2.14.2
+dpkg-buildpackage: source version 2.14.3-1
+ dpkg-source --before-build bedtools-2.14.3
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -336,21 +336,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Entering directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -525,9 +525,11 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
- Building in src/multiIntersectBed
* compiling multiIntersectBed.cpp
* compiling multiIntersectBedMain.cpp
-multiIntersectBedMain.cpp:24:31: fatal error: MultiIntersectBed.h: No such file or directory
-compilation terminated.
-make[2]: *** [../../obj//multiIntersectBedMain.o] Error 1
+multiIntersectBedMain.cpp: In function 'int main(int, char**)':
+multiIntersectBedMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
+multiIntersectBedMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
+ * linking multiIntersectBed
- Building in src/nucBed
* compiling nucBedMain.cpp
@@ -604,7 +606,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O/bedtools-2.14.2'
+make[1]: Leaving directory `/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx/bedtools-2.14.3'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -649,56 +651,56 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.14.2-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org> >../bedtools_2.14.2-1_sparc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.14.3-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (spontini) <buildd_sparc-spontini at buildd.debian.org> >../bedtools_2.14.3-1_sparc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.14.2
+ dpkg-source --after-build bedtools-2.14.3
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111103-0411
+Build finished at 20111105-0227
-bedtools_2.14.2-1_sparc.changes:
+bedtools_2.14.3-1_sparc.changes:
Format: 1.8
-Date: Thu, 03 Nov 2011 12:15:32 +0900
+Date: Fri, 04 Nov 2011 09:25:38 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.14.2-1
+Version: 2.14.3-1
Distribution: sid
Urgency: low
-Maintainer: sparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org>
+Maintainer: sparc Build Daemon (spontini) <buildd_sparc-spontini at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.14.2-1) unstable; urgency=low
+ bedtools (2.14.3-1) unstable; urgency=low
.
- [356313d] Bugfix release.
+ [04f6aa3] Bugfix release.
Checksums-Sha1:
- 592e74505b07a85fdfeb12a91f53ea9dbb7f5f12 569290 bedtools_2.14.2-1_sparc.deb
+ 875ab669db90062d342af236009f54c575b5ba2e 587132 bedtools_2.14.3-1_sparc.deb
Checksums-Sha256:
- f43e599ad33f7a494758aa6110f7e76f4d858b990efc6f01a4fd919b0780967b 569290 bedtools_2.14.2-1_sparc.deb
+ 7e2c91cf09451a4198cf79aa4fc0abff36f7db60fc2be2cca47198ff1a9e19fb 587132 bedtools_2.14.3-1_sparc.deb
Files:
- f98a2c510f45c02ba5b1d477d5b1dd9f 569290 science optional bedtools_2.14.2-1_sparc.deb
+ bd4a759944dd5c0c1c556fcef8cef218 587132 science optional bedtools_2.14.3-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.14.2-1_sparc.deb
+bedtools_2.14.3-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 569290 bytes: control archive= 1733 bytes.
+ size 587132 bytes: control archive= 1767 bytes.
865 bytes, 19 lines control
- 2025 bytes, 35 lines md5sums
+ 2085 bytes, 36 lines md5sums
Package: bedtools
- Version: 2.14.2-1
+ Version: 2.14.3-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4589
+ Installed-Size: 4722
Pre-Depends: dpkg (>= 1.15.6)
Depends: libc6 (>= 2.6), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
Suggests: filo
@@ -714,49 +716,50 @@ bedtools_2.14.2-1_sparc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-11-03 04:11 ./
-drwxr-xr-x root/root 0 2011-11-03 04:11 ./usr/
-drwxr-xr-x root/root 0 2011-11-03 04:11 ./usr/bin/
--rwxr-xr-x root/root 224720 2011-11-03 04:11 ./usr/bin/bamToBed
--rwxr-xr-x root/root 109568 2011-11-03 04:11 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 60340 2011-11-03 04:11 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 139536 2011-11-03 04:11 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 118900 2011-11-03 04:11 ./usr/bin/closestBed
--rwxr-xr-x root/root 103204 2011-11-03 04:11 ./usr/bin/complementBed
--rwxr-xr-x root/root 117776 2011-11-03 04:11 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 293276 2011-11-03 04:11 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 127360 2011-11-03 04:11 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110508 2011-11-03 04:11 ./usr/bin/flankBed
--rwxr-xr-x root/root 93984 2011-11-03 04:11 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 104044 2011-11-03 04:11 ./usr/bin/linksBed
--rwxr-xr-x root/root 298604 2011-11-03 04:11 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 277964 2011-11-03 04:11 ./usr/bin/coverageBed
--rwxr-xr-x root/root 224712 2011-11-03 04:11 ./usr/bin/bedToBam
--rwxr-xr-x root/root 84868 2011-11-03 04:11 ./usr/bin/overlap
--rwxr-xr-x root/root 282188 2011-11-03 04:11 ./usr/bin/windowBed
--rwxr-xr-x root/root 364188 2011-11-03 04:11 ./usr/bin/pairToBed
--rwxr-xr-x root/root 143908 2011-11-03 04:11 ./usr/bin/sortBed
--rwxr-xr-x root/root 274036 2011-11-03 04:11 ./usr/bin/tagBam
--rwxr-xr-x root/root 105968 2011-11-03 04:11 ./usr/bin/mergeBed
--rwxr-xr-x root/root 347776 2011-11-03 04:11 ./usr/bin/intersectBed
--rwxr-xr-x root/root 101500 2011-11-03 04:11 ./usr/bin/annotateBed
--rwxr-xr-x root/root 109848 2011-11-03 04:11 ./usr/bin/subtractBed
--rwxr-xr-x root/root 142564 2011-11-03 04:11 ./usr/bin/nucBed
--rwxr-xr-x root/root 175004 2011-11-03 04:11 ./usr/bin/pairToPair
--rwxr-xr-x root/root 102632 2011-11-03 04:11 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-11-03 04:11 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-03 04:11 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-03 04:11 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11638 2011-11-02 23:56 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-11-03 03:15 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 661 2011-11-03 03:15 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 1442 2011-11-02 23:56 ./usr/share/doc/bedtools/README.rst
-drwxr-xr-x root/root 0 2011-11-03 04:11 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-11-03 04:01 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-11-02 23:56 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 565 2011-11-02 23:56 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-11-05 02:26 ./
+drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/
+drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-11-03 07:14 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-11-04 00:24 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 686 2011-11-04 00:26 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 11638 2011-11-03 07:14 ./usr/share/doc/bedtools/changelog.gz
+drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-11-05 02:01 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-11-03 07:14 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-11-03 07:14 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-11-05 02:26 ./usr/bin/
+-rwxr-xr-x root/root 143908 2011-11-05 02:26 ./usr/bin/sortBed
+-rwxr-xr-x root/root 84868 2011-11-05 02:26 ./usr/bin/overlap
+-rwxr-xr-x root/root 105968 2011-11-05 02:26 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 277964 2011-11-05 02:26 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 293276 2011-11-05 02:26 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 93984 2011-11-05 02:26 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 103204 2011-11-05 02:26 ./usr/bin/complementBed
+-rwxr-xr-x root/root 364188 2011-11-05 02:26 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 109848 2011-11-05 02:26 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 110508 2011-11-05 02:26 ./usr/bin/flankBed
+-rwxr-xr-x root/root 175004 2011-11-05 02:26 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 136940 2011-11-05 02:26 ./usr/bin/multiIntersectBed
+-rwxr-xr-x root/root 60340 2011-11-05 02:26 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 109568 2011-11-05 02:26 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 347776 2011-11-05 02:26 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 274036 2011-11-05 02:26 ./usr/bin/tagBam
+-rwxr-xr-x root/root 118900 2011-11-05 02:26 ./usr/bin/closestBed
+-rwxr-xr-x root/root 224720 2011-11-05 02:26 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 139536 2011-11-05 02:26 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 102632 2011-11-05 02:26 ./usr/bin/slopBed
+-rwxr-xr-x root/root 127360 2011-11-05 02:26 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 117776 2011-11-05 02:26 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 298604 2011-11-05 02:26 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 142564 2011-11-05 02:26 ./usr/bin/nucBed
+-rwxr-xr-x root/root 101500 2011-11-05 02:26 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 104044 2011-11-05 02:26 ./usr/bin/linksBed
+-rwxr-xr-x root/root 224712 2011-11-05 02:26 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 282188 2011-11-05 02:26 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -770,7 +773,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-0fa400a1-bc41-4822-819d-a988d8aa4b9e/build/buildd-bedtools_2.14.2-1-sparc-NDA_8O
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-e63feb8a-788a-4423-bcb4-9ab130d2897d/build/buildd-bedtools_2.14.3-1-sparc-1_m3gx
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -778,18 +781,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 102596
-Build-Time: 628
+Build-Space: 104408
+Build-Time: 1596
Distribution: sid
-Install-Time: 56
-Job: bedtools_2.14.2-1
+Install-Time: 83
+Job: bedtools_2.14.3-1
Package: bedtools
-Package-Time: 739
-Source-Version: 2.14.2-1
-Space: 102596
+Package-Time: 1789
+Source-Version: 2.14.3-1
+Space: 104408
Status: successful
-Version: 2.14.2-1
+Version: 2.14.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111103-0411
-Build needed 00:12:19, 102596k disc space
-Signature with key '7C392B18' requested:
+Finished at 20111105-0227
+Build needed 00:29:49, 104408k disc space
+Signature with key '0D4C040C' requested:
--
Suite of utilities for comparing genomic features.
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