[med-svn] [SCM] BEDtools branch, meta, updated. meta/2.13.3-1-2-gafe81aa
Charles Plessy
plessy at debian.org
Mon Oct 31 13:46:12 UTC 2011
The following commit has been merged in the meta branch:
commit afe81aa83f988144166da211b98051acee01b734
Author: Charles Plessy <plessy at debian.org>
Date: Mon Oct 31 22:45:36 2011 +0900
Collected build logs for 2.13.4-1.
diff --git a/armel.log b/armel.log
index 20b62bd..d1dc18c 100644
--- a/armel.log
+++ b/armel.log
@@ -1,4 +1,4 @@
-From buildd at ancina.debian.org Wed Oct 05 09:58:28 2011
+From buildd at ancina.debian.org Sat Oct 29 03:27:48 2011
Return-path: <buildd at ancina.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,
@@ -6,70 +6,62 @@ 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 ancina.debian.org>)
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- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:58:28 +0000
+ id 1RJzaG-0003iC-8y
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:27:48 +0000
Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
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by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
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- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:58:27 +0000
+ id 1RJzaF-0008Uh-Gc
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:27:47 +0000
Received: from buildd by ancina.debian.org with local (Exim 4.69)
(envelope-from <buildd at ancina.debian.org>)
- id 1RBOF8-0002ZS-Ha; Wed, 05 Oct 2011 09:58:26 +0000
+ id 1RJzaE-0005bG-Qb; Sat, 29 Oct 2011 03:27:46 +0000
MIME-Version: 1.0
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-Date: Wed, 5 Oct 2011 09:58:26 +0000
+Date: Sat, 29 Oct 2011 03:27:46 +0000
From: Build Daemon <buildd at ancina.debian.org>
To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on armel (dist=sid)
+Subject: Log for successful build of bedtools_2.13.4-1 on armel (dist=sid)
Key-Id: 534B6930
-Message-Id: <E1RBOF8-0002ZS-Ha at ancina.debian.org>
+Message-Id: <E1RJzaE-0005bG-Qb at ancina.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (armel) 05 Oct 2011 09:35 ║
+║ bedtools 2.13.4-1 (armel) 29 Oct 2011 03:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: armel
-Get:1 http://ftp.de.debian.org sid InRelease [146 kB]
-Get:2 http://incoming.debian.org sid InRelease [146 kB]
-Get:3 http://ftp.de.debian.org sid/main Sources/DiffIndex [2038 B]
+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
Ign http://incoming.debian.org InRelease
Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Get:4 http://ftp.de.debian.org sid/main armel Packages/DiffIndex [2038 B]
+Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Get:5 http://ftp.de.debian.org sid/main TranslationIndex [2045 B]
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://ftp.de.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:8 http://ftp.de.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
-Get:9 http://ftp.de.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:10 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://ftp.de.debian.org sid/main TranslationIndex
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Ign http://ftp.de.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:11 http://incoming.debian.org sid/main armel Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/main armel Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:12 http://incoming.debian.org sid/main TranslationIndex [2045 B]
-Get:13 http://incoming.debian.org Release [1604 B]
-Get:14 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:15 http://incoming.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
-Get:16 http://ftp.de.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
-Ign http://ftp.de.debian.org sid/contrib Translation-en
-Get:17 http://incoming.debian.org Sources [36.7 kB]
-Get:18 http://incoming.debian.org Packages [271 kB]
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [36.2 kB]
+Get:4 http://incoming.debian.org Packages [324 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Get:19 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:20 http://incoming.debian.org sid/main armel 2011-10-05-0826.58.pdiff [3994 B]
-Fetched 632 kB in 24s (26.0 kB/s)
+Fetched 362 kB in 10s (35.2 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 1s (502 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 1s (626 kB/s)
Download complete and in download only mode
Check arch
@@ -108,18 +100,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 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 38 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -131,32 +123,32 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-09-16-1)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.4)
+diffutils: already installed (1:3.2-1)
+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 (5.9-1)
+ncurses-base: already installed (5.9-2)
ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-5)
+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-13.11)
-sysvinit: already installed (2.88dsf-13.11)
+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 (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: already installed (8.9.8 >= 8 is satisfied)
quilt: missing
@@ -174,15 +166,15 @@ Recommended packages:
autotools-dev
The following NEW packages will be installed:
cdbs diffstat quilt
-0 upgraded, 3 newly installed, 0 to remove and 38 not upgraded.
+0 upgraded, 3 newly installed, 0 to remove and 8 not upgraded.
Need to get 0 B/461 kB of archives.
After this operation, 1215 kB of additional disk space will be used.
-Selecting previously deselected package cdbs.
-(Reading database ... 28011 files and directories currently installed.)
+Selecting previously unselected package cdbs.
+(Reading database ... 23123 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
-Selecting previously deselected package diffstat.
+Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
-Selecting previously deselected package quilt.
+Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.48-8_all.deb) ...
Processing triggers for man-db ...
Setting up cdbs (0.4.99) ...
@@ -192,11 +184,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.53.20110910-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
-Package versions: adduser_3.113 apex-nslu2_1.6.10 apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 bc_1.06.95-2 bf-utf-source_0.05-0.1 binutils_2.21.53.20110910-1 bison_1:2.4.1.dfsg-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 cramfsprogs_1.1-6 dash_0.5.7-1 dbus_1.4.16-1 dbus-x11_1.4.16-1 dctrl-tools_2.18 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debiandoc-sgml_1.2.25 debianutils_4.0.2 devio_1.2-1+b1 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 dns323-firmware-tools_0.3-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.16.0.3 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-16-1 e2fsprogs_1.42~WIP-2011-09-16-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.6_4.6.1-13 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gconf2_2.32.4-1 gconf2-common_2.32.4-1 genext2fs_1.4.1-3 genisoimage_9:1.1.11-2 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gir1.2-atk-1.0_2.2.0-1 gir1.2-freedesktop_0.10.8-2+b1 gir1.2-gdkpixbuf-2.0_2.24.0-1 gir1.2-glib-2.0_0.10.8-2+b1 gir1.2-pango-1.0_1.28.4-3 gnome-mime-data_2.18.0-1 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gvfs_1.6.4-4 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libart-2.0-2_2.3.21-1 libasound2_1.0.24.1-4 libaspell15_0.60.7~20110707-1 libatasmart4_0.17+git20100219-3 libatk1.0-0_2.2.0-1 libatk1.0-data_2.2.0-1 libatk1.0-dev_2.2.0-1 libattr1_1:2.4.46-3 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common3_0.6.30-5 libavahi-glib1_0.6.30-5 libblas3gf_1.2.20110419-2 libblkid1_2.19.1-5 libbluetooth-dev_4.96-2 libbluetooth3_4.96-2 libbogl-dev_0.1.18-5 libbogl0_0.1.18-5 libbonobo2-0_2.24.3-1 libbonobo2-common_2.24.3-1 libbonoboui2-0_2.24.3-1 libbonoboui2-common_2.24.3-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-pic_2.13-21 libcairo-gobject2_1.10.2-6.1 libcairo-script-interpreter2_1.10.2-6.1 libcairo2_1.10.2-6.1 libcairo2-dev_1.10.2-6.1 libcanberra0_0.28-1 libcomerr2_1.42~WIP-2011-10-01-2 libcroco3_0.6.2-1 libcups2_1.5.0-8 libdatrie1_0.2.4-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdbus-glib-1-2_0.98-1 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.1 libdrm2_2.4.26-1 libenchant1c2a_1.6.0-3 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfam0_2.7.0-17 libffi-dev_3.0.10-1 libffi5_3.0.10-1 libfontconfig1_2.8.0-3 libfontconfig1-dev_2.8.0-3 libfontenc1_1:1.1.0-1 libfreetype6_2.4.6-2 libfreetype6-dev_2.4.6-2 libgail18_2.24.6-1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgconf2-4_2.32.4-1 libgcrypt11_1.5.0-3 libgd2-noxpm_2.0.36~rc1~dfsg-5.1+b1 libgdbm3_1.8.3-10 libgdk-pixbuf2.0-0_2.24.0-1 libgdk-pixbuf2.0-dev_2.24.0-1 libgdu0_2.32.1-1 libgfortran3_4.6.1-13 libgirepository-1.0-1_0.10.8-2+b1 libgl1-mesa-glx_7.11-6 libglade2-0_1:2.6.4-1 libglapi-mesa_7.11-6 libglib2.0-0_2.28.6-1 libglib2.0-bin_2.28.6-1 libglib2.0-data_2.28.6-1 libglib2.0-dev_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnome-keyring0_3.2.0-2 libgnome2-0_2.32.1-1 libgnome2-common_2.32.1-1 libgnomecanvas2-0_2.30.3-1 libgnomecanvas2-common_2.30.3-1 libgnomeui-0_2.24.5-2 libgnomeui-common_2.24.5-2 libgnomevfs2-0_1:2.24.4-1 libgnomevfs2-common_1:2.24.4-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgpm2_1.20.4-4 libgssapi-krb5-2_1.9.1+dfsg-3 libgtk2.0-0_2.24.6-1 libgtk2.0-common_2.24.6-1 libgtk2.0-dev_2.24.6-1 libgtkspell0_2.0.16-1 libgudev-1.0-0_172-1 libhtml-parser-perl_3.68-1+b1 libhtml-tagset-perl_3.20-2 libhunspell-1.2-0_1.2.14-4 libice-dev_2:1.0.7-2 libice6_2:1.0.7-2 libidl0_0.8.14-0.2 libidn11_1.22-3 libjasper1_1.900.1-10 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1+b1 libldap-2.4-2_2.4.25-3 libltdl7_2.4-4 liblvm2app2.2_2.02.86-1 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libmysqlclient16_5.1.58-1 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-1 libnewt-dev_0.52.11-2.1 libnewt-pic_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libogg0_1.2.2~dfsg-1 liborbit2_1:2.14.18-0.2 libp11-kit0_0.7-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-4 libpango1.0-0_1.28.4-3 libpango1.0-dev_1.28.4-3 libparted0debian1_2.3-8 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpisock-dev_0.12.5-4 libpisock9_0.12.5-4 libpisync1_0.12.5-4 libpixman-1-0_0.22.2-1 libpixman-1-dev_0.22.2-1 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpolkit-gobject-1-0_0.102-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1 libpthread-stubs0-dev_0.3-2.1 libpython2.6_2.6.7-4 libpython2.7_2.7.2-5 libreadline5_5.2-10 libreadline6_6.2-6 libroman-perl_1.23-1 libruby1.8_1.8.7.352-2 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libsgmls-perl_1.03ii-32 libsgutils2-2_1.32-1 libsigsegv2_2.9-4 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libslang2-pic_2.2.4-3 libsm-dev_2:1.2.0-2 libsm6_2:1.2.0-2 libsp1c2_1.3.4-1.2.1-47.1 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-09-25-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtasn1-3_2.9-4 libtdb1_1.2.9-4+b1 libtext-format-perl_0.53-1 libthai-data_0.1.15-2 libthai0_0.1.15-2 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libudev0_172-1 libunistring0_0.9.3-4 liburi-perl_1.59-1 libusb-0.1-4_2:0.1.12-19 libusb-dev_2:0.1.12-19 libuuid1_2.19.1-5 libvolume-id1_0.141-2 libvorbis0a_1.3.2-1 libvorbisfile3_1.3.2-1 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libx11-dev_2:1.4.4-2 libxau-dev_1:1.0.6-3 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb-render0_1.7-3 libxcb-render0-dev_1.7-3 libxcb-shape0_1.7-3 libxcb-shm0_1.7-3 libxcb-shm0-dev_1.7-3 libxcb1_1.7-3 libxcb1-dev_1.7-3 libxcomposite-dev_1:0.4.3-2 libxcomposite1_1:0.4.3-2 libxcursor-dev_1:1.1.12-1 libxcursor1_1:1.1.12-1 libxdamage-dev_1:1.1.3-2 libxdamage1_1:1.1.3-2 libxdmcp-dev_1:1.1.0-3 libxdmcp6_1:1.1.0-3 libxext-dev_2:1.3.0-3 libxext6_2:1.3.0-3 libxfixes-dev_1:5.0-4 libxfixes3_1:5.0-4 libxft-dev_2.2.0-3 libxft2_2.2.0-3 libxi-dev_2:1.4.3-3 libxi6_2:1.4.3-3 libxinerama-dev_2:1.1.1-3 libxinerama1_2:1.1.1-3 libxml2_2.7.8.dfsg-4 libxml2-utils_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxmuu1_2:1.1.0-2 libxpm4_1:3.5.9-1 libxrandr-dev_2:1.3.2-2 libxrandr2_2:1.3.2-2 libxrender-dev_1:0.9.6-2 libxrender1_1:0.9.6-2 libxslt1.1_1.1.26-8 libxt6_1:1.1.1-2 libxtst6_2:1.2.0-3 libxv1_2:1.0.6-2 libxxf86dga1_2:1.1.2-1 libxxf86vm1_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 m4_1.4.16-2 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 mklibs_0.1.33 mklibs-copy_0.1.33 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-18 mysql-common_5.1.58-1 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 nullmailer_1:1.05-1 openssl_1.0.0d-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.14-1 python_2.7.2-7 python-all_2.7.2-7 python-all-dev_2.7.2-7 python-cairo_1.8.8-1+b2 python-central_0.6.17 python-dateutil_1.5-1 python-dev_2.7.2-7 python-egenix-mx-base-dev_3.2.1-1 python-egenix-mxdatetime_3.2.1-1 python-egenix-mxtools_3.2.1-1 python-gconf_2.28.1-3 python-glade2_2.24.0-2 python-gnome2_2.28.1-3 python-gobject_2.28.6-5 python-gobject-dev_2.28.6-5 python-gtk2_2.24.0-2 python-gtk2-dev_2.24.0-2 python-gtkspell_2.25.3-10.1 python-imaging_1.1.7-4 python-minimal_2.7.2-7 python-mysqldb_1.2.2-10+b3 python-numpy_1:1.5.1-2+b1 python-pisock_0.12.5-4 python-pyorbit_2.24.0-6+b1 python-pyparsing_1.5.2-2 python-reportlab_2.5-1.1 python-support_1.0.14 python-tz_2011h-0.1 python-vobject_0.8.1c-4 python2.6_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-5 python2.7-dev_2.7.2-5 python2.7-minimal_2.7.2-5 quilt_0.48-8 readline-common_6.2-4 ruby1.8_1.8.7.352-2 scons_2.1.0-1 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sgmlspl_1.03ii-32 shared-mime-info_0.90-1 slugimage_1:0.0+r104-5 sp_1.3.4-1.2.1-47.1 sudo_1.8.2-1 swig_2.0.4-4 swig2.0_2.0.4-4 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 ttf-dejavu-core_2.33-2 tzdata_2011k-1 u-boot-tools_2011.06-4 uboot-mkimage_2011.06-4 ucf_3.0025+nmu2 udev_172-1 udisks_1.0.4-1 util-linux_2.19.1-5 wget_1.13-1 x11-common_1:7.6+9 x11-utils_7.6+3 x11proto-composite-dev_1:0.4.2-2 x11proto-core-dev_7.0.22-1 x11proto-damage-dev_1:1.2.1-2 x11proto-fixes-dev_1:5.0-2 x11proto-input-dev_2.0.2-2 x11proto-kb-dev_1.0.5-2 x11proto-randr-dev_1.3.2-2 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.2.0-3 x11proto-xinerama-dev_1.2.1-2 xml-core_0.13 xorg-sgml-doctools_1:1.8-2 xsltproc_1.1.26-8 xtrans-dev_1.2.6-2 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+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_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 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_2.1.0-1 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_2.9-4 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_2011m-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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -207,12 +199,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -222,30 +214,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+/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_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -258,21 +245,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
+/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_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -290,7 +277,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -350,10 +337,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -523,7 +506,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -595,22 +578,22 @@ dpkg-shlibdeps: warning: debian/bedtools/usr/bin/complementBed contains an unres
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.13.3-1_armel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bedtools_2.13.4-1_armel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-0958
+Build finished at 20111029-0327
-bedtools_2.13.3-1_armel.changes:
+bedtools_2.13.4-1_armel.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: armel
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
@@ -618,33 +601,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- 6dffa715e001bd06b2d6b28414ecdbf56a3c6970 533770 bedtools_2.13.3-1_armel.deb
+ 9f3ddd65de23e3d9f429aeed4acf58dbe9d74006 536930 bedtools_2.13.4-1_armel.deb
Checksums-Sha256:
- 701dd9294529c8cc82f74e9aa19200b76e2f4ce4d59558552327f80d215acc17 533770 bedtools_2.13.3-1_armel.deb
+ 1fc8440979c587c0331388d62f020c01e7da0684cb06e2226f32da365d43a988 536930 bedtools_2.13.4-1_armel.deb
Files:
- 23bf2ca7e0bd482f6452b11b81e3d317 533770 science optional bedtools_2.13.3-1_armel.deb
+ cbe86889ba6a8d9ca338addb04f4bc70 536930 science optional bedtools_2.13.4-1_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_armel.deb
+bedtools_2.13.4-1_armel.deb
───────────────────────────
new debian package, version 2.0.
- size 533770 bytes: control archive= 1713 bytes.
- 835 bytes, 18 lines control
+ size 536930 bytes: control archive= 1729 bytes.
+ 865 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 3942
+ Installed-Size: 3948
+ 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
Section: science
@@ -659,7 +643,7 @@ bedtools_2.13.3-1_armel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-armel-sbuild-6403b615-c722-4314-b6b7-19773bad4d98/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo/bedtools_2.13.3-1_armel.deb' contains ununderstood data member data.tar.xz , giving up
+dpkg-deb: file `/var/lib/schroot/mount/sid-armel-sbuild-e9c05b69-e231-4b61-a0b6-46d1571b58ec/build/buildd-bedtools_2.13.4-1-armel-YeGMVB/bedtools_2.13.4-1_armel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -673,19 +657,19 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armel-sbuild-6403b615-c722-4314-b6b7-19773bad4d98/build/buildd-bedtools_2.13.3-1-armel-Bl0Obo
+Purging /var/lib/schroot/mount/sid-armel-sbuild-e9c05b69-e231-4b61-a0b6-46d1571b58ec/build/buildd-bedtools_2.13.4-1-armel-YeGMVB
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
cdbs* diffstat* quilt*
-0 upgraded, 0 newly installed, 3 to remove and 38 not upgraded.
+0 upgraded, 0 newly installed, 3 to remove and 8 not upgraded.
After this operation, 1215 kB disk space will be freed.
-(Reading database ... 28146 files and directories currently installed.)
+(Reading database ... 23257 files and directories currently installed.)
Removing cdbs ...
Removing quilt ...
Purging configuration files for quilt ...
@@ -697,18 +681,18 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 98156
-Build-Time: 1263
+Build-Space: 97844
+Build-Time: 1247
Distribution: sid
Install-Time: 29
-Job: bedtools_2.13.3-1
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 1344
-Source-Version: 2.13.3-1
-Space: 98156
+Package-Time: 1312
+Source-Version: 2.13.4-1
+Space: 97844
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-0958
-Build needed 00:22:24, 98156k disc space
+Finished at 20111029-0327
+Build needed 00:21:52, 97844k disc space
Signature with key '534B6930' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index b155467..a3e5029 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,110 +1,83 @@
-From buildd at mozart.debian.net Wed Oct 05 12:11:40 2011
-Return-path: <buildd at mozart.debian.net>
+From buildd at bach.debian.net Sat Oct 29 03:17:08 2011
+Return-path: <buildd at bach.debian.net>
Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
- id 1RBQK2-0004mT-UM
- for logs at buildd.debian.org; Wed, 05 Oct 2011 12:11:40 +0000
-Received: from mozart.debian.net ([10.1.0.1])
+ (Exim 4.72) (envelope-from <buildd at bach.debian.net>)
+ id 1RJzPv-0002AA-LE
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:17:08 +0000
+Received: from bach.debian.net ([10.3.0.1])
by callisto.debian.net with esmtp (Exim 4.69)
- (envelope-from <buildd at mozart.debian.net>)
- id 1RBQJp-0006nQ-Va; Wed, 05 Oct 2011 13:11:26 +0100
-Received: from buildd by mozart.debian.net with local (Exim 4.76)
- (envelope-from <buildd at mozart.debian.net>)
- id 1RBQJq-0002OF-8b; Wed, 05 Oct 2011 12:11:26 +0000
-From: Build Daemon <buildd at mozart.debian.net>
+ (envelope-from <buildd at bach.debian.net>)
+ id 1RJzPr-0004eT-Fo; Sat, 29 Oct 2011 04:17:03 +0100
+Received: from buildd by bach.debian.net with local (Exim 4.72)
+ (envelope-from <buildd at bach.debian.net>)
+ id 1RJzPt-00079l-Fw; Sat, 29 Oct 2011 03:17:05 +0000
+Date: Sat, 29 Oct 2011 03:17:05 +0000
+Message-Id: <E1RJzPt-00079l-Fw at bach.debian.net>
+From: Build Daemon <buildd at bach.debian.net>
To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
- logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on hurd-i386 (dist=sid)
+ logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.4-1 on hurd-i386
+ (dist=unstable)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RBQJq-0002OF-8b at mozart.debian.net>
-Date: Wed, 05 Oct 2011 12:11:26 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mozart.debian.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on bach.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (hurd-i386) 05 oct. 2011 11:56 ║
+║ bedtools 2.13.4-1 (hurd-i386) 29 oct. 2011 03:04 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: hurd-i386
-Get:1 http://ftp.uk.debian.org sid InRelease [146 kB]
-Get:2 http://ftp.fr.debian.org sid InRelease [146 kB]
-Ign http://ftp.debian-ports.org unreleased InRelease
-Get:3 http://ftp.debian-ports.org unreleased Release.gpg [836 B]
-Get:4 http://ftp.debian-ports.org unreleased Release [25.8 kB]
-Get:5 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://ftp.uk.debian.org sid InRelease
+Hit http://ftp.fr.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
+Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
+Ign http://ftp.debian-ports.org unreleased InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
-Get:6 http://ftp.uk.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:7 http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
+Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Get:8 http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
+Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
-Get:9 http://ftp.uk.debian.org sid/main TranslationIndex [2045 B]
+Hit http://ftp.uk.debian.org sid/main TranslationIndex
Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
-Get:10 http://ftp.uk.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
-Get:11 http://ftp.uk.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
-Get:12 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
-Get:13 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
-Get:14 http://ftp.fr.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:15 http://ftp.debian-ports.org unreleased/main hurd-i386 Packages [49.7 kB]
-Get:16 http://incoming.debian.org Release.gpg [836 B]
-Get:17 http://ftp.uk.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
+Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.debian-ports.org unreleased Release.gpg
+Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.uk.debian.org sid/main Translation-fr
Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
-Get:18 http://ftp.fr.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:19 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
+Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex
Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Get:20 http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
+Hit http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex
Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
-Get:21 http://ftp.fr.debian.org sid/main TranslationIndex [2045 B]
+Hit http://ftp.fr.debian.org sid/main TranslationIndex
Ign http://ftp.fr.debian.org sid/non-free TranslationIndex
-Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Get:22 http://incoming.debian.org Release [1604 B]
-Get:23 http://ftp.fr.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
-Get:24 http://ftp.uk.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
-Get:25 http://ftp.fr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
-Get:26 http://ftp.uk.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
-Get:27 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
-Get:28 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
-Get:29 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
-Get:30 http://ftp.uk.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
+Hit http://ftp.debian-ports.org unreleased Release
+Get:3 http://incoming.debian.org Sources [36.2 kB]
+Hit http://ftp.fr.debian.org sid/main Translation-fr
Ign http://ftp.uk.debian.org sid/contrib Translation-en
+Ign http://ftp.uk.debian.org sid/contrib Translation-fr
Ign http://ftp.uk.debian.org sid/non-free Translation-en
-Get:31 http://incoming.debian.org Sources [36.5 kB]
+Ign http://ftp.uk.debian.org sid/non-free Translation-fr
+Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Get:4 http://incoming.debian.org Packages [324 kB]
+Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
Ign http://ftp.fr.debian.org sid/contrib Translation-en
+Ign http://ftp.fr.debian.org sid/contrib Translation-fr
Ign http://ftp.fr.debian.org sid/non-free Translation-en
-Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Get:32 http://incoming.debian.org Packages [279 kB]
-Get:33 http://ftp.uk.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
-Get:34 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
+Ign http://ftp.fr.debian.org sid/non-free Translation-fr
Ign http://incoming.debian.org Translation-en
-Get:35 http://ftp.fr.debian.org sid/main 2011-10-04-2014.04.pdiff [14.1 kB]
-Get:36 http://ftp.fr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
-Get:37 http://ftp.fr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
-Get:38 http://ftp.uk.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
-Get:39 http://ftp.fr.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
-Get:40 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-04-2014.04.pdiff [8590 B]
-Get:41 http://ftp.uk.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:42 http://ftp.fr.debian.org sid/non-free hurd-i386 2011-10-05-0214.30.pdiff [54 B]
-Get:43 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
-Get:44 http://ftp.uk.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
-Get:45 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
-Get:46 http://ftp.fr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
-Get:47 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
-Get:48 http://ftp.fr.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
-Get:49 http://ftp.fr.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:50 http://ftp.uk.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:51 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0214.30.pdiff [9284 B]
-Get:52 http://ftp.uk.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
-Get:53 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
-Get:54 http://ftp.fr.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:55 http://ftp.fr.debian.org sid/main hurd-i386 2011-10-05-0826.58.pdiff [593 B]
-Fetched 809 kB in 4min 6s (3275 B/s)
+Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Ign http://incoming.debian.org Translation-fr
+Ign http://ftp.debian-ports.org unreleased/main Translation-fr
+Fetched 362 kB in 1min 59s (3030 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -125,11 +98,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 3s (181 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 3s (255 kB/s)
Download complete and in download only mode
Check arch
@@ -149,18 +122,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 68 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 68 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -169,17 +136,17 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, cdbs, debhelper (>= 8), quilt, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
+base-files: already installed (6.4)
+base-passwd: already installed (3.5.22)
bash: already installed (4.1-3+hurd.1)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
+dash: already installed (0.5.5.1-7.4)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
+grep: already installed (2.9-1)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
hurd: already installed (20110519-3)
@@ -187,19 +154,19 @@ ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-2)
perl-base: already installed (5.12.4-4)
sed: already installed (4.2.1-9)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-util-linux: already installed (2.19.1-5)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
+tar: already installed (1.25-2)
+bsdutils: already installed (1:2.16.2-0)
+util-linux: already installed (2.16.2-0)
libc0.3-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
hurd-dev: already installed (20110519-3)
cdbs: missing
-debhelper: already installed (8.9.6 >= 8 is satisfied)
+debhelper: already installed (8.9.8 >= 8 is satisfied)
quilt: missing
zlib1g-dev: missing
Checking for dependency conflicts...
@@ -207,9 +174,6 @@ Installing positive dependencies: cdbs quilt zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
diffstat
Suggested packages:
@@ -218,14 +182,14 @@ Recommended packages:
autotools-dev
The following NEW packages will be installed:
cdbs diffstat quilt zlib1g-dev
-0 upgraded, 4 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 4 newly installed, 0 to remove and 68 not upgraded.
Need to get 0 B/648 kB of archives.
After this operation, 1633 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
cdbs diffstat quilt zlib1g-dev
Authentication warning overridden.
Selecting previously deselected package cdbs.
-(Reading database ... 13812 files and directories currently installed.)
+(Reading database ... 14844 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
@@ -242,14 +206,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 68 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_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 hurd-dev_20110519-3 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.6 apt-utils_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-119 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-2 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-2 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-2 gfortran-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-10 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 libept1_1.0.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libldap-2.4-2_2.4.25-3 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncursesw5_5.9-2 libobjc2_4.5.3-8 libp11-kit0_0.4-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-4 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-5 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsigsegv2_2.9-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libuuid1_2.19.1-5 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-4 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 ttf-dejavu-core_2.33-2 type-handling_0.2.23 tzdata_2011i-2 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 hurd-dev_20110519-3 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 autopoint_0.18.1.1-4 base-files_6.4 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsd-mailx_8.1.2-0.20100314cvs-1 bsdmainutils_8.2.3 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20110502+nmu1 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-118 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.6-2 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 exim4-base_4.76-2+b3 exim4-config_4.76-2 exim4-daemon-light_4.76-2+b3 fakeroot_1.15.1-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.0-6 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran_4:4.6.0-6 gfortran-4.6_4.6.1-9+hurd.1 git_1:1.7.6.3-1 git-man_1:1.7.6.3-1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.7-3 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 liberror-perl_0.17-1 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 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 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libidn11_1.22-3 libldap-2.4-2_2.4.25-3 liblockfile-bin_1.09-3 liblockfile1_1.09-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libncursesw5_5.9-2 libp11-kit0_0.7-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 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 librtmp0_2.4~20110711.gitc28f1bab-1 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libtext-charwidth-perl_0.04-6+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 netcat-traditional_1.10-39 openssl_1.0.0e-2 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 quilt_0.48-8 random-egd_0.5-0+hurd.1 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-2 ttf-bitstream-vera_1.10-8 ttf-freefont_20100919-1 type-handling_0.2.23 tzdata_2011h-3 ucf_3.0025+nmu2 util-linux_2.16.2-0 xml-core_0.13 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -260,12 +221,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -281,24 +242,24 @@ 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 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -311,21 +272,21 @@ 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_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -408,9 +369,9 @@ Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t,
Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
-
genomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
genomeFile.cpp:61:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
+
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
@@ -492,12 +453,12 @@ mergeMain.cpp: In function 'int main(int, char**)':
mergeMain.cpp:40:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
* compiling mergeBed.cpp
* linking mergeBed
-multiBamCovMain.cpp: In function 'int main(int, char**)':
-multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
-multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
- Building in src/multiBamCov
* compiling multiBamCovMain.cpp
+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
@@ -507,9 +468,9 @@ multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunus
* 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]
- * compiling overlap.cpp
* linking overlap
- Building in src/pairToBed
@@ -524,13 +485,13 @@ pairToBed.cpp:307:9: warning: variable 'spanLength' set but not used [-Wunused-b
* linking pairToBed
- Building in src/pairToPair
- * compiling pairToPairMain.cpp
pairToPairMain.cpp: In function 'int main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
- * compiling pairToPair.cpp
+ * compiling pairToPairMain.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]
+ * compiling pairToPair.cpp
* linking pairToPair
- Building in src/shuffleBed
@@ -575,10 +536,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowMain.cpp
* compiling windowBed.cpp
* linking windowBed
+ /usr/bin/fakeroot debian/rules binary-arch
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T/bedtools-2.13.4'
touch debian/stamp-makefile-build
- /usr/bin/fakeroot debian/rules binary-arch
DEB_MAKE_CHECK_TARGET unset, not running checks
test -x debian/rules
dh_testroot
@@ -621,56 +582,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../bedtools_2.13.3-1_hurd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org> >../bedtools_2.13.4-1_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-1210
+Build finished at 20111029-0316
-bedtools_2.13.3-1_hurd-i386.changes:
+bedtools_2.13.4-1_hurd-i386.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: hurd-i386
-Version: 2.13.3-1
-Distribution: sid
+Version: 2.13.4-1
+Distribution: unstable
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- b8f8978122b27a7402e9fa902685fc677d2ac7c4 678846 bedtools_2.13.3-1_hurd-i386.deb
+ 3e478dd7008cb15ce49f0cf83e9ef66ae21f9e19 683322 bedtools_2.13.4-1_hurd-i386.deb
Checksums-Sha256:
- 414f9666e227f4b4cba6047795d07ffa6f84bc158be12420a282019c5cf78d18 678846 bedtools_2.13.3-1_hurd-i386.deb
+ 6311af5c57c8063f27409e5ba4c6209bc08d77727d06ae307ba99b78c8a44ce7 683322 bedtools_2.13.4-1_hurd-i386.deb
Files:
- d5b29d71b7eeb4ebba86cf64ceca6e87 678846 science optional bedtools_2.13.3-1_hurd-i386.deb
+ dcefb0c3be1ae1e076048557aabfb4b7 683322 science optional bedtools_2.13.4-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_hurd-i386.deb
+bedtools_2.13.4-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 678846 bytes: control archive= 1722 bytes.
- 839 bytes, 18 lines control
+ size 683322 bytes: control archive= 1742 bytes.
+ 869 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4638
+ Installed-Size: 4649
+ 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
Section: science
@@ -685,49 +647,49 @@ bedtools_2.13.3-1_hurd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 12:08 ./
-drwxr-xr-x root/root 0 2011-10-05 12:08 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 12:08 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 12:01 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-05 12:09 ./usr/bin/
--rwxr-xr-x root/root 104532 2011-10-05 12:09 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223448 2011-10-05 12:09 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96364 2011-10-05 12:09 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227776 2011-10-05 12:09 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121332 2011-10-05 12:09 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120924 2011-10-05 12:09 ./usr/bin/closestBed
--rwxr-xr-x root/root 105476 2011-10-05 12:09 ./usr/bin/complementBed
--rwxr-xr-x root/root 280928 2011-10-05 12:09 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142360 2011-10-05 12:09 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 114464 2011-10-05 12:09 ./usr/bin/flankBed
--rwxr-xr-x root/root 297332 2011-10-05 12:09 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350580 2011-10-05 12:09 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105660 2011-10-05 12:09 ./usr/bin/linksBed
--rwxr-xr-x root/root 109572 2011-10-05 12:09 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 107068 2011-10-05 12:09 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297320 2011-10-05 12:09 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 142468 2011-10-05 12:09 ./usr/bin/nucBed
--rwxr-xr-x root/root 88172 2011-10-05 12:09 ./usr/bin/overlap
--rwxr-xr-x root/root 366976 2011-10-05 12:09 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178292 2011-10-05 12:09 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129588 2011-10-05 12:09 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105348 2011-10-05 12:09 ./usr/bin/slopBed
--rwxr-xr-x root/root 143492 2011-10-05 12:09 ./usr/bin/sortBed
--rwxr-xr-x root/root 113080 2011-10-05 12:09 ./usr/bin/subtractBed
--rwxr-xr-x root/root 272752 2011-10-05 12:09 ./usr/bin/tagBam
--rwxr-xr-x root/root 59976 2011-10-05 12:09 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285032 2011-10-05 12:09 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-10-29 03:14 ./
+drwxr-xr-x root/root 0 2011-10-29 03:14 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 03:14 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 03:07 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-29 03:15 ./usr/bin/
+-rwxr-xr-x root/root 104532 2011-10-29 03:15 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223904 2011-10-29 03:15 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96364 2011-10-29 03:15 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227776 2011-10-29 03:15 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121332 2011-10-29 03:15 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 122588 2011-10-29 03:15 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105476 2011-10-29 03:15 ./usr/bin/complementBed
+-rwxr-xr-x root/root 285024 2011-10-29 03:15 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142360 2011-10-29 03:15 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 114464 2011-10-29 03:15 ./usr/bin/flankBed
+-rwxr-xr-x root/root 301428 2011-10-29 03:15 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350580 2011-10-29 03:15 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105660 2011-10-29 03:15 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109572 2011-10-29 03:15 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 107068 2011-10-29 03:15 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297320 2011-10-29 03:15 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 142468 2011-10-29 03:15 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88172 2011-10-29 03:15 ./usr/bin/overlap
+-rwxr-xr-x root/root 366976 2011-10-29 03:15 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178292 2011-10-29 03:15 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129588 2011-10-29 03:15 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 105348 2011-10-29 03:15 ./usr/bin/slopBed
+-rwxr-xr-x root/root 143492 2011-10-29 03:15 ./usr/bin/sortBed
+-rwxr-xr-x root/root 113080 2011-10-29 03:15 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 272752 2011-10-29 03:15 ./usr/bin/tagBam
+-rwxr-xr-x root/root 59976 2011-10-29 03:15 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285032 2011-10-29 03:15 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -741,25 +703,19 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-sid/build/buildd-bedtools_2.13.3-1-hurd-i386-nTcZJq
+Purging /home/buildd/build/chroot-unstable/build/buildd-bedtools_2.13.4-1-hurd-i386-LTYA2T
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 68 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
-Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
cdbs* diffstat* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 4 to remove and 32 not upgraded.
+0 upgraded, 0 newly installed, 4 to remove and 68 not upgraded.
After this operation, 1633 kB disk space will be freed.
-(Reading database ... 13983 files and directories currently installed.)
+(Reading database ... 15015 files and directories currently installed.)
Removing cdbs ...
Removing quilt ...
Purging configuration files for quilt ...
@@ -772,18 +728,18 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 94336
-Build-Time: 539
-Distribution: sid
-Install-Time: 31
-Job: bedtools_2.13.3-1
+Build-Space: 94480
+Build-Time: 556
+Distribution: unstable
+Install-Time: 26
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 863
-Source-Version: 2.13.3-1
-Space: 94336
+Package-Time: 742
+Source-Version: 2.13.4-1
+Space: 94480
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-1210
-Build needed 00:14:23, 94336k disc space
+Finished at 20111029-0316
+Build needed 00:12:22, 94480k disc space
diff --git a/i386.log b/i386.log
index b558ff0..e807ad5 100644
--- a/i386.log
+++ b/i386.log
@@ -1,71 +1,68 @@
-From buildd at murphy.debian.org Wed Oct 05 09:38:19 2011
-Return-path: <buildd at murphy.debian.org>
+From buildd at biber.debian.org Sat Oct 29 03:08:51 2011
+Return-path: <buildd at biber.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 murphy.debian.org>)
- id 1RBNvf-00073x-8c
- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:38:19 +0000
-Received: from murphy.debian.org ([70.103.162.31])
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1RJzHv-0001DR-1j
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:08:51 +0000
+Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=murphy.debian.org, EMAIL=hostmaster at murphy.debian.org (verified)
+ 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 murphy.debian.org>)
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- id 1RBNvc-00013f-OA; Wed, 05 Oct 2011 09:38:16 +0000
-Message-Id: <E1RBNvc-00013f-OA at murphy.debian.org>
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1RJzHu-0007r6-BX; Sat, 29 Oct 2011 03:08:50 +0000
+Received: from buildd by biber.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at biber.debian.org>)
+ id 1RJzHY-0002T7-Py; Sat, 29 Oct 2011 03:08:28 +0000
+Message-Id: <E1RJzHY-0002T7-Py at biber.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 5 Oct 2011 09:38:16 +0000
-From: buildd on murphy <buildd at murphy.debian.org>
-To: logs at buildd.debian.org,buildd-admin at murphy.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on i386 (dist=sid)
-Key-Id: AC7BC9C1
+Date: Sat, 29 Oct 2011 03:08:28 +0000
+From: buildd on biber <buildd at biber.debian.org>
+To: kurt at roeckx.be,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.4-1 on i386 (dist=sid)
+Key-Id: E4786BDC
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (i386) 05 Oct 2011 09:34 ║
+║ bedtools 2.13.4-1 (i386) 29 Oct 2011 03:03 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: i386
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
-Hit http://ftp.us.debian.org sid InRelease
-Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
Get:2 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.us.debian.org sid/main i386 Packages/DiffIndex
-Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
-Ign http://ftp.us.debian.org sid/contrib TranslationIndex
-Hit http://ftp.us.debian.org sid/main TranslationIndex
-Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:4 http://incoming.debian.org sid/main i386 Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:5 http://incoming.debian.org sid/main TranslationIndex [2045 B]
-Get:6 http://incoming.debian.org Release [1604 B]
-Get:7 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:8 http://incoming.debian.org sid/main i386 2011-10-05-0826.58.pdiff [5592 B]
-Get:9 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:10 http://incoming.debian.org Sources [36.7 kB]
-Ign http://ftp.us.debian.org sid/contrib Translation-en
-Get:11 http://incoming.debian.org Packages [271 kB]
-Get:12 http://incoming.debian.org sid/main i386 2011-10-05-0826.58.pdiff [5592 B]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:3 http://incoming.debian.org unstable/main Sources [5874 kB]
+Get:4 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:5 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:6 http://incoming.debian.org unstable/main i386 Packages [7815 kB]
+Get:7 http://incoming.debian.org unstable/contrib i386 Packages [67.9 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:8 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:9 http://incoming.debian.org Release [1604 B]
+Get:10 http://incoming.debian.org Sources [36.2 kB]
+Get:11 http://incoming.debian.org Packages [324 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 473 kB in 7s (64.8 kB/s)
+Get:12 http://ftp.gr.debian.org unstable InRelease [146 kB]
+Get:13 http://ftp.gr.debian.org unstable/main Sources [5868 kB]
+Get:14 http://ftp.gr.debian.org unstable/contrib Sources [56.5 kB]
+Get:15 http://ftp.gr.debian.org unstable/non-free Sources [104 kB]
+Get:16 http://ftp.gr.debian.org unstable/main i386 Packages [7812 kB]
+Get:17 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.1 kB]
+Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
+Get:18 http://ftp.gr.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.gr.debian.org unstable/contrib Translation-en
+Fetched 28.5 MB in 27s (1043 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 2s (327 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 1s (472 kB/s)
Download complete and in download only mode
Check arch
@@ -104,18 +101,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 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 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -127,23 +124,23 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.13-2)
+coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.2)
+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-2011-09-25-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
+ncurses-base: already installed (5.9-2)
ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-5)
+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-13.11)
-sysvinit: already installed (2.88dsf-13.11)
+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)
@@ -152,46 +149,134 @@ libc6-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
-debhelper: already installed (8.9.8 >= 8 is satisfied)
+debhelper: missing
+Using default version 8.9.8
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 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
+ 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 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 1.2.0-3 [37.6 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-4 [223 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main 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
-0 upgraded, 3 newly installed, 0 to remove and 15 not upgraded.
-Need to get 0 B/461 kB of archives.
-After this operation, 1215 kB of additional disk space will be used.
+Fetched 9694 kB in 21s (445 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10633 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_i386.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_i386.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_i386.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_i386.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.09-2_i386.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.09-2_i386.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_i386.deb) ...
Selecting previously unselected package cdbs.
-(Reading database ... 20082 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_i386.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_i386.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_i386.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_i386.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+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 (8.9.8) ...
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 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.8 autoconf_2.68-1 automake_1:1.11.1-1 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20110502+nmu1 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 dconf-gsettings-backend_0.7.5-3 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool_0.41.1-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libasound2_1.0.24.1-4 libasound2-dev_1.0.24.1-4 libasyncns0_0.8-4 libatk1.0-0_2.2.0-1 libatk1.0-data_2.2.0-1 libattr1_1:2.4.46-3 libavahi-client-dev_0.6.30-5 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common-dev_0.6.30-5 libavahi-common3_0.6.30-5 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcaca-dev_0.99.beta17-2.1 libcaca0_0.99.beta17-2.1 libcairo-gobject2_1.10.2-6.1 libcairo2_1.10.2-6.1 libcap2_1:2.22-1 libcomerr2_1.42~WIP-2011-10-01-1 libcroco3_0.6.2-1 libcups2_1.5.0-8 libdatrie1_0.2.4-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdbus-1-dev_1.4.16-1 libdirectfb-1.2-9_1.2.10.0-4.2 libdirectfb-dev_1.2.10.0-4.2 libdirectfb-extra_1.2.10.0-4.2 libdpkg-perl_1.16.1 libdrm2_2.4.26-1 libencode-locale-perl_1.02-2 libexpat1_2.0.1-7 libfile-listing-perl_6.03-1 libflac8_1.2.1-5 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libfreetype6-dev_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgdk-pixbuf2.0-0_2.24.0-1 libgl1-mesa-dev_7.11-6 libgl1-mesa-glx_7.11-6 libglapi-mesa_7.11-6 libglib2.0-0_2.28.6-1 libglib2.0-bin_2.28.6-1 libglib2.0-data_2.28.6-1 libglib2.0-dev_2.28.6-1 libglu1-mesa_7.11-6 libglu1-mesa-dev_7.11-6 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgssapi-krb5-2_1.9.1+dfsg-3 libgtk-3-0_3.0.12-2 libgtk-3-common_3.0.12-2 libgtk2.0-0_2.24.6-1 libgtk2.0-common_2.24.6-1 libhtml-parser-perl_3.68-1+b1 libhtml-tagset-perl_3.20-2 libhtml-tree-perl_4.2-1 libhttp-cookies-perl_6.00-2 libhttp-date-perl_6.00-1 libhttp-message-perl_6.01-1 libhttp-negotiate-perl_6.00-2 libice-dev_2:1.0.7-2 libice6_2:1.0.7-2 libio-socket-ssl-perl_1.44-1 libjasper1_1.900.1-10 libjpeg8_8c-2 libjpeg8-dev_8c-2 libjson0_0.9-1 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblwp-mediatypes-perl_6.01-1 liblwp-protocol-https-perl_6.02-1 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-2 libnet-http-perl_6.01-1 libnet-ssleay-perl_1.41-1 libode-sp-dev_2:0.11.1-4 libode1sp_2:0.11.1-4 libogg0_1.2.2~dfsg-1 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpango1.0-0_1.29.4-1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpixman-1-0_0.22.2-1 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1 libpthread-stubs0-dev_0.3-2.1 libpulse-dev_1.0-3 libpulse-mainloop-glib0_1.0-3 libpulse0_1.0-3 libquadmath0_4.6.1-13 libreadline6_6.2-6 librsvg2-2_2.34.1-2 librsvg2-bin_2.34.1-2 librsvg2-common_2.34.1-2 libsamplerate0_0.1.8-1 libsdl-image1.2_1.2.10-2.1+b1 libsdl-image1.2-dev_1.2.10-2.1+b1 libsdl-ttf2.0-0_2.0.9-1.1 libsdl-ttf2.0-dev_2.0.9-1.1 libsdl1.2-dev_1.2.14-6.4 libsdl1.2debian_1.2.14-6.4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libsm-dev_2:1.2.0-2 libsm6_2:1.2.0-2 libsndfile1_1.0.25-3 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-10-01-1 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libsysfs-dev_2.1.0+repack-1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libthai-data_0.1.15-2 libthai0_0.1.15-2 libtiff4_3.9.5-2 libtiff4-dev_3.9.5-2 libtiffxx0c2_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libtool_2.4-4 libts-0.0-0_1.0-9 libunistring0_0.9.3-4 liburi-perl_1.59-1 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libvorbis0a_1.3.2-1 libvorbisenc2_1.3.2-1 libwrap0_7.6.q-21 libwww-perl_6.02-1 libwww-robotrules-perl_6.01-1 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libx11-dev_2:1.4.4-2 libx11-xcb1_2:1.4.4-2 libxau-dev_1:1.0.6-3 libxau6_1:1.0.6-3 libxcb-render0_1.7-3 libxcb-shm0_1.7-3 libxcb1_1.7-3 libxcb1-dev_1.7-3 libxcomposite1_1:0.4.3-2 libxcursor1_1:1.1.12-1 libxdamage1_1:1.1.3-2 libxdmcp-dev_1:1.1.0-3 libxdmcp6_1:1.1.0-3 libxext-dev_2:1.3.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxft2_2.2.0-3 libxi6_2:1.4.3-3 libxinerama1_2:1.1.1-3 libxml-parser-perl_2.41-1 libxml2_2.7.8.dfsg-4 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.6-2 libxt-dev_1:1.1.1-2 libxt6_1:1.1.1-2 libxtst6_2:1.2.0-3 libxxf86vm1_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 m4_1.4.16-2 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mesa-common-dev_7.11-6 mime-support_3.51-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-2 netbase_4.46 openssl_1.0.0e-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 python_2.7.2-7 python-minimal_2.7.2-7 python2.7_2.7.2-6 python2.7-minimal_2.7.2-6 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 shared-mime-info_0.90-1 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tsconf_1.0-9 ttf-dejavu-core_2.33-2 tzdata_2011k-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 x11-common_1:7.6+9 x11proto-core-dev_7.0.22-1 x11proto-input-dev_2.0.2-2 x11proto-kb-dev_1.0.5-2 x11proto-xext-dev_7.2.0-3 xorg-sgml-doctools_1:1.8-2 xtrans-dev_1.2.6-2 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
+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 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-4.6_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 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_1.2.0-3 libquadmath0_4.6.1-15 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-13.12 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -202,12 +287,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -217,30 +302,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+/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_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -253,21 +333,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
+/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_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -285,7 +365,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -345,10 +425,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -518,7 +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_2.13.3-1-i386-PCGCnt/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-i386-kdo61W/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -563,56 +639,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../bedtools_2.13.3-1_i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bedtools_2.13.4-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-0938
+Build finished at 20111029-0308
-bedtools_2.13.3-1_i386.changes:
+bedtools_2.13.4-1_i386.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: i386
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
+Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- fd9b0d36d582794ca0512453dae58a63b4f79730 676004 bedtools_2.13.3-1_i386.deb
+ 52cfafd73701e0abd7582a7b03d02ee6b9192e0b 681952 bedtools_2.13.4-1_i386.deb
Checksums-Sha256:
- ac2ca581306581c962ebf435c0c85c5c41aa58a656305a86886b596ac2907a43 676004 bedtools_2.13.3-1_i386.deb
+ 9555c63da4b13366aa9ac61676b3d2f52e0bf0b2a77aa77a95b1af819999d9ad 681952 bedtools_2.13.4-1_i386.deb
Files:
- 7aa3403311f6bf782a997b633c70bb3c 676004 science optional bedtools_2.13.3-1_i386.deb
+ cd2a8dafb349927a435b85fbf0650e52 681952 science optional bedtools_2.13.4-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_i386.deb
+bedtools_2.13.4-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 676004 bytes: control archive= 1715 bytes.
- 834 bytes, 18 lines control
+ size 681952 bytes: control archive= 1728 bytes.
+ 864 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4633
+ Installed-Size: 4634
+ 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
Section: science
@@ -627,49 +704,49 @@ bedtools_2.13.3-1_i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/bin/
--rwxr-xr-x root/root 121164 2011-10-05 09:38 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 297324 2011-10-05 09:38 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 272744 2011-10-05 09:38 ./usr/bin/tagBam
--rwxr-xr-x root/root 96356 2011-10-05 09:38 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 142236 2011-10-05 09:38 ./usr/bin/nucBed
--rwxr-xr-x root/root 143260 2011-10-05 09:38 ./usr/bin/sortBed
--rwxr-xr-x root/root 285024 2011-10-05 09:38 ./usr/bin/windowBed
--rwxr-xr-x root/root 120916 2011-10-05 09:38 ./usr/bin/closestBed
--rwxr-xr-x root/root 280920 2011-10-05 09:38 ./usr/bin/coverageBed
--rwxr-xr-x root/root 109276 2011-10-05 09:38 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 103124 2011-10-05 09:38 ./usr/bin/annotateBed
--rwxr-xr-x root/root 142064 2011-10-05 09:38 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 129356 2011-10-05 09:38 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 366968 2011-10-05 09:38 ./usr/bin/pairToBed
--rwxr-xr-x root/root 106836 2011-10-05 09:38 ./usr/bin/mergeBed
--rwxr-xr-x root/root 105244 2011-10-05 09:38 ./usr/bin/complementBed
--rwxr-xr-x root/root 297312 2011-10-05 09:38 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 88164 2011-10-05 09:38 ./usr/bin/overlap
--rwxr-xr-x root/root 178284 2011-10-05 09:38 ./usr/bin/pairToPair
--rwxr-xr-x root/root 105332 2011-10-05 09:38 ./usr/bin/linksBed
--rwxr-xr-x root/root 112848 2011-10-05 09:38 ./usr/bin/subtractBed
--rwxr-xr-x root/root 227628 2011-10-05 09:38 ./usr/bin/bedToBam
--rwxr-xr-x root/root 59648 2011-10-05 09:38 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 223440 2011-10-05 09:38 ./usr/bin/bamToBed
--rwxr-xr-x root/root 114232 2011-10-05 09:38 ./usr/bin/flankBed
--rwxr-xr-x root/root 350572 2011-10-05 09:38 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105116 2011-10-05 09:38 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 09:34 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/bin/
+-rwxr-xr-x root/root 142064 2011-10-29 03:08 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 59648 2011-10-29 03:08 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 96356 2011-10-29 03:08 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227628 2011-10-29 03:08 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 113880 2011-10-29 03:08 ./usr/bin/flankBed
+-rwxr-xr-x root/root 142652 2011-10-29 03:08 ./usr/bin/sortBed
+-rwxr-xr-x root/root 297312 2011-10-29 03:08 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 105332 2011-10-29 03:08 ./usr/bin/linksBed
+-rwxr-xr-x root/root 141980 2011-10-29 03:08 ./usr/bin/nucBed
+-rwxr-xr-x root/root 350572 2011-10-29 03:08 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 112716 2011-10-29 03:08 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 285024 2011-10-29 03:08 ./usr/bin/windowBed
+-rwxr-xr-x root/root 109276 2011-10-29 03:08 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 272744 2011-10-29 03:08 ./usr/bin/tagBam
+-rwxr-xr-x root/root 129160 2011-10-29 03:08 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 281508 2011-10-29 03:08 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 106740 2011-10-29 03:08 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 102964 2011-10-29 03:08 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 88164 2011-10-29 03:08 ./usr/bin/overlap
+-rwxr-xr-x root/root 121664 2011-10-29 03:08 ./usr/bin/closestBed
+-rwxr-xr-x root/root 178284 2011-10-29 03:08 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 105148 2011-10-29 03:08 ./usr/bin/complementBed
+-rwxr-xr-x root/root 223548 2011-10-29 03:08 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 298132 2011-10-29 03:08 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 366968 2011-10-29 03:08 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 121164 2011-10-29 03:08 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 104988 2011-10-29 03:08 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 03:05 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -683,42 +760,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-20013937-43eb-4fc3-ac1e-54fde9be699d/build/buildd-bedtools_2.13.3-1-i386-PCGCnt
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- cdbs* diffstat* quilt*
-0 upgraded, 0 newly installed, 3 to remove and 15 not upgraded.
-After this operation, 1215 kB disk space will be freed.
-(Reading database ... 20217 files and directories currently installed.)
-Removing cdbs ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-i386-sbuild-1cf97047-5a84-4be2-9ed7-799ebad2a5c3/build/buildd-bedtools_2.13.4-1-i386-kdo61W
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 94292
-Build-Time: 204
+Build-Space: 94000
+Build-Time: 168
Distribution: sid
-Install-Time: 7
-Job: bedtools_2.13.3-1
+Install-Time: 60
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 227
-Source-Version: 2.13.3-1
-Space: 94292
+Package-Time: 272
+Source-Version: 2.13.4-1
+Space: 94000
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-0938
-Build needed 00:03:47, 94292k disc space
-Signature with key 'AC7BC9C1' requested:
+Finished at 20111029-0308
+Build needed 00:04:32, 94000k disc space
+Signature with key 'E4786BDC' requested:
diff --git a/ia64.log b/ia64.log
index a1374cd..e973ea4 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,67 +1,66 @@
-From buildd at alkman.debian.org Wed Oct 05 09:54:29 2011
-Return-path: <buildd at alkman.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at mundy.debian.org Sat Oct 29 05:16:53 2011
+Return-path: <buildd at mundy.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1RBOBJ-0001t9-G3
- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:54:29 +0000
-Received: from alkman.debian.org ([192.25.206.63])
+ (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
+ id 1RK1Hp-00033I-4W
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 05:16:53 +0000
+Received: from mundy.debian.org ([192.25.206.62])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
- 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 1RBOBI-0002Tr-6m
- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:54:28 +0000
-Received: from buildd by alkman.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alkman.debian.org>)
- id 1RBOBF-0007bB-Vu; Wed, 05 Oct 2011 09:54:26 +0000
-Date: Wed, 05 Oct 2011 09:54:25 +0000
-Message-Id: <E1RBOBF-0007bB-Vu at alkman.debian.org>
-From: buildd on alkman <buildd at alkman.debian.org>
-To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on ia64 (dist=sid)
+ 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 1RK1Hn-0005PA-UV; Sat, 29 Oct 2011 05:16:52 +0000
+Received: from buildd by mundy.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mundy.debian.org>)
+ id 1RK1Hl-0007TC-EB; Sat, 29 Oct 2011 05:16:49 +0000
+Date: Sat, 29 Oct 2011 05:16:49 +0000
+Message-Id: <E1RK1Hl-0007TC-EB at mundy.debian.org>
+From: buildd on mundy <buildd at mundy.debian.org>
+To: dannf at master.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.4-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mundy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (ia64) 05 Oct 2011 09:42 ║
+║ bedtools 2.13.4-1 (ia64) 29 Oct 2011 05:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: ia64
Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://spohr.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
-Get:3 http://spohr.debian.org unstable/main Sources [5816 kB]
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5816 kB]
-Get:6 http://spohr.debian.org unstable/contrib Sources [57.1 kB]
-Get:7 http://spohr.debian.org unstable/non-free Sources [103 kB]
-Get:8 http://spohr.debian.org unstable/main ia64 Packages [7490 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [55.5 kB]
-Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://spohr.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [7490 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [55.5 kB]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org Release [1604 B]
+Get:4 http://incoming.debian.org unstable/main Sources [5874 kB]
+Get:5 http://spohr.debian.org unstable InRelease [146 kB]
+Get:6 http://spohr.debian.org unstable/main Sources [5874 kB]
+Get:7 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:8 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:9 http://incoming.debian.org unstable/main ia64 Packages [7508 kB]
+Get:10 http://incoming.debian.org unstable/contrib ia64 Packages [55.7 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.7 kB]
-Get:18 http://incoming.debian.org Packages [271 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:12 http://incoming.debian.org Sources [37.0 kB]
+Get:13 http://incoming.debian.org Packages [331 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 27.6 MB in 23s (1200 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:14 http://spohr.debian.org unstable/contrib Sources [56.5 kB]
+Get:15 http://spohr.debian.org unstable/non-free Sources [104 kB]
+Get:16 http://spohr.debian.org unstable/main ia64 Packages [7508 kB]
+Get:17 http://spohr.debian.org unstable/contrib ia64 Packages [55.7 kB]
+Ign http://spohr.debian.org unstable/contrib TranslationIndex
+Get:18 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://spohr.debian.org unstable/contrib Translation-en
+Fetched 27.9 MB in 19s (1433 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +81,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 0s (677 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 1s (860 kB/s)
Download complete and in download only mode
Check arch
@@ -109,7 +108,7 @@ Reading state information...
The following packages were automatically installed and are no longer required:
libppl9 libpwl5 libppl-c4 libcloog-ppl0 libgmpxx4ldbl
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -117,7 +116,7 @@ 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 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -182,24 +181,24 @@ 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 11 not upgraded.
+0 upgraded, 21 newly installed, 0 to remove and 46 not upgraded.
Need to get 11.4 MB of archives.
-After this operation, 42.4 MB of additional disk space will be used.
+After this operation, 38.5 MB of additional disk space will be used.
Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-3 [47.8 kB]
Get:2 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-2 [1118 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.08-1 [272 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main file ia64 5.08-1 [54.0 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-4 [173 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-4 [1177 kB]
-Get:10 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:12 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.6-1 [1973 kB]
-Get:13 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
-Get:14 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-4 [467 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-4 [2441 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]
@@ -207,12 +206,20 @@ Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9
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 0s (14.4 MB/s)
+Fetched 11.4 MB in 28s (403 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10538 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_ia64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_ia64.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_ia64.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_ia64.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_ia64.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_ia64.deb) ...
Selecting previously unselected package groff-base.
@@ -220,25 +227,17 @@ Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_ia64.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_ia64.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_ia64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.08-1_ia64.deb) ...
+Unpacking file (from .../archives/file_5.09-2_ia64.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_ia64.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_ia64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_ia64.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_ia64.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_ia64.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_ia64.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_ia64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_ia64.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
@@ -253,23 +252,23 @@ Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
+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 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up 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) ...
@@ -283,11 +282,11 @@ 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 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 46 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_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6.1_2.13-21 libc6.1-dev_2.13-21 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-5 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+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_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-13 libreadline6_6.2-5 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 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 │
@@ -298,12 +297,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -319,24 +318,24 @@ 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 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -349,21 +348,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -614,7 +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_2.13.3-1-ia64-2lzIyS/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -656,60 +655,61 @@ 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/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" were not uselessly linked against it (they use none of its symbols).
+dpkg-shlibdeps: warning: dependency on libm.so.6.1 could be avoided if "debian/bedtools/usr/bin/flankBed debian/bedtools/usr/bin/unionBedGraphs debian/bedtools/usr/bin/multiBamCov debian/bedtools/usr/bin/pairToBed debian/bedtools/usr/bin/bed12ToBed6 debian/bedtools/usr/bin/bamToBed debian/bedtools/usr/bin/coverageBed debian/bedtools/usr/bin/closestBed debian/bedtools/usr/bin/fastaFromBed debian/bedtools/usr/bin/overlap debian/bedtools/usr/bin/maskFastaFromBed debian/bedtools/usr/bin/bedToBam debian/bedtools/usr/bin/genomeCoverageBed debian/bedtools/usr/bin/annotateBed debian/bedtools/usr/bin/subtractBed debian/bedtools/usr/bin/sortBed debian/bedtools/usr/bin/pairToPair debian/bedtools/usr/bin/shuffleBed debian/bedtools/usr/bin/mergeBed debian/bedtools/usr/bin/nucBed debian/bedtools/usr/bin/bedToIgv debian/bedtools/usr/bin/windowBed debian/bedtools/usr/bin/linksBed debian/bedtools/usr/bin/tagBam debian/bedtools/usr/bin/slopBed debian/bedtools/usr/bin/intersectBed debian/bedtools/usr/bin/complementBed" were not uselessly linked against it (they use none of its symbols).
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bedtools_2.13.3-1_ia64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../bedtools_2.13.4-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-0954
+Build finished at 20111029-0516
-bedtools_2.13.3-1_ia64.changes:
+bedtools_2.13.4-1_ia64.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: ia64
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
+Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- dd23cfe6292d224600f7403762e8675aa10914d2 745358 bedtools_2.13.3-1_ia64.deb
+ 4525b15f5c544c46765a435343c520168a04b333 744358 bedtools_2.13.4-1_ia64.deb
Checksums-Sha256:
- 359ac4198e69fb333ed8ecbc2a21f787a7a68fd4abd08d6e8e45007a0670f8e9 745358 bedtools_2.13.3-1_ia64.deb
+ 35d902ba7ff65a7b30a8418cde058b7e67503a2559c51b8782db5e7f0e346d5d 744358 bedtools_2.13.4-1_ia64.deb
Files:
- c47d2b2ce55524bafe7af5bcdee2a2f9 745358 science optional bedtools_2.13.3-1_ia64.deb
+ 22ea6bd90c3943f471b8b04b14b99447 744358 science optional bedtools_2.13.4-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_ia64.deb
+bedtools_2.13.4-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 745358 bytes: control archive= 1729 bytes.
- 850 bytes, 18 lines control
+ size 744358 bytes: control archive= 1742 bytes.
+ 880 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 9504
+ Installed-Size: 9560
+ 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
Section: science
@@ -724,49 +724,49 @@ bedtools_2.13.3-1_ia64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 09:53 ./
-drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/bin/
--rwxr-xr-x root/root 216544 2011-10-05 09:53 ./usr/bin/annotateBed
--rwxr-xr-x root/root 456976 2011-10-05 09:53 ./usr/bin/bamToBed
--rwxr-xr-x root/root 199440 2011-10-05 09:53 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 471856 2011-10-05 09:53 ./usr/bin/bedToBam
--rwxr-xr-x root/root 246744 2011-10-05 09:53 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 249488 2011-10-05 09:53 ./usr/bin/closestBed
--rwxr-xr-x root/root 219880 2011-10-05 09:53 ./usr/bin/complementBed
--rwxr-xr-x root/root 574072 2011-10-05 09:53 ./usr/bin/coverageBed
--rwxr-xr-x root/root 293648 2011-10-05 09:53 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 234456 2011-10-05 09:53 ./usr/bin/flankBed
--rwxr-xr-x root/root 605816 2011-10-05 09:53 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 727904 2011-10-05 09:53 ./usr/bin/intersectBed
--rwxr-xr-x root/root 220280 2011-10-05 09:53 ./usr/bin/linksBed
--rwxr-xr-x root/root 226280 2011-10-05 09:53 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 221064 2011-10-05 09:53 ./usr/bin/mergeBed
--rwxr-xr-x root/root 620624 2011-10-05 09:53 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 297768 2011-10-05 09:53 ./usr/bin/nucBed
--rwxr-xr-x root/root 178672 2011-10-05 09:53 ./usr/bin/overlap
--rwxr-xr-x root/root 767632 2011-10-05 09:53 ./usr/bin/pairToBed
--rwxr-xr-x root/root 378032 2011-10-05 09:53 ./usr/bin/pairToPair
--rwxr-xr-x root/root 270696 2011-10-05 09:53 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 217208 2011-10-05 09:53 ./usr/bin/slopBed
--rwxr-xr-x root/root 305760 2011-10-05 09:53 ./usr/bin/sortBed
--rwxr-xr-x root/root 234968 2011-10-05 09:53 ./usr/bin/subtractBed
--rwxr-xr-x root/root 564992 2011-10-05 09:53 ./usr/bin/tagBam
--rwxr-xr-x root/root 120416 2011-10-05 09:53 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 587368 2011-10-05 09:53 ./usr/bin/windowBed
-drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 09:44 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 09:53 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-10-29 05:16 ./
+drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 05:07 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 05:16 ./usr/bin/
+-rwxr-xr-x root/root 463184 2011-10-29 05:16 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 178672 2011-10-29 05:16 ./usr/bin/overlap
+-rwxr-xr-x root/root 270696 2011-10-29 05:16 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 471856 2011-10-29 05:16 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 219880 2011-10-29 05:16 ./usr/bin/complementBed
+-rwxr-xr-x root/root 587752 2011-10-29 05:16 ./usr/bin/windowBed
+-rwxr-xr-x root/root 217208 2011-10-29 05:16 ./usr/bin/slopBed
+-rwxr-xr-x root/root 305760 2011-10-29 05:16 ./usr/bin/sortBed
+-rwxr-xr-x root/root 226280 2011-10-29 05:16 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 297768 2011-10-29 05:16 ./usr/bin/nucBed
+-rwxr-xr-x root/root 293648 2011-10-29 05:16 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 221064 2011-10-29 05:16 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 234968 2011-10-29 05:16 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 251952 2011-10-29 05:16 ./usr/bin/closestBed
+-rwxr-xr-x root/root 728240 2011-10-29 05:16 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 199440 2011-10-29 05:16 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 564992 2011-10-29 05:16 ./usr/bin/tagBam
+-rwxr-xr-x root/root 246744 2011-10-29 05:16 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 220280 2011-10-29 05:16 ./usr/bin/linksBed
+-rwxr-xr-x root/root 216544 2011-10-29 05:16 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 580280 2011-10-29 05:16 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 378032 2011-10-29 05:16 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 612040 2011-10-29 05:16 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 620624 2011-10-29 05:16 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 120416 2011-10-29 05:16 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 767632 2011-10-29 05:16 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 234456 2011-10-29 05:16 ./usr/bin/flankBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -780,7 +780,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-4dfe5cf8-691a-4d39-abfe-e242ff2b1e0c/build/buildd-bedtools_2.13.3-1-ia64-2lzIyS
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-1ae39a2e-4d0c-42e1-a216-bdc745d88862/build/buildd-bedtools_2.13.4-1-ia64-EGuzfI
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -788,19 +788,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 162092
-Build-Time: 585
+Build-Space: 156600
+Build-Time: 543
Distribution: sid
-Install-Time: 65
-Job: bedtools_2.13.3-1
+Install-Time: 84
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 700
-Source-Version: 2.13.3-1
-Space: 162092
+Package-Time: 677
+Source-Version: 2.13.4-1
+Space: 156600
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-0954
-Build needed 00:11:40, 162092k disc space
-Signature with key 'C6591CE9' requested:
+Finished at 20111029-0516
+Build needed 00:11:17, 156600k disc space
+Signature with key '96FA48F4' requested:
diff --git a/info b/info
index bf985a9..3258c06 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-i386~1317807504~sid~successful
-powerpc~1317807719~sid~successful
-kfreebsd-amd64~1317807732~sid~successful
-kfreebsd-i386~1317807765~sid~successful
-ia64~1317808470~sid~successful
-armel~1317808708~sid~successful
-mipsel~1317809171~sid~successful
-mips~1317809615~sid~successful
-sparc~1317809672~sid~successful
-s390~1317811073~sid~successful
-hurd-i386~1317816700~sid~successful
+i386~1319857731~sid~successful
+powerpc~1319857796~sid~successful
+hurd-i386~1319858228~sid~successful
+kfreebsd-amd64~1319858240~sid~successful
+mips~1319858838~sid~successful
+armel~1319858868~sid~successful
+kfreebsd-i386~1319860896~sid~successful
+mipsel~1319862768~sid~successful
+sparc~1319863353~sid~successful
+s390~1319863708~sid~successful
+ia64~1319865413~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 8f40470..0116b63 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,83 +1,93 @@
-From buildd at fasch.debian.org Wed Oct 05 09:42:04 2011
-Return-path: <buildd at fasch.debian.org>
+From buildd at fano.debian.org Sat Oct 29 03:17:20 2011
+Return-path: <buildd at fano.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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 fasch.debian.org>)
- id 1RBNzI-0007ii-3e
- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:42:04 +0000
-Received: from fasch.debian.org ([194.177.211.201])
+ (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
+ id 1RJzQ7-0002Au-VY
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:17:20 +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=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
+ CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
- id 1RBNzG-0001as-JR; Wed, 05 Oct 2011 09:42:02 +0000
-Received: from buildd by fasch.debian.org with local (Exim 4.72)
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- id 1RBNzF-0000nq-Hx; Wed, 05 Oct 2011 09:42:01 +0000
-Message-Id: <E1RBNzF-0000nq-Hx at fasch.debian.org>
+ (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
+ id 1RJzQ6-0008RR-QB; Sat, 29 Oct 2011 03:17:19 +0000
+Received: from buildd by fano.debian.org with local (Exim 4.72)
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+ id 1RJzQ4-00097p-43; Sat, 29 Oct 2011 03:17:16 +0000
+Message-Id: <E1RJzQ4-00097p-43 at fano.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 5 Oct 2011 09:42:01 +0000
-From: buildd on fasch <buildd at fasch.debian.org>
+Date: Sat, 29 Oct 2011 03:17:16 +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_2.13.3-1 on kfreebsd-amd64
+Subject: Log for successful build of bedtools_2.13.4-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 56BAE008
+Key-Id: 911EAB69
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (kfreebsd-amd64) 05 Oct 2011 09:36 ║
+║ bedtools 2.13.4-1 (kfreebsd-amd64) 29 Oct 2011 03:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: kfreebsd-amd64
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
Get:1 http://incoming.debian.org sid InRelease [146 kB]
-Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.gr.debian.org sid/main TranslationIndex
-Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
-Ign http://ftp.gr.debian.org sid/contrib Translation-en
-Ign http://ftp.gr.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org InRelease
Get:2 http://incoming.debian.org Release.gpg [836 B]
Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Get:4 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
Get:5 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Get:6 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex [2023 B]
+Get:6 http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex [2023 B]
+Get:7 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex [2023 B]
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:7 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Get:8 http://incoming.debian.org sid/main TranslationIndex [2045 B]
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:8 http://incoming.debian.org Release [1604 B]
-Get:9 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:10 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
-Get:11 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-05-0826.58.pdiff [3796 B]
-Get:12 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:13 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [87.7 kB]
-Get:14 http://incoming.debian.org Sources [36.7 kB]
-Get:15 http://incoming.debian.org Packages [271 kB]
-Get:16 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
-Get:17 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-05-0826.58.pdiff [3796 B]
+Get:9 http://mirror-ubc.debian.org sid InRelease [146 kB]
+Get:10 http://incoming.debian.org Release [1604 B]
+Get:11 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:12 http://incoming.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
+Get:13 http://incoming.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
+Get:14 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
+Get:15 http://incoming.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
+Get:16 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [86.9 kB]
+Get:17 http://incoming.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
+Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
+Get:18 http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:19 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Get:20 http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex [2023 B]
+Get:21 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex [2023 B]
+Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
+Get:22 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
+Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
+Get:23 http://mirror-ubc.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
+Get:24 http://mirror-ubc.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
+Get:25 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
+Get:26 http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
+Get:27 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [86.9 kB]
+Get:28 http://incoming.debian.org Sources [36.2 kB]
+Get:29 http://incoming.debian.org Packages [324 kB]
+Get:30 http://incoming.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
+Get:31 http://incoming.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
+Ign http://mirror-ubc.debian.org sid/contrib Translation-en
+Ign http://mirror-ubc.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org sid/contrib Translation-en
+Get:32 http://incoming.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
+Get:33 http://mirror-ubc.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 563 kB in 5s (102 kB/s)
+Get:34 http://mirror-ubc.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
+Get:35 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-10-29-0215.35.pdiff [17.9 kB]
+Get:36 http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 2011-10-29-0215.35.pdiff [31 B]
+Fetched 914 kB in 15s (57.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -98,11 +108,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 2s (230 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 1s (635 kB/s)
Download complete and in download only mode
Check arch
@@ -122,12 +132,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -141,10 +151,10 @@ base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.3)
+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-2011-07-02-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.2+ds2-5)
grep: already installed (2.9-2)
@@ -152,11 +162,11 @@ gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-2)
ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-5)
+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-13.11)
-sysvinit: already installed (2.88dsf-13.11)
+sysvinit-utils: already installed (2.88dsf-13.12)
+sysvinit: already installed (2.88dsf-13.12)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
@@ -164,7 +174,7 @@ libc6-dev: already installed (~*=PROVIDED=*=)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
Using default version 8.9.8
@@ -176,9 +186,8 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
- po-debconf
+ diffstat file gettext gettext-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
devscripts dh-make gettext-doc groff less www-browser libmail-box-perl
procmail graphviz
@@ -186,40 +195,38 @@ Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/9350 kB of archives.
-After this operation, 25.8 MB of additional disk space will be used.
+0 upgraded, 18 newly installed, 0 to remove and 10 not upgraded.
+Need to get 0 B/8237 kB of archives.
+After this operation, 21.7 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 11972 files and directories currently installed.)
+(Reading database ... 12406 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-amd64.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_kfreebsd-amd64.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.08-1_kfreebsd-amd64.deb) ...
+Unpacking file (from .../file_5.09-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-amd64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_kfreebsd-amd64.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_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-amd64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
@@ -233,20 +240,19 @@ 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_kfreebsd-amd64.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
-Setting up groff-base (1.21-6) ...
+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 man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up 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) ...
@@ -257,11 +263,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.90.20111004-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libncursesw5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-13 libreadline6_6.2-6 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+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 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_2.21.90.20111004-2 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 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_1:3.0-1 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 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-4.6_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 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 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 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 libquadmath0_4.6.1-15 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libsigsegv2_2.9-4 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 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_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 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_1.8.2-2 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_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 │
@@ -272,12 +278,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -287,30 +293,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+/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_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4/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 +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_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
+/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_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -355,7 +356,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -415,10 +416,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -588,7 +585,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -633,56 +630,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../bedtools_2.13.3-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bedtools_2.13.4-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-0941
+Build finished at 20111029-0316
-bedtools_2.13.3-1_kfreebsd-amd64.changes:
+bedtools_2.13.4-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-amd64
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- a5a804611be9905baa3aabfca216e3a04af2e3d3 667732 bedtools_2.13.3-1_kfreebsd-amd64.deb
+ a4cd93bbd55049562234e90038e5de946a39575d 668126 bedtools_2.13.4-1_kfreebsd-amd64.deb
Checksums-Sha256:
- cd5c5e1cc10b11382c2a12636d9159aa8f765229cde743477f4893102d8de153 667732 bedtools_2.13.3-1_kfreebsd-amd64.deb
+ d8603b9d6826c48fa3d4c838d699cef7b90da8d68ebed7f195ed9d357c3845e5 668126 bedtools_2.13.4-1_kfreebsd-amd64.deb
Files:
- bec7217b9b6137d5059c57125771f27f 667732 science optional bedtools_2.13.3-1_kfreebsd-amd64.deb
+ 21afb051f4c03c7e2b238801fd6b0c8c 668126 science optional bedtools_2.13.4-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_kfreebsd-amd64.deb
+bedtools_2.13.4-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 667732 bytes: control archive= 1723 bytes.
- 846 bytes, 18 lines control
+ size 668126 bytes: control archive= 1741 bytes.
+ 876 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4660
+ Installed-Size: 4663
+ 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
Section: science
@@ -697,49 +695,49 @@ bedtools_2.13.3-1_kfreebsd-amd64.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 09:40 ./
-drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 09:37 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-05 09:40 ./usr/bin/
--rwxr-xr-x root/root 110000 2011-10-05 09:40 ./usr/bin/annotateBed
--rwxr-xr-x root/root 215992 2011-10-05 09:40 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101856 2011-10-05 09:40 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 229232 2011-10-05 09:40 ./usr/bin/bedToBam
--rwxr-xr-x root/root 126480 2011-10-05 09:40 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 126400 2011-10-05 09:40 ./usr/bin/closestBed
--rwxr-xr-x root/root 114168 2011-10-05 09:40 ./usr/bin/complementBed
--rwxr-xr-x root/root 274440 2011-10-05 09:40 ./usr/bin/coverageBed
--rwxr-xr-x root/root 147112 2011-10-05 09:40 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 119160 2011-10-05 09:40 ./usr/bin/flankBed
--rwxr-xr-x root/root 291216 2011-10-05 09:40 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 346336 2011-10-05 09:40 ./usr/bin/intersectBed
--rwxr-xr-x root/root 110096 2011-10-05 09:40 ./usr/bin/linksBed
--rwxr-xr-x root/root 118328 2011-10-05 09:40 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 114112 2011-10-05 09:40 ./usr/bin/mergeBed
--rwxr-xr-x root/root 294864 2011-10-05 09:40 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 147136 2011-10-05 09:40 ./usr/bin/nucBed
--rwxr-xr-x root/root 93664 2011-10-05 09:40 ./usr/bin/overlap
--rwxr-xr-x root/root 357216 2011-10-05 09:40 ./usr/bin/pairToBed
--rwxr-xr-x root/root 180072 2011-10-05 09:40 ./usr/bin/pairToPair
--rwxr-xr-x root/root 135520 2011-10-05 09:40 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 110176 2011-10-05 09:40 ./usr/bin/slopBed
--rwxr-xr-x root/root 150952 2011-10-05 09:40 ./usr/bin/sortBed
--rwxr-xr-x root/root 268040 2011-10-05 09:40 ./usr/bin/tagBam
--rwxr-xr-x root/root 118192 2011-10-05 09:40 ./usr/bin/subtractBed
--rwxr-xr-x root/root 65032 2011-10-05 09:40 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 279240 2011-10-05 09:40 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-10-29 03:16 ./
+drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 03:13 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-29 03:16 ./usr/bin/
+-rwxr-xr-x root/root 110000 2011-10-29 03:16 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 218376 2011-10-29 03:16 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101856 2011-10-29 03:16 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 229232 2011-10-29 03:16 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 126480 2011-10-29 03:16 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 126496 2011-10-29 03:16 ./usr/bin/closestBed
+-rwxr-xr-x root/root 114168 2011-10-29 03:16 ./usr/bin/complementBed
+-rwxr-xr-x root/root 276440 2011-10-29 03:16 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 147112 2011-10-29 03:16 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 118768 2011-10-29 03:16 ./usr/bin/flankBed
+-rwxr-xr-x root/root 294888 2011-10-29 03:16 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 345520 2011-10-29 03:16 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 110096 2011-10-29 03:16 ./usr/bin/linksBed
+-rwxr-xr-x root/root 118328 2011-10-29 03:16 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 114112 2011-10-29 03:16 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 292760 2011-10-29 03:16 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 147136 2011-10-29 03:16 ./usr/bin/nucBed
+-rwxr-xr-x root/root 93664 2011-10-29 03:16 ./usr/bin/overlap
+-rwxr-xr-x root/root 356352 2011-10-29 03:16 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 179944 2011-10-29 03:16 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 135232 2011-10-29 03:16 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 110056 2011-10-29 03:16 ./usr/bin/slopBed
+-rwxr-xr-x root/root 150952 2011-10-29 03:16 ./usr/bin/sortBed
+-rwxr-xr-x root/root 267640 2011-10-29 03:16 ./usr/bin/tagBam
+-rwxr-xr-x root/root 118192 2011-10-29 03:16 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 65032 2011-10-29 03:16 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 278800 2011-10-29 03:16 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -753,21 +751,21 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1317807374-99849/build/buildd-bedtools_2.13.3-1-kfreebsd-amd64-foEYN9
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1319857958-32760/build/buildd-bedtools_2.13.4-1-kfreebsd-amd64-BHNVG8
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
- libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
-After this operation, 25.8 MB disk space will be freed.
-(Reading database ... 13328 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
+ libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 18 to remove and 10 not upgraded.
+After this operation, 21.7 MB disk space will be freed.
+(Reading database ... 13582 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -778,10 +776,6 @@ Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
@@ -790,6 +784,8 @@ Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
+Removing man-db ...
+Purging configuration files for man-db ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
@@ -803,18 +799,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 136132
-Build-Time: 197
+Build-Space: 135716
+Build-Time: 196
Distribution: sid
-Install-Time: 79
-Job: bedtools_2.13.3-1
+Install-Time: 32
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 295
-Source-Version: 2.13.3-1
-Space: 136132
+Package-Time: 257
+Source-Version: 2.13.4-1
+Space: 135716
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-0941
-Build needed 00:04:55, 136132k disc space
-Signature with key '56BAE008' requested:
+Finished at 20111029-0316
+Build needed 00:04:17, 135716k disc space
+Signature with key '911EAB69' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 232d49c..de8f309 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,30 +1,30 @@
-From buildd at field.debian.org Wed Oct 05 09:42:44 2011
+From buildd at field.debian.org Sat Oct 29 04:01:35 2011
Return-path: <buildd at field.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 field.debian.org>)
- id 1RBNzw-0007kN-Mv
- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:42:44 +0000
+ id 1RK06x-0000Ax-Lv
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 04:01:35 +0000
Received: from field.debian.org ([194.177.211.210])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
- by 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 field.debian.org>)
- id 1RBNzw-0001b7-0O; Wed, 05 Oct 2011 09:42:44 +0000
+ id 1RK06w-0001Sw-5c; Sat, 29 Oct 2011 04:01:34 +0000
Received: from buildd by field.debian.org with local (Exim 4.72)
(envelope-from <buildd at field.debian.org>)
- id 1RBNzv-000HGc-5s; Wed, 05 Oct 2011 09:42:43 +0000
-Message-Id: <E1RBNzv-000HGc-5s at field.debian.org>
+ id 1RK06v-000OcF-B1; Sat, 29 Oct 2011 04:01:33 +0000
+Message-Id: <E1RK06v-000OcF-B1 at field.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 5 Oct 2011 09:42:42 +0000
+Date: Sat, 29 Oct 2011 04:01:33 +0000
From: buildd on field <buildd at field.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on kfreebsd-i386
+Subject: Log for successful build of bedtools_2.13.4-1 on kfreebsd-i386
(dist=sid)
Key-Id: 6B8016EE
Delivered-To: logs at buildd.debian.org
@@ -32,60 +32,54 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (kfreebsd-i386) 05 Oct 2011 09:37 ║
+║ bedtools 2.13.4-1 (kfreebsd-i386) 29 Oct 2011 03:55 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: kfreebsd-i386
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Get:1 http://ftp.gr.debian.org sid InRelease [146 kB]
+Get:2 http://ftp.gr.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Get:3 http://ftp.gr.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:4 http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
+Get:5 http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex [2023 B]
+Get:6 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex [2023 B]
Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Get:7 http://ftp.gr.debian.org sid/main TranslationIndex [2045 B]
Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Get:2 http://ftp.gr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
-Get:3 http://ftp.gr.debian.org sid/main 2011-10-05-0214.30.pdiff [12.7 kB]
-Get:4 http://ftp.gr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
-Get:5 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-05-0214.30.pdiff [14.9 kB]
+Get:8 http://ftp.gr.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:6 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-05-0214.30.pdiff [54 B]
+Get:9 http://ftp.gr.debian.org sid/main 2011-10-29-0215.35.pdiff [12.5 kB]
+Get:10 http://ftp.gr.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
+Get:11 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-29-0215.35.pdiff [17.0 kB]
+Get:12 http://ftp.gr.debian.org sid/contrib kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
+Get:13 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
Ign http://ftp.gr.debian.org sid/contrib Translation-en
Ign http://ftp.gr.debian.org sid/non-free Translation-en
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:14 http://incoming.debian.org Release.gpg [836 B]
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:9 http://incoming.debian.org sid/non-free Sources/DiffIndex [2023 B]
-Get:10 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/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
-Get:11 http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex [2023 B]
+Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:12 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:13 http://ftp.gr.debian.org sid/non-free 2011-10-05-0214.30.pdiff [843 B]
-Get:14 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-05-0214.30.pdiff [14.9 kB]
Get:15 http://incoming.debian.org Release [1604 B]
-Get:16 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
-Get:17 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
-Get:18 http://incoming.debian.org sid/main kfreebsd-i386 2011-10-05-0826.58.pdiff [2824 B]
-Get:19 http://incoming.debian.org sid/non-free kfreebsd-i386 2011-10-05-0826.58.pdiff [1227 B]
-Get:20 http://incoming.debian.org Sources [36.7 kB]
-Get:21 http://incoming.debian.org Packages [271 kB]
-Get:22 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-05-0214.30.pdiff [54 B]
-Get:23 http://incoming.debian.org sid/main 2011-10-05-0826.58.pdiff [5108 B]
+Get:16 http://ftp.gr.debian.org sid/non-free 2011-10-29-0215.35.pdiff [376 B]
+Get:17 http://ftp.gr.debian.org sid/main kfreebsd-i386 2011-10-29-0215.35.pdiff [17.0 kB]
+Get:18 http://incoming.debian.org Sources [36.6 kB]
+Get:19 http://incoming.debian.org Packages [331 kB]
+Get:20 http://ftp.gr.debian.org sid/contrib kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
+Get:21 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2011-10-29-0215.35.pdiff [31 B]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Get:24 http://incoming.debian.org sid/non-free 2011-10-05-0826.58.pdiff [31 B]
-Get:25 http://incoming.debian.org sid/main kfreebsd-i386 2011-10-05-0826.58.pdiff [2824 B]
-Get:26 http://incoming.debian.org sid/non-free kfreebsd-i386 2011-10-05-0826.58.pdiff [1227 B]
-Fetched 504 kB in 8s (58.8 kB/s)
+Fetched 558 kB in 6s (90.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -106,11 +100,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 2s (258 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 2s (347 kB/s)
Download complete and in download only mode
Check arch
@@ -130,12 +124,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -149,10 +143,10 @@ base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.3)
+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-2011-07-02-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.2+ds2-5)
grep: already installed (2.9-2)
@@ -160,11 +154,11 @@ gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-2)
ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-5)
+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-13.11)
-sysvinit: already installed (2.88dsf-13.11)
+sysvinit-utils: already installed (2.88dsf-13.12)
+sysvinit: already installed (2.88dsf-13.12)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
@@ -172,7 +166,7 @@ libc6-dev: already installed (~*=PROVIDED=*=)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
Using default version 8.9.8
@@ -198,36 +192,36 @@ The following NEW packages will be installed:
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/9047 kB of archives.
-After this operation, 24.9 MB of additional disk space will be used.
+0 upgraded, 19 newly installed, 0 to remove and 10 not upgraded.
+Need to get 0 B/9192 kB of archives.
+After this operation, 24.2 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 12056 files and directories currently installed.)
+(Reading database ... 12054 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-i386.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-i386.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_kfreebsd-i386.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-i386.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_kfreebsd-i386.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_kfreebsd-i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.08-1_kfreebsd-i386.deb) ...
+Unpacking file (from .../file_5.09-2_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-i386.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_kfreebsd-i386.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_kfreebsd-i386.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-i386.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_kfreebsd-i386.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
@@ -241,20 +235,20 @@ 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_kfreebsd-i386.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
+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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
-Setting up libmagic1 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up 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) ...
@@ -265,11 +259,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.90.20111004-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.3 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18.1-1 file_5.08-1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-3 libmpfr4_3.1.0-1 libncurses5_5.9-2 libncursesw5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-13 libreadline6_6.2-6 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-8 readline-common_6.2-6 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 type-handling_0.2.23 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-1 gcc-4.6_4.6.2-1 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-21 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 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_4.6.2-1 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_1:3.0-1 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_4.6.2-1 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_4.6.2-1 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 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 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-1 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_4.6.2-1 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 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 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 libquadmath0_4.6.2-1 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.2-1 libstdc++6-4.6-dev_4.6.2-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 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_1.3.3-15 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 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_1.8.2-2 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_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 │
@@ -280,12 +274,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -295,30 +289,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+/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_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -331,21 +320,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
+/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_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -363,7 +352,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -423,10 +412,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -596,7 +581,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -641,22 +626,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.13.3-1_kfreebsd-i386.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../bedtools_2.13.4-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-0941
+Build finished at 20111029-0400
-bedtools_2.13.3-1_kfreebsd-i386.changes:
+bedtools_2.13.4-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: kfreebsd-i386
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
@@ -664,33 +649,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- e1571e7aee77c783b08e6e12e752b1bbb7a57d1e 676492 bedtools_2.13.3-1_kfreebsd-i386.deb
+ 92a56f473957115d23cd8906ee1928760a93e063 679346 bedtools_2.13.4-1_kfreebsd-i386.deb
Checksums-Sha256:
- 73cb86bd852b2932c943e78ec3c1c0fa33a245b4243db588c8adf388b78ae723 676492 bedtools_2.13.3-1_kfreebsd-i386.deb
+ 6927d84913f1bd96a7c3b07aca308a08807125f0f3a4a6f5cbbb1d3fbbe30580 679346 bedtools_2.13.4-1_kfreebsd-i386.deb
Files:
- 173d79bec66e0f6402792eac39a8fec2 676492 science optional bedtools_2.13.3-1_kfreebsd-i386.deb
+ 0fe4a69daf0e253938a20f1eb6f67412 679346 science optional bedtools_2.13.4-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_kfreebsd-i386.deb
+bedtools_2.13.4-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 676492 bytes: control archive= 1724 bytes.
- 845 bytes, 18 lines control
+ size 679346 bytes: control archive= 1742 bytes.
+ 875 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 4602
+ 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
Section: science
@@ -705,49 +691,49 @@ bedtools_2.13.3-1_kfreebsd-i386.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 09:38 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/bin/
--rwxr-xr-x root/root 103092 2011-10-05 09:41 ./usr/bin/annotateBed
--rwxr-xr-x root/root 223440 2011-10-05 09:41 ./usr/bin/bamToBed
--rwxr-xr-x root/root 96356 2011-10-05 09:41 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 227628 2011-10-05 09:41 ./usr/bin/bedToBam
--rwxr-xr-x root/root 121132 2011-10-05 09:41 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 120916 2011-10-05 09:41 ./usr/bin/closestBed
--rwxr-xr-x root/root 105212 2011-10-05 09:41 ./usr/bin/complementBed
--rwxr-xr-x root/root 280920 2011-10-05 09:41 ./usr/bin/coverageBed
--rwxr-xr-x root/root 142096 2011-10-05 09:41 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 114200 2011-10-05 09:41 ./usr/bin/flankBed
--rwxr-xr-x root/root 297324 2011-10-05 09:41 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 350572 2011-10-05 09:41 ./usr/bin/intersectBed
--rwxr-xr-x root/root 105300 2011-10-05 09:41 ./usr/bin/linksBed
--rwxr-xr-x root/root 109244 2011-10-05 09:41 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 106804 2011-10-05 09:41 ./usr/bin/mergeBed
--rwxr-xr-x root/root 297312 2011-10-05 09:41 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 142268 2011-10-05 09:41 ./usr/bin/nucBed
--rwxr-xr-x root/root 88164 2011-10-05 09:41 ./usr/bin/overlap
--rwxr-xr-x root/root 366968 2011-10-05 09:41 ./usr/bin/pairToBed
--rwxr-xr-x root/root 178284 2011-10-05 09:41 ./usr/bin/pairToPair
--rwxr-xr-x root/root 129324 2011-10-05 09:41 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 105084 2011-10-05 09:41 ./usr/bin/slopBed
--rwxr-xr-x root/root 143228 2011-10-05 09:41 ./usr/bin/sortBed
--rwxr-xr-x root/root 272744 2011-10-05 09:41 ./usr/bin/tagBam
--rwxr-xr-x root/root 112816 2011-10-05 09:41 ./usr/bin/subtractBed
--rwxr-xr-x root/root 59616 2011-10-05 09:41 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 285024 2011-10-05 09:41 ./usr/bin/windowBed
+drwxr-xr-x root/root 0 2011-10-29 04:00 ./
+drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 03:57 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-29 04:00 ./usr/bin/
+-rwxr-xr-x root/root 102932 2011-10-29 04:00 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 223468 2011-10-29 04:00 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 96356 2011-10-29 04:00 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 227628 2011-10-29 04:00 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121132 2011-10-29 04:00 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 121600 2011-10-29 04:00 ./usr/bin/closestBed
+-rwxr-xr-x root/root 105084 2011-10-29 04:00 ./usr/bin/complementBed
+-rwxr-xr-x root/root 281428 2011-10-29 04:00 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 142096 2011-10-29 04:00 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 113848 2011-10-29 04:00 ./usr/bin/flankBed
+-rwxr-xr-x root/root 298052 2011-10-29 04:00 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 350572 2011-10-29 04:00 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 105300 2011-10-29 04:00 ./usr/bin/linksBed
+-rwxr-xr-x root/root 109244 2011-10-29 04:00 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 106708 2011-10-29 04:00 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 297312 2011-10-29 04:00 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 142012 2011-10-29 04:00 ./usr/bin/nucBed
+-rwxr-xr-x root/root 88164 2011-10-29 04:00 ./usr/bin/overlap
+-rwxr-xr-x root/root 366968 2011-10-29 04:00 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 178284 2011-10-29 04:00 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 129160 2011-10-29 04:00 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 104956 2011-10-29 04:00 ./usr/bin/slopBed
+-rwxr-xr-x root/root 142620 2011-10-29 04:00 ./usr/bin/sortBed
+-rwxr-xr-x root/root 272744 2011-10-29 04:00 ./usr/bin/tagBam
+-rwxr-xr-x root/root 112716 2011-10-29 04:00 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 59616 2011-10-29 04:00 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 285024 2011-10-29 04:00 ./usr/bin/windowBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -761,11 +747,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1317807422-63202/build/buildd-bedtools_2.13.3-1-kfreebsd-i386-wXytxm
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1319860544-91264/build/buildd-bedtools_2.13.4-1-kfreebsd-i386-4jA5YH
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -773,9 +759,9 @@ The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
-After this operation, 24.9 MB disk space will be freed.
-(Reading database ... 13412 files and directories currently installed.)
+0 upgraded, 0 newly installed, 19 to remove and 10 not upgraded.
+After this operation, 24.2 MB disk space will be freed.
+(Reading database ... 13410 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -811,18 +797,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 95358
-Build-Time: 193
+Build-Space: 95096
+Build-Time: 187
Distribution: sid
-Install-Time: 77
-Job: bedtools_2.13.3-1
+Install-Time: 80
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 290
-Source-Version: 2.13.3-1
-Space: 95358
+Package-Time: 294
+Source-Version: 2.13.4-1
+Space: 95096
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-0941
-Build needed 00:04:50, 95358k disc space
+Finished at 20111029-0400
+Build needed 00:04:54, 95096k disc space
Signature with key '6B8016EE' requested:
diff --git a/mips.log b/mips.log
index 2c41ba3..d14b130 100644
--- a/mips.log
+++ b/mips.log
@@ -1,68 +1,67 @@
-From buildd2 at lucatelli.debian.org Wed Oct 05 10:13:34 2011
-Return-path: <buildd2 at lucatelli.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at ball.debian.org Sat Oct 29 03:27:17 2011
+Return-path: <buildd at ball.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
- id 1RBOTm-0005Jc-E9
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:13:34 +0000
-Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1RJzZl-0003dp-Ml
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:27:17 +0000
+Received: from ball.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d09])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lucatelli.debian.org,
- EMAIL=hostmaster at lucatelli.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
- id 1RBOTl-0003M0-5Y
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:13:33 +0000
-Received: from buildd2 by lucatelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd2 at lucatelli.debian.org>) id 1RBOTj-0003bv-JI
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:13:31 +0000
-From: buildd on lucatelli <buildd2 at lucatelli.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on mips (dist=sid)
+ CN=ball.debian.org, EMAIL=hostmaster at ball.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1RJzZl-0000Ss-0B
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:27:17 +0000
+Received: from buildd by ball.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at ball.debian.org>)
+ id 1RJzZk-0004Ud-A5; Sat, 29 Oct 2011 03:27:16 +0000
+Date: Sat, 29 Oct 2011 03:27:16 +0000
+Message-Id: <E1RJzZk-0004Ud-A5 at ball.debian.org>
+From: buildd on ball <buildd at ball.debian.org>
+To: logs at buildd.debian.org,buildd-porters at ball.debian.org
+Subject: Log for successful build of bedtools_2.13.4-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RBOTj-0003bv-JI at lucatelli.debian.org>
-Date: Wed, 05 Oct 2011 10:13:31 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ball.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (mips) 05 Oct 2011 09:35 ║
+║ bedtools 2.13.4-1 (mips) 29 Oct 2011 03:04 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
+Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5816 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5868 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 [5816 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [57.1 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [103 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7555 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib mips Packages [55.3 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:12 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7555 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [55.3 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5874 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.5 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [104 kB]
+Get:8 http://ftp.de.debian.org unstable/main mips Packages [7593 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib mips Packages [55.7 kB]
+Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.de.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7596 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [55.5 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.7 kB]
-Get:18 http://incoming.debian.org Packages [271 kB]
+Get:17 http://incoming.debian.org Sources [36.2 kB]
+Get:18 http://incoming.debian.org Packages [324 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 27.8 MB in 1min 15s (369 kB/s)
+Fetched 28.0 MB in 51s (544 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 1s (628 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 1s (714 kB/s)
Download complete and in download only mode
Check arch
@@ -101,18 +100,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -124,19 +123,19 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.13-2)
+coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.2)
+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-2011-07-02-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
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 (5.12.4-5)
+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-13.11)
@@ -174,37 +173,45 @@ 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 7 not upgraded.
-Need to get 9537 kB of archives.
-After this operation, 29.4 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-3 [35.6 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.08-1 [250 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.08-1 [51.8 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-4 [142 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-4 [858 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.6-1 [1509 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-4 [415 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-4 [2025 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+0 upgraded, 21 newly installed, 0 to remove and 32 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://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-3 [35.6 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.8-1 [1565 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-5 [858 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-2 [104 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libmagic1 mips 5.09-2 [249 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main file mips 5.09-2 [51.8 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-5 [136 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 mips 1.3.2a-15 [103 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext mips 0.18.1.1-5 [2032 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:19 http://ftp.de.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9537 kB in 1s (6136 kB/s)
+Fetched 9581 kB in 1s (6315 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10545 files and directories currently installed.)
+(Reading database ... 10544 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mips.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mips.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mips.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mips.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mips.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mips.deb) ...
Selecting previously unselected package groff-base.
@@ -212,25 +219,17 @@ Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_mips.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_mips.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_mips.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.08-1_mips.deb) ...
+Unpacking file (from .../archives/file_5.09-2_mips.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mips.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mips.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mips.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_mips.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mips.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mips.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_mips.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_mips.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
@@ -245,23 +244,23 @@ Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
+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 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up 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) ...
@@ -272,11 +271,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 32 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-sb1-bcm91250a 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_1.2.0-3 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 │
@@ -286,13 +285,13 @@ Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -308,24 +307,24 @@ 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 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4/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 +337,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -603,7 +602,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -648,56 +647,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org> >../bedtools_2.13.3-1_mips.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_mips.deb'.
+ dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../bedtools_2.13.4-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-1013
+Build finished at 20111029-0327
-bedtools_2.13.3-1_mips.changes:
+bedtools_2.13.4-1_mips.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: mips
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org>
+Maintainer: Debian Build Daemon <buildd_mips-ball at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- 35a7cbc2dc148e2d205ed6360fdc59d4620d9c2b 596414 bedtools_2.13.3-1_mips.deb
+ e545407436619ad8024731ff1087ca1352c82ab5 596388 bedtools_2.13.4-1_mips.deb
Checksums-Sha256:
- a9ec77b26c39b83942ea1d7fde04876a3d35e92ca677a99864fbe1444ad14e04 596414 bedtools_2.13.3-1_mips.deb
+ 5012df456da793ae416d33afd9d28b8a4929cc09ca542280f263b45f0dbfe099 596388 bedtools_2.13.4-1_mips.deb
Files:
- c875ca9e8e4c4c8312981c08170c5494 596414 science optional bedtools_2.13.3-1_mips.deb
+ 8e2542ad9b10589c3f205b77ed0dde1f 596388 science optional bedtools_2.13.4-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_mips.deb
+bedtools_2.13.4-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 596414 bytes: control archive= 1725 bytes.
- 836 bytes, 18 lines control
+ size 596388 bytes: control archive= 1732 bytes.
+ 866 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4999
+ Installed-Size: 5008
+ 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
Section: science
@@ -712,7 +712,49 @@ bedtools_2.13.3-1_mips.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-778e4d3e-5ab4-4fae-b70e-0f59c0e4067a/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd/bedtools_2.13.3-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2011-10-29 03:25 ./
+drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 03:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 03:08 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+drwxr-xr-x root/root 0 2011-10-29 03:26 ./usr/bin/
+-rwxr-xr-x root/root 112024 2011-10-29 03:26 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 103848 2011-10-29 03:26 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 114184 2011-10-29 03:26 ./usr/bin/linksBed
+-rwxr-xr-x root/root 128600 2011-10-29 03:26 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 299084 2011-10-29 03:26 ./usr/bin/tagBam
+-rwxr-xr-x root/root 139592 2011-10-29 03:26 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 307068 2011-10-29 03:26 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 118552 2011-10-29 03:26 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 116536 2011-10-29 03:26 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 152828 2011-10-29 03:26 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 152552 2011-10-29 03:26 ./usr/bin/sortBed
+-rwxr-xr-x root/root 63960 2011-10-29 03:26 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 326540 2011-10-29 03:26 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 324412 2011-10-29 03:26 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 248076 2011-10-29 03:26 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 187048 2011-10-29 03:26 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 152956 2011-10-29 03:26 ./usr/bin/nucBed
+-rwxr-xr-x root/root 129224 2011-10-29 03:26 ./usr/bin/closestBed
+-rwxr-xr-x root/root 311532 2011-10-29 03:26 ./usr/bin/windowBed
+-rwxr-xr-x root/root 93976 2011-10-29 03:26 ./usr/bin/overlap
+-rwxr-xr-x root/root 121576 2011-10-29 03:26 ./usr/bin/flankBed
+-rwxr-xr-x root/root 244460 2011-10-29 03:26 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 120440 2011-10-29 03:26 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 378380 2011-10-29 03:26 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 114664 2011-10-29 03:26 ./usr/bin/slopBed
+-rwxr-xr-x root/root 391308 2011-10-29 03:26 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 114776 2011-10-29 03:26 ./usr/bin/complementBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -726,94 +768,86 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-778e4d3e-5ab4-4fae-b70e-0f59c0e4067a/build/buildd2-bedtools_2.13.3-1-mips-XP4hTd
+Purging /var/lib/schroot/mount/sid-mips-sbuild-8d522319-ac2d-4b70-b8ed-91a448eb589f/build/buildd-bedtools_2.13.4-1-mips-dNl1Yd
Not cleaning session: cloned chroot in use
-Can't open average time db /var/lib/sbuild/avg-build-times
-Can't open average space db /var/lib/sbuild/avg-build-space
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 102152
-Build-Time: 2052
+Build-Space: 102348
+Build-Time: 1145
Distribution: sid
-Install-Time: 74
-Job: bedtools_2.13.3-1
+Install-Time: 91
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 2248
-Source-Version: 2.13.3-1
-Space: 102152
+Package-Time: 1374
+Source-Version: 2.13.4-1
+Space: 102348
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-1013
-Build needed 00:37:28, 102152k disc space
-Signature with key 'FDFDA76A' requested:
-
-From buildd at mayer.debian.org Wed Oct 05 10:06:11 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+Finished at 20111029-0327
+Build needed 00:22:54, 102348k disc space
+Signature with key '2D578AB1' requested:
+
+From buildd at phrixos.ayous.org Sat Oct 29 04:32:47 2011
+Return-path: <buildd at phrixos.ayous.org>
+Received: from phrixos.ayous.org ([2001:a60:f006:deb:223:9eff:fe00:f7c]
+ helo=alius.ayous.org)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RBOMd-0004JL-8U
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:11 +0000
-Received: from mayer.debian.org ([140.211.166.78])
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- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RBOMc-00034a-01
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:10 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1RBOMX-0004yO-0Q
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:05 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on mipsel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at phrixos.ayous.org>)
+ id 1RK0b7-0004Vw-IW
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 04:32:47 +0000
+Received: from buildd by phrixos.ayous.org with local (Exim 4.72)
+ (envelope-from <buildd at phrixos.ayous.org>)
+ id 1RK0b5-0006uY-3C; Sat, 29 Oct 2011 04:32:43 +0000
+Date: Sat, 29 Oct 2011 04:32:43 +0000
+Message-Id: <E1RK0b5-0006uY-3C at phrixos.ayous.org>
+From: buildd on phrixos <buildd at phrixos.ayous.org>
+To: aba+buildd_phrixos at not.so.argh.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.4-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RBOMX-0004yO-0Q at mayer.debian.org>
-Date: Wed, 05 Oct 2011 10:06:05 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on phrixos.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (mipsel) 05 Oct 2011 09:44 ║
+║ bedtools 2.13.4-1 (mipsel) 29 Oct 2011 04:10 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
-Get:2 http://debian.oregonstate.edu sid/main Sources [5816 kB]
-Hit http://incoming.debian.org sid InRelease
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
+Start Time: 20111029-0410
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://mirror.ayous.org unstable InRelease [146 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Get:4 http://mirror.ayous.org unstable/main Sources [7388 kB]
Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Get:3 http://debian.oregonstate.edu sid/contrib Sources [57.1 kB]
-Get:4 http://debian.oregonstate.edu sid/main mipsel Packages [7572 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:5 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:6 http://mirror.ayous.org unstable/contrib Sources [67.7 kB]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://mirror.ayous.org unstable/non-free Sources [125 kB]
+Get:9 http://incoming.debian.org unstable/main Sources [7388 kB]
+Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9956 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [67.7 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [125 kB]
+Get:13 http://incoming.debian.org unstable/main mipsel Packages [9956 kB]
+Get:14 http://mirror.ayous.org unstable/contrib mipsel Packages [68.0 kB]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [68.0 kB]
+Get:16 http://incoming.debian.org Release [1604 B]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:17 http://incoming.debian.org Sources [43.1 kB]
+Get:18 http://incoming.debian.org Packages [515 kB]
Ign http://incoming.debian.org Translation-en
-Get:5 http://debian.oregonstate.edu sid/contrib mipsel Packages [55.6 kB]
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Fetched 13.6 MB in 27s (501 kB/s)
+Fetched 36.1 MB in 31s (1140 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -834,109 +868,147 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 1s (663 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 3s (272 kB/s)
Download complete and in download only mode
Check arch
──────────
+** Using build dependencies supplied by package:
+Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install bedtools build dependencies (internal resolver) │
+│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.13-2)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
-cdbs: already installed (0.4.99)
-debhelper: already installed (8.9.8 >= 8 is satisfied)
+Checking for already installed source dependencies...
+cdbs: missing
+debhelper: missing
+Using default version 8.9.8
quilt: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for dependency conflicts...
-Installing positive dependencies: quilt
+zlib1g-dev: missing
+Checking for source 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:
- 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:
- procmail graphviz
+ 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:
- diffstat quilt
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 21 newly installed, 0 to remove and 20 not upgraded.
+Need to get 9532 kB of archives.
+After this operation, 28.2 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 2 newly installed, 0 to remove and 12 not upgraded.
-Need to get 0 B/385 kB of archives.
-After this operation, 835 kB of additional disk space will be used.
+Fetched 9532 kB in 1s (6774 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10569 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
+Selecting previously unselected package libglib2.0-0.
+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) ...
+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.
+Unpacking file (from .../file_5.09-2_mipsel.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
Selecting previously unselected package diffstat.
-(Reading database ... 26387 files and directories currently installed.)
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.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_mipsel.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+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 (8.9.8) ...
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 12 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 dh-buildinfo_0.9 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 docutils-common_0.8.1-3 doxygen_1.7.4-4 doxygen-latex_1.7.4-4 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 ed_1.5-3 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-3 gfortran-4.6_4.6.1-13 ghostscript_9.02~dfsg-3 gnupg_1.4.11-3 gperf_3.0.3-1+b1 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gs-cjk-resource_1.20100103-2 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 latex-xcolor_2.11-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libaudio2_1.9.2-9 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common3_0.6.30-5 libblas3gf_1.2.20110419-2 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcnf-dev_4.0-2 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libcups2_1.5.0-8 libcupsimage2_1.5.0-8 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-13 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgs9_9.02~dfsg-3 libgs9-common_9.02~dfsg-3 libgssapi-krb5-2_1.9.1+dfsg-3 libice6_2:1.0.7-2 libidn11_1.22-3 libijs-0.35_0.35-8 libjasper1_1.900.1-10 libjbig2dec0_0.11-1 libjpeg62_6b1-2 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkpathsea5_2009-11 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1+b1 libltdl-dev_2.4-4 libltdl7_2.4-4 liblua5.1-0_5.1.4-10 liblua5.1-0-dev_5.1.4-10 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-2 libodbc1_2.2.14p2-3 libodbcinstq1c2_2.2.14p2-3 libopenjpeg2_1.3+dfsg-4 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpoppler13_0.16.7-2+b1 libpopt-dev_1.16-1 libpopt0_1.16-1 libpython2.7_2.7.2-5 libqt3-mt_3:3.3.8b-11 libreadline-dev_6.2-4 libreadline6_6.2-4 libreadline6-dev_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm6_2:1.2.0-2 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-07-02-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtasn1-3_2.9-4 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libtut-dev_0.0.20070706-1 libudev0_172-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb1_1.7-3 libxcursor1_1:1.1.12-1 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxft2_2.2.0-3 libxi6_2:1.4.3-3 libxinerama1_2:1.1.1-3 libxml2_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxpm4_1:3.5.9-1 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.6-2 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 luatex_0.70.1-1+b1 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 odbcinst_2.2.14p2-3 odbcinst1debian2_2.2.14p2-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 preview-latex-style_11.86-4 procps_1:3.2.8-11 python_2.7.2-7 python-central_0.6.17 python-dev_2.7.2-7 python-docutils_0.8.1-3 python-minimal_2.7.2-7 python-numpy_1:1.5.1-2+b1 python-roman_0.8.1-3 python-support_1.0.14 python2.7_2.7.2-5 python2.7-dev_2.7.2-5 python2.7-minimal_2.7.2-5 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 swig_2.0.4-4 swig2.0_2.0.4-4 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tex-common_2.10 texlive-base_2009-14 texlive-binaries_2009-11 texlive-common_2009-14 texlive-doc-base_2009-2 texlive-extra-utils_2009-10 texlive-font-utils_2009-10 texlive-latex-base_2009-14 texlive-latex-extra_2009-10 texlive-latex-recommended_2009-14 texlive-pictures_2009-14 ttf-dejavu-core_2.33-2 tzdata_2011k-1 ucf_3.0025+nmu2 udev_172-1 unixodbc_2.2.14p2-3 unixodbc-dev_2.2.14p2-3 util-linux_2.19.1-5 x11-common_1:7.6+9 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Checking correctness of source dependencies...
+Kernel: Linux 2.6.36-rc6-loongson-2f mipsel (mips64)
+Toolchain package versions: libc6-dev_2.13-21 dpkg-dev_1.16.1.1 linux-libc-dev_3.0.0-5 gcc-4.6_4.6.1-15 g++-4.6_4.6.1-15 binutils_2.21.90.20111004-2 libstdc++6-4.6-dev_4.6.1-15 libstdc++6_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_2.21.90.20111004-2 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-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_1:3.0-1 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 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_1.2.0-3 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 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -946,13 +1018,14 @@ Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
+dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -962,30 +1035,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
dpkg-buildpackage: host architecture mipsel
- fakeroot debian/rules clean
+ /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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+/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_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -998,21 +1066,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+/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_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -1030,7 +1098,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -1090,10 +1158,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -1263,10 +1327,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- fakeroot debian/rules binary-arch
+ /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -1296,7 +1360,6 @@ dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
dh_link -pbedtools
-dh_buildinfo -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
@@ -1309,57 +1372,58 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.13.3-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org> >../bedtools_2.13.4-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-1005
+Build finished at 20111029-0432
-bedtools_2.13.3-1_mipsel.changes:
+bedtools_2.13.4-1_mipsel.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
+Maintainer: mipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- 70a401adf167a606f58bc85ca0ea18b6b9363498 629960 bedtools_2.13.3-1_mipsel.deb
+ fccac36642ee6d1d37fae42e017baea1bafbaf28 629804 bedtools_2.13.4-1_mipsel.deb
Checksums-Sha256:
- d67904e6bc4035d5261c3dd4f42b6d92f00add1b96f581a8debbc20697ff8b7e 629960 bedtools_2.13.3-1_mipsel.deb
+ d9186686420740adbd60f662f729c891bb225bc438982cd59044dc33143c130c 629804 bedtools_2.13.4-1_mipsel.deb
Files:
- 592b28403eb5b89cceb2eb041fb710e8 629960 science optional bedtools_2.13.3-1_mipsel.deb
+ 171d817f4b1fe188910778259ae8b95c 629804 science optional bedtools_2.13.4-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_mipsel.deb
+bedtools_2.13.4-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 629960 bytes: control archive= 1751 bytes.
- 838 bytes, 18 lines control
- 2095 bytes, 36 lines md5sums
+ size 629804 bytes: control archive= 1736 bytes.
+ 866 bytes, 19 lines control
+ 2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5000
- Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 5005
+ 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
Section: science
Priority: optional
@@ -1373,7 +1437,49 @@ bedtools_2.13.3-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools_2.13.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 04:12 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/bin/
+-rwxr-xr-x root/root 116424 2011-10-29 04:31 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 299084 2011-10-29 04:31 ./usr/bin/tagBam
+-rwxr-xr-x root/root 378380 2011-10-29 04:31 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 93944 2011-10-29 04:31 ./usr/bin/overlap
+-rwxr-xr-x root/root 128600 2011-10-29 04:31 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 120104 2011-10-29 04:31 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 114776 2011-10-29 04:31 ./usr/bin/complementBed
+-rwxr-xr-x root/root 248076 2011-10-29 04:31 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121272 2011-10-29 04:31 ./usr/bin/flankBed
+-rwxr-xr-x root/root 118552 2011-10-29 04:31 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 139592 2011-10-29 04:31 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 128696 2011-10-29 04:31 ./usr/bin/closestBed
+-rwxr-xr-x root/root 390940 2011-10-29 04:31 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 103784 2011-10-29 04:31 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 311532 2011-10-29 04:31 ./usr/bin/windowBed
+-rwxr-xr-x root/root 186888 2011-10-29 04:31 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 326540 2011-10-29 04:31 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 111928 2011-10-29 04:31 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 63960 2011-10-29 04:31 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 152876 2011-10-29 04:31 ./usr/bin/nucBed
+-rwxr-xr-x root/root 114664 2011-10-29 04:31 ./usr/bin/slopBed
+-rwxr-xr-x root/root 306972 2011-10-29 04:31 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 152828 2011-10-29 04:31 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 152104 2011-10-29 04:31 ./usr/bin/sortBed
+-rwxr-xr-x root/root 114184 2011-10-29 04:31 ./usr/bin/linksBed
+-rwxr-xr-x root/root 324412 2011-10-29 04:31 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 244460 2011-10-29 04:31 ./usr/bin/bamToBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1382,47 +1488,9 @@ dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464
Built successfully
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- diffstat* quilt*
-0 upgraded, 0 newly installed, 2 to remove and 12 not upgraded.
-After this operation, 835 kB disk space will be freed.
-(Reading database ... 26467 files and directories currently installed.)
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Processing triggers for man-db ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: mipsel
-Build-Space: 102184
-Build-Time: 1168
-Distribution: sid
-Install-Time: 33
-Job: bedtools_2.13.3-1
-Package: bedtools
-Package-Time: 1264
-Source-Version: 2.13.3-1
-Space: 102184
-Status: successful
-Version: 2.13.3-1
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-1005
-Build needed 00:21:04, 102184k disc space
-Signature with key 'A5633F94' requested:
+Finished at 20111029-0432
+Build needed 00:22:23, 101932k disc space
diff --git a/mipsel.log b/mipsel.log
index e36fd63..52648a6 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,65 +1,59 @@
-From buildd at mayer.debian.org Wed Oct 05 10:06:11 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+From buildd at phrixos.ayous.org Sat Oct 29 04:32:47 2011
+Return-path: <buildd at phrixos.ayous.org>
+Received: from phrixos.ayous.org ([2001:a60:f006:deb:223:9eff:fe00:f7c]
+ helo=alius.ayous.org)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RBOMd-0004JL-8U
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:11 +0000
-Received: from mayer.debian.org ([140.211.166.78])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RBOMc-00034a-01
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:10 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1RBOMX-0004yO-0Q
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:06:05 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on mipsel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at phrixos.ayous.org>)
+ id 1RK0b7-0004Vw-IW
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 04:32:47 +0000
+Received: from buildd by phrixos.ayous.org with local (Exim 4.72)
+ (envelope-from <buildd at phrixos.ayous.org>)
+ id 1RK0b5-0006uY-3C; Sat, 29 Oct 2011 04:32:43 +0000
+Date: Sat, 29 Oct 2011 04:32:43 +0000
+Message-Id: <E1RK0b5-0006uY-3C at phrixos.ayous.org>
+From: buildd on phrixos <buildd at phrixos.ayous.org>
+To: aba+buildd_phrixos at not.so.argh.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.4-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RBOMX-0004yO-0Q at mayer.debian.org>
-Date: Wed, 05 Oct 2011 10:06:05 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on phrixos.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (mipsel) 05 Oct 2011 09:44 ║
+║ bedtools 2.13.4-1 (mipsel) 29 Oct 2011 04:10 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
-Get:2 http://debian.oregonstate.edu sid/main Sources [5816 kB]
-Hit http://incoming.debian.org sid InRelease
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
+Start Time: 20111029-0410
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://mirror.ayous.org unstable InRelease [146 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:3 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Get:4 http://mirror.ayous.org unstable/main Sources [7388 kB]
Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Get:3 http://debian.oregonstate.edu sid/contrib Sources [57.1 kB]
-Get:4 http://debian.oregonstate.edu sid/main mipsel Packages [7572 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:5 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:6 http://mirror.ayous.org unstable/contrib Sources [67.7 kB]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://mirror.ayous.org unstable/non-free Sources [125 kB]
+Get:9 http://incoming.debian.org unstable/main Sources [7388 kB]
+Get:10 http://mirror.ayous.org unstable/main mipsel Packages [9956 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [67.7 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [125 kB]
+Get:13 http://incoming.debian.org unstable/main mipsel Packages [9956 kB]
+Get:14 http://mirror.ayous.org unstable/contrib mipsel Packages [68.0 kB]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [68.0 kB]
+Get:16 http://incoming.debian.org Release [1604 B]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:17 http://incoming.debian.org Sources [43.1 kB]
+Get:18 http://incoming.debian.org Packages [515 kB]
Ign http://incoming.debian.org Translation-en
-Get:5 http://debian.oregonstate.edu sid/contrib mipsel Packages [55.6 kB]
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Fetched 13.6 MB in 27s (501 kB/s)
+Fetched 36.1 MB in 31s (1140 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,109 +74,147 @@ 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 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 1s (663 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 3s (272 kB/s)
Download complete and in download only mode
Check arch
──────────
+** Using build dependencies supplied by package:
+Build-Depends: cdbs, debhelper (>= 8), quilt, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
+│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install bedtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), cdbs, debhelper (>= 8), quilt, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.13-2)
-dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-21)
-gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
-cdbs: already installed (0.4.99)
-debhelper: already installed (8.9.8 >= 8 is satisfied)
+Checking for already installed source dependencies...
+cdbs: missing
+debhelper: missing
+Using default version 8.9.8
quilt: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for dependency conflicts...
-Installing positive dependencies: quilt
+zlib1g-dev: missing
+Checking for source 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:
- 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:
- procmail graphviz
+ 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:
- diffstat quilt
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 21 newly installed, 0 to remove and 20 not upgraded.
+Need to get 9532 kB of archives.
+After this operation, 28.2 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-2 [986 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 2 newly installed, 0 to remove and 12 not upgraded.
-Need to get 0 B/385 kB of archives.
-After this operation, 835 kB of additional disk space will be used.
+Fetched 9532 kB in 1s (6774 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10569 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
+Selecting previously unselected package libglib2.0-0.
+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) ...
+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.
+Unpacking file (from .../file_5.09-2_mipsel.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_mipsel.deb) ...
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.99_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_mipsel.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.8_all.deb) ...
Selecting previously unselected package diffstat.
-(Reading database ... 26387 files and directories currently installed.)
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.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_mipsel.deb) ...
+Setting up libpipeline1 (1.2.0-3) ...
+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 (8.9.8) ...
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 12 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 dh-buildinfo_0.9 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 docutils-common_0.8.1-3 doxygen_1.7.4-4 doxygen-latex_1.7.4-4 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 ed_1.5-3 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-3 gfortran-4.6_4.6.1-13 ghostscript_9.02~dfsg-3 gnupg_1.4.11-3 gperf_3.0.3-1+b1 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gs-cjk-resource_1.20100103-2 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 latex-xcolor_2.11-1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libaudio2_1.9.2-9 libavahi-client3_0.6.30-5 libavahi-common-data_0.6.30-5 libavahi-common3_0.6.30-5 libblas3gf_1.2.20110419-2 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcnf-dev_4.0-2 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libcups2_1.5.0-8 libcupsimage2_1.5.0-8 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-13 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgnutls26_2.12.11-1 libgomp1_4.6.1-13 libgpg-error0_1.10-1 libgs9_9.02~dfsg-3 libgs9-common_9.02~dfsg-3 libgssapi-krb5-2_1.9.1+dfsg-3 libice6_2:1.0.7-2 libidn11_1.22-3 libijs-0.35_0.35-8 libjasper1_1.900.1-10 libjbig2dec0_0.11-1 libjpeg62_6b1-2 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkpathsea5_2009-11 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblapack3gf_3.3.1-1 liblcms1_1.19.dfsg-1+b1 libltdl-dev_2.4-4 libltdl7_2.4-4 liblua5.1-0_5.1.4-10 liblua5.1-0-dev_5.1.4-10 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-2 libncurses5-dev_5.9-2 libncursesw5_5.9-2 libodbc1_2.2.14p2-3 libodbcinstq1c2_2.2.14p2-3 libopenjpeg2_1.3+dfsg-4 libp11-kit0_0.7-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpoppler13_0.16.7-2+b1 libpopt-dev_1.16-1 libpopt0_1.16-1 libpython2.7_2.7.2-5 libqt3-mt_3:3.3.8b-11 libreadline-dev_6.2-4 libreadline6_6.2-4 libreadline6-dev_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libsm6_2:1.2.0-2 libsqlite3-0_3.7.8-1 libss2_1.42~WIP-2011-07-02-1 libssl-dev_1.0.0e-2 libssl1.0.0_1.0.0e-2 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtasn1-3_2.9-4 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-2 libtinfo5_5.9-2 libtut-dev_0.0.20070706-1 libudev0_172-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libx11-6_2:1.4.4-2 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-3 libxaw7_2:1.0.9-2 libxcb1_1.7-3 libxcursor1_1:1.1.12-1 libxdmcp6_1:1.1.0-3 libxext6_2:1.3.0-3 libxfixes3_1:5.0-4 libxft2_2.2.0-3 libxi6_2:1.4.3-3 libxinerama1_2:1.1.1-3 libxml2_2.7.8.dfsg-4 libxmu6_2:1.1.0-2 libxpm4_1:3.5.9-1 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.6-2 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 luatex_0.70.1-1+b1 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 odbcinst_2.2.14p2-3 odbcinst1debian2_2.2.14p2-3 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 preview-latex-style_11.86-4 procps_1:3.2.8-11 python_2.7.2-7 python-central_0.6.17 python-dev_2.7.2-7 python-docutils_0.8.1-3 python-minimal_2.7.2-7 python-numpy_1:1.5.1-2+b1 python-roman_0.8.1-3 python-support_1.0.14 python2.7_2.7.2-5 python2.7-dev_2.7.2-5 python2.7-minimal_2.7.2-5 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 swig_2.0.4-4 swig2.0_2.0.4-4 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tex-common_2.10 texlive-base_2009-14 texlive-binaries_2009-11 texlive-common_2009-14 texlive-doc-base_2009-2 texlive-extra-utils_2009-10 texlive-font-utils_2009-10 texlive-latex-base_2009-14 texlive-latex-extra_2009-10 texlive-latex-recommended_2009-14 texlive-pictures_2009-14 ttf-dejavu-core_2.33-2 tzdata_2011k-1 ucf_3.0025+nmu2 udev_172-1 unixodbc_2.2.14p2-3 unixodbc-dev_2.2.14p2-3 util-linux_2.19.1-5 x11-common_1:7.6+9 xml-core_0.13 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Checking correctness of source dependencies...
+Kernel: Linux 2.6.36-rc6-loongson-2f mipsel (mips64)
+Toolchain package versions: libc6-dev_2.13-21 dpkg-dev_1.16.1.1 linux-libc-dev_3.0.0-5 gcc-4.6_4.6.1-15 g++-4.6_4.6.1-15 binutils_2.21.90.20111004-2 libstdc++6-4.6-dev_4.6.1-15 libstdc++6_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_2.21.90.20111004-2 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-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_1:3.0-1 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 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_1.2.0-3 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 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -192,13 +224,14 @@ Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
+dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -208,30 +241,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
dpkg-buildpackage: host architecture mipsel
- fakeroot debian/rules clean
+ /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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+/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_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/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 +272,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
+/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_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -276,7 +304,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -336,10 +364,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -509,10 +533,10 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
- fakeroot debian/rules binary-arch
+ /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -542,7 +566,6 @@ dh_lintian -pbedtools
dh_bugfiles -pbedtools
dh_install -pbedtools
dh_link -pbedtools
-dh_buildinfo -pbedtools
dh_installmime -pbedtools
dh_installgsettings -pbedtools
dh_strip -pbedtools
@@ -555,57 +578,58 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bedtools_2.13.3-1_mipsel.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org> >../bedtools_2.13.4-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-1005
+Build finished at 20111029-0432
-bedtools_2.13.3-1_mipsel.changes:
+bedtools_2.13.4-1_mipsel.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: mipsel
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
+Maintainer: mipsel Build Daemon (phrixos) <buildd_mipsel-phrixos at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- 70a401adf167a606f58bc85ca0ea18b6b9363498 629960 bedtools_2.13.3-1_mipsel.deb
+ fccac36642ee6d1d37fae42e017baea1bafbaf28 629804 bedtools_2.13.4-1_mipsel.deb
Checksums-Sha256:
- d67904e6bc4035d5261c3dd4f42b6d92f00add1b96f581a8debbc20697ff8b7e 629960 bedtools_2.13.3-1_mipsel.deb
+ d9186686420740adbd60f662f729c891bb225bc438982cd59044dc33143c130c 629804 bedtools_2.13.4-1_mipsel.deb
Files:
- 592b28403eb5b89cceb2eb041fb710e8 629960 science optional bedtools_2.13.3-1_mipsel.deb
+ 171d817f4b1fe188910778259ae8b95c 629804 science optional bedtools_2.13.4-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_mipsel.deb
+bedtools_2.13.4-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 629960 bytes: control archive= 1751 bytes.
- 838 bytes, 18 lines control
- 2095 bytes, 36 lines md5sums
+ size 629804 bytes: control archive= 1736 bytes.
+ 866 bytes, 19 lines control
+ 2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 5000
- Depends: libc6 (>= 2.3.4), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), zlib1g (>= 1:1.1.4)
+ Installed-Size: 5005
+ 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
Section: science
Priority: optional
@@ -619,7 +643,49 @@ bedtools_2.13.3-1_mipsel.deb
.
The groupBy utility is distribued in the filo package.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM/bedtools_2.13.3-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 04:12 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 04:31 ./usr/bin/
+-rwxr-xr-x root/root 116424 2011-10-29 04:31 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 299084 2011-10-29 04:31 ./usr/bin/tagBam
+-rwxr-xr-x root/root 378380 2011-10-29 04:31 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 93944 2011-10-29 04:31 ./usr/bin/overlap
+-rwxr-xr-x root/root 128600 2011-10-29 04:31 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 120104 2011-10-29 04:31 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 114776 2011-10-29 04:31 ./usr/bin/complementBed
+-rwxr-xr-x root/root 248076 2011-10-29 04:31 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 121272 2011-10-29 04:31 ./usr/bin/flankBed
+-rwxr-xr-x root/root 118552 2011-10-29 04:31 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 139592 2011-10-29 04:31 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 128696 2011-10-29 04:31 ./usr/bin/closestBed
+-rwxr-xr-x root/root 390940 2011-10-29 04:31 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 103784 2011-10-29 04:31 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 311532 2011-10-29 04:31 ./usr/bin/windowBed
+-rwxr-xr-x root/root 186888 2011-10-29 04:31 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 326540 2011-10-29 04:31 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 111928 2011-10-29 04:31 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 63960 2011-10-29 04:31 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 152876 2011-10-29 04:31 ./usr/bin/nucBed
+-rwxr-xr-x root/root 114664 2011-10-29 04:31 ./usr/bin/slopBed
+-rwxr-xr-x root/root 306972 2011-10-29 04:31 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 152828 2011-10-29 04:31 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 152104 2011-10-29 04:31 ./usr/bin/sortBed
+-rwxr-xr-x root/root 114184 2011-10-29 04:31 ./usr/bin/linksBed
+-rwxr-xr-x root/root 324412 2011-10-29 04:31 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 244460 2011-10-29 04:31 ./usr/bin/bamToBed
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -628,47 +694,9 @@ dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464
Built successfully
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-8c9248b3-89ee-4e22-b464-96dd4dc502fb/build/buildd-bedtools_2.13.3-1-mipsel-EOYlXM
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- diffstat* quilt*
-0 upgraded, 0 newly installed, 2 to remove and 12 not upgraded.
-After this operation, 835 kB disk space will be freed.
-(Reading database ... 26467 files and directories currently installed.)
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Processing triggers for man-db ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: mipsel
-Build-Space: 102184
-Build-Time: 1168
-Distribution: sid
-Install-Time: 33
-Job: bedtools_2.13.3-1
-Package: bedtools
-Package-Time: 1264
-Source-Version: 2.13.3-1
-Space: 102184
-Status: successful
-Version: 2.13.3-1
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-30419245-bcd1-4c75-8da2-a8d7e08091c4/build/buildd-bedtools_2.13.4-1-mipsel-yZbvCk
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-1005
-Build needed 00:21:04, 102184k disc space
-Signature with key 'A5633F94' requested:
+Finished at 20111029-0432
+Build needed 00:22:23, 101932k disc space
diff --git a/powerpc.log b/powerpc.log
index 5552de0..15abb42 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,68 @@
-From buildd at porpora.debian.org Wed Oct 05 09:41:50 2011
-Return-path: <buildd at porpora.debian.org>
+From buildd at praetorius.debian.org Sat Oct 29 03:09:55 2011
+Return-path: <buildd at praetorius.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1RBNz4-0007iQ-GN
- for logs at buildd.debian.org; Wed, 05 Oct 2011 09:41:50 +0000
-Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
- helo=porpora.debian.org)
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1RJzIx-0001GN-D5
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 03:09:55 +0000
+Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
+ (helo=praetorius.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
+ CN=praetorius.debian.org,
+ EMAIL=hostmaster at praetorius.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1RBNz3-0001xK-Go; Wed, 05 Oct 2011 09:41:49 +0000
-Received: from buildd by porpora.debian.org with local (Exim 4.72)
- (envelope-from <buildd at porpora.debian.org>)
- id 1RBNz1-00017M-G5; Wed, 05 Oct 2011 09:41:47 +0000
-Message-Id: <E1RBNz1-00017M-G5 at porpora.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 5 Oct 2011 09:41:47 +0000
-From: buildd on porpora <buildd at porpora.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on powerpc (dist=sid)
-Key-Id: 6CB21D9F
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1RJzIw-0007kP-Hw; Sat, 29 Oct 2011 03:09:54 +0000
+Received: from buildd by praetorius.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at praetorius.debian.org>)
+ id 1RJzIv-0006eJ-Qt; Sat, 29 Oct 2011 03:09:53 +0000
+Date: Sat, 29 Oct 2011 03:09:53 +0000
+Message-Id: <E1RJzIv-0006eJ-Qt at praetorius.debian.org>
+From: buildd on praetorius <buildd at praetorius.debian.org>
+To: wouter at debian.org,logs at buildd.debian.org
+Subject: Log for successful build of bedtools_2.13.4-1 on powerpc (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (powerpc) 05 Oct 2011 09:35 ║
+║ bedtools 2.13.4-1 (powerpc) 29 Oct 2011 03:03 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5815 kB]
-Get:4 http://ftp.uk.debian.org unstable/contrib Sources [57.1 kB]
-Get:5 http://ftp.uk.debian.org unstable/non-free Sources [104 kB]
-Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [7638 kB]
+Get:1 http://ftp.se.debian.org unstable InRelease [146 kB]
+Get:2 http://ftp.se.debian.org unstable/main Sources [5868 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:4 http://ftp.se.debian.org unstable/contrib Sources [56.5 kB]
+Get:5 http://ftp.se.debian.org unstable/non-free Sources [104 kB]
+Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [7698 kB]
+Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [55.4 kB]
+Ign http://ftp.se.debian.org unstable/contrib TranslationIndex
+Get:8 http://ftp.se.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.se.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5816 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.0 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7638 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.0 kB]
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [5874 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7699 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.2 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 [36.7 kB]
-Get:18 http://incoming.debian.org Packages [271 kB]
+Get:17 http://incoming.debian.org Sources [36.2 kB]
+Get:18 http://incoming.debian.org Packages [324 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 27.9 MB in 22s (1228 kB/s)
+Fetched 28.2 MB in 17s (1652 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 1s (536 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 1s (536 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +107,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 42 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 42 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -135,8 +134,8 @@ findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -175,37 +174,45 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 12 not upgraded.
-Need to get 9691 kB of archives.
-After this operation, 29.0 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-3 [37.2 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.08-1 [253 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.08-1 [51.9 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-4 [134 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-4 [837 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.6-1 [1611 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-4 [422 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-4 [2032 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+0 upgraded, 21 newly installed, 0 to remove and 42 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.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-3 [37.2 kB]
+Get:2 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
+Get:3 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
+Get:4 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
+Get:5 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
+Get:6 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:7 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
+Get:8 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
+Get:9 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
+Get:10 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
+Get:11 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
+Get:12 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
+Get:13 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:15 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
+Get:16 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:17 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:18 http://ftp.se.debian.org/debian/ unstable/main debhelper all 8.9.8 [552 kB]
+Get:19 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
+Get:20 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
+Get:21 http://ftp.se.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9691 kB in 1s (6358 kB/s)
+Fetched 9676 kB in 1s (8750 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10782 files and directories currently installed.)
+(Reading database ... 10788 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_powerpc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_powerpc.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_powerpc.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_powerpc.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_powerpc.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_powerpc.deb) ...
Selecting previously unselected package groff-base.
@@ -213,25 +220,17 @@ Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_powerpc.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_powerpc.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_powerpc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.08-1_powerpc.deb) ...
+Unpacking file (from .../file_5.09-2_powerpc.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_powerpc.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_powerpc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_powerpc.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_powerpc.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_powerpc.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_powerpc.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_powerpc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_powerpc.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
@@ -246,23 +245,23 @@ Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
+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 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up 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) ...
@@ -273,11 +272,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 42 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-09-25-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-25-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.5-1 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.09-2 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-2011-09-25-1 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 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_3.0.1-6 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-25-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 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_3.0.0-4 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_5.12.4-5 perl-base_5.12.4-5 perl-modules_5.12.4-5 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -288,12 +287,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -309,24 +308,24 @@ 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 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4/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 +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_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -604,7 +603,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -649,56 +648,57 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bedtools_2.13.3-1_powerpc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../bedtools_2.13.4-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-0941
+Build finished at 20111029-0309
-bedtools_2.13.3-1_powerpc.changes:
+bedtools_2.13.4-1_powerpc.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: powerpc
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
+Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- 4452933abda5cd318820804da673cbcb6ecac8ab 594494 bedtools_2.13.3-1_powerpc.deb
+ 530eb4bd481acaea490f723825e54eeee9f98404 593104 bedtools_2.13.4-1_powerpc.deb
Checksums-Sha256:
- e8999dfb8da086be7ea85c2a3f8d9dd365869dba7769e36f957e7fb8ca89b849 594494 bedtools_2.13.3-1_powerpc.deb
+ 9817df66bc57db8e4564d0df33e00a01fe307d0e2cf34605c4b557243721314d 593104 bedtools_2.13.4-1_powerpc.deb
Files:
- 589ac7c0e911a19e9d94e25885309acc 594494 science optional bedtools_2.13.3-1_powerpc.deb
+ b7442900d5145a744cfc9457688086b9 593104 science optional bedtools_2.13.4-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_powerpc.deb
+bedtools_2.13.4-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 594494 bytes: control archive= 1718 bytes.
- 837 bytes, 18 lines control
+ size 593104 bytes: control archive= 1731 bytes.
+ 867 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4834
+ Installed-Size: 4841
+ 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
Section: science
@@ -713,49 +713,49 @@ bedtools_2.13.3-1_powerpc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/bin/
--rwxr-xr-x root/root 149868 2011-10-05 09:41 ./usr/bin/nucBed
--rwxr-xr-x root/root 363104 2011-10-05 09:41 ./usr/bin/intersectBed
--rwxr-xr-x root/root 113332 2011-10-05 09:41 ./usr/bin/mergeBed
--rwxr-xr-x root/root 145636 2011-10-05 09:41 ./usr/bin/sortBed
--rwxr-xr-x root/root 240116 2011-10-05 09:41 ./usr/bin/bedToBam
--rwxr-xr-x root/root 122484 2011-10-05 09:41 ./usr/bin/closestBed
--rwxr-xr-x root/root 313952 2011-10-05 09:41 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 108772 2011-10-05 09:41 ./usr/bin/annotateBed
--rwxr-xr-x root/root 149860 2011-10-05 09:41 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 110972 2011-10-05 09:41 ./usr/bin/complementBed
--rwxr-xr-x root/root 375408 2011-10-05 09:41 ./usr/bin/pairToBed
--rwxr-xr-x root/root 297552 2011-10-05 09:41 ./usr/bin/coverageBed
--rwxr-xr-x root/root 100652 2011-10-05 09:41 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 109684 2011-10-05 09:41 ./usr/bin/linksBed
--rwxr-xr-x root/root 110324 2011-10-05 09:41 ./usr/bin/slopBed
--rwxr-xr-x root/root 115364 2011-10-05 09:41 ./usr/bin/subtractBed
--rwxr-xr-x root/root 301656 2011-10-05 09:41 ./usr/bin/windowBed
--rwxr-xr-x root/root 232804 2011-10-05 09:41 ./usr/bin/bamToBed
--rwxr-xr-x root/root 289608 2011-10-05 09:41 ./usr/bin/tagBam
--rwxr-xr-x root/root 133724 2011-10-05 09:41 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 63772 2011-10-05 09:41 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 174836 2011-10-05 09:41 ./usr/bin/pairToPair
--rwxr-xr-x root/root 125204 2011-10-05 09:41 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 318048 2011-10-05 09:41 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 117412 2011-10-05 09:41 ./usr/bin/flankBed
--rwxr-xr-x root/root 113948 2011-10-05 09:41 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 92620 2011-10-05 09:41 ./usr/bin/overlap
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 09:36 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 09:41 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 03:09 ./
+drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/bin/
+-rwxr-xr-x root/root 363104 2011-10-29 03:09 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 113948 2011-10-29 03:09 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 149868 2011-10-29 03:09 ./usr/bin/nucBed
+-rwxr-xr-x root/root 63772 2011-10-29 03:09 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 133724 2011-10-29 03:09 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 125204 2011-10-29 03:09 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 113332 2011-10-29 03:09 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 301656 2011-10-29 03:09 ./usr/bin/windowBed
+-rwxr-xr-x root/root 92620 2011-10-29 03:09 ./usr/bin/overlap
+-rwxr-xr-x root/root 108772 2011-10-29 03:09 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 235964 2011-10-29 03:09 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 100652 2011-10-29 03:09 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 375408 2011-10-29 03:09 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 149860 2011-10-29 03:09 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 110972 2011-10-29 03:09 ./usr/bin/complementBed
+-rwxr-xr-x root/root 125164 2011-10-29 03:09 ./usr/bin/closestBed
+-rwxr-xr-x root/root 297552 2011-10-29 03:09 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 110324 2011-10-29 03:09 ./usr/bin/slopBed
+-rwxr-xr-x root/root 174836 2011-10-29 03:09 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 318048 2011-10-29 03:09 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 240116 2011-10-29 03:09 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 314808 2011-10-29 03:09 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 109684 2011-10-29 03:09 ./usr/bin/linksBed
+-rwxr-xr-x root/root 145636 2011-10-29 03:09 ./usr/bin/sortBed
+-rwxr-xr-x root/root 115364 2011-10-29 03:09 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 117412 2011-10-29 03:09 ./usr/bin/flankBed
+-rwxr-xr-x root/root 289608 2011-10-29 03:09 ./usr/bin/tagBam
+drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+drwxr-xr-x root/root 0 2011-10-29 03:09 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 03:05 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -769,7 +769,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-2854bbaa-0a5c-40ef-88cf-9869c9042605/build/buildd-bedtools_2.13.3-1-powerpc-aWJ_0J
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-9ccd0ef2-1517-4631-b157-0cb77cbfd890/build/buildd-bedtools_2.13.4-1-powerpc-_pjTlX
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -777,18 +777,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 105056
-Build-Time: 302
+Build-Space: 105208
+Build-Time: 261
Distribution: sid
-Install-Time: 42
-Job: bedtools_2.13.3-1
+Install-Time: 61
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 383
-Source-Version: 2.13.3-1
-Space: 105056
+Package-Time: 364
+Source-Version: 2.13.4-1
+Space: 105208
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-0941
-Build needed 00:06:23, 105056k disc space
-Signature with key '6CB21D9F' requested:
+Finished at 20111029-0309
+Build needed 00:06:04, 105208k disc space
+
diff --git a/s390.log b/s390.log
index 4070110..881a391 100644
--- a/s390.log
+++ b/s390.log
@@ -1,69 +1,69 @@
-From buildd at zandonai.debian.org Wed Oct 05 10:37:52 2011
+From buildd at zandonai.debian.org Sat Oct 29 04:48:27 2011
Return-path: <buildd at zandonai.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 zandonai.debian.org>)
- id 1RBOrI-00026m-Rb
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:37:52 +0000
+ id 1RK0qJ-0006yN-D1
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 04:48:27 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ 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 1RBOrI-0004F4-6l; Wed, 05 Oct 2011 10:37:52 +0000
+ id 1RK0qI-00036v-JB; Sat, 29 Oct 2011 04:48:26 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1RBOrH-0002Jl-Nr; Wed, 05 Oct 2011 10:37:51 +0000
-Message-Id: <E1RBOrH-0002Jl-Nr at zandonai.debian.org>
+ id 1RK0qI-0006qI-9M; Sat, 29 Oct 2011 04:48:26 +0000
+Message-Id: <E1RK0qI-0006qI-9M 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: Wed, 5 Oct 2011 10:37:51 +0000
+Date: Sat, 29 Oct 2011 04:48:26 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on s390 (dist=sid)
+Subject: Log for successful build of bedtools_2.13.4-1 on s390 (dist=sid)
Key-Id: 2D941D26
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (s390) 05 Oct 2011 10:33 ║
+║ bedtools 2.13.4-1 (s390) 29 Oct 2011 04:44 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
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 [5816 kB]
+Get:2 http://ftp.de.debian.org unstable/main Sources [5874 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 [5816 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [57.1 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [103 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7557 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.0 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5874 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [56.5 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [104 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7610 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.2 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7557 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.0 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7610 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.2 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 [36.2 kB]
-Get:18 http://incoming.debian.org Packages [277 kB]
+Get:17 http://incoming.debian.org Sources [37.0 kB]
+Get:18 http://incoming.debian.org Packages [332 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 27.8 MB in 30s (908 kB/s)
+Fetched 28.1 MB in 24s (1137 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 1s (348 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 2s (461 kB/s)
Download complete and in download only mode
Check arch
@@ -102,18 +102,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -125,19 +125,19 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.13-2)
+coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.2)
+debianutils: already installed (4.0.3)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-09-25-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-05-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-5)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.11)
@@ -175,24 +175,24 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 21 newly installed, 0 to remove and 17 not upgraded.
-Need to get 9823 kB of archives.
-After this operation, 28.8 MB of additional disk space will be used.
+0 upgraded, 21 newly installed, 0 to remove and 40 not upgraded.
+Need to get 9864 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 1.2.0-3 [39.0 kB]
Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-2 [1029 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.08-1 [255 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main file s390 5.08-1 [52.2 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-4 [143 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-4 [879 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.6-1 [1639 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-4 [431 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-4 [2073 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]
@@ -200,12 +200,20 @@ Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4
Get:20 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9823 kB in 6s (1414 kB/s)
+Fetched 9864 kB in 2s (3441 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10624 files and directories currently installed.)
+(Reading database ... 10631 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_s390.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_s390.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_s390.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_s390.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_s390.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390.deb) ...
Selecting previously unselected package groff-base.
@@ -213,25 +221,17 @@ Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_s390.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_s390.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_s390.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.08-1_s390.deb) ...
+Unpacking file (from .../archives/file_5.09-2_s390.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_s390.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_s390.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_s390.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_s390.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_s390.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_s390.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_s390.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_s390.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
@@ -246,23 +246,23 @@ Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
+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 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up 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) ...
@@ -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 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-09-25-1 e2fsprogs_1.42~WIP-2011-09-25-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-09-25-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-09-25-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+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_1.2.0-3 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 Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.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 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -339,21 +339,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -604,7 +604,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-s390-oUtfeu/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-s390-7mfGTR/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -649,22 +649,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.13.3-1_s390.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bedtools_2.13.4-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-1037
+Build finished at 20111029-0448
-bedtools_2.13.3-1_s390.changes:
+bedtools_2.13.4-1_s390.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: s390
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -672,33 +672,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- 75733846d436cd069c4f45c0bc3798046ff65052 523834 bedtools_2.13.3-1_s390.deb
+ 5a423ec434d0e8494e2755a11c65c73c4f5a07c2 525452 bedtools_2.13.4-1_s390.deb
Checksums-Sha256:
- 9e78f4027e5e57d87c901ddda8dc8777945d60e788ba990cf4a9c01a5db542a9 523834 bedtools_2.13.3-1_s390.deb
+ 7063b5d1a3abcd47378e8ba6a7d7c1dd03f7cdf75938fd3273babd57a1cbf801 525452 bedtools_2.13.4-1_s390.deb
Files:
- 31c6269b3eb5b0d34373c12aa2bf4869 523834 science optional bedtools_2.13.3-1_s390.deb
+ 187fcb45404b6b106e22b00762fc49c3 525452 science optional bedtools_2.13.4-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_s390.deb
+bedtools_2.13.4-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 523834 bytes: control archive= 1717 bytes.
- 834 bytes, 18 lines control
+ size 525452 bytes: control archive= 1732 bytes.
+ 864 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4734
+ Installed-Size: 4740
+ 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
Section: science
@@ -713,49 +714,49 @@ bedtools_2.13.3-1_s390.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 10:37 ./
-drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/bin/
--rwxr-xr-x root/root 285616 2011-10-05 10:37 ./usr/bin/coverageBed
--rwxr-xr-x root/root 105796 2011-10-05 10:37 ./usr/bin/linksBed
--rwxr-xr-x root/root 293148 2011-10-05 10:37 ./usr/bin/windowBed
--rwxr-xr-x root/root 113560 2011-10-05 10:37 ./usr/bin/subtractBed
--rwxr-xr-x root/root 280868 2011-10-05 10:37 ./usr/bin/tagBam
--rwxr-xr-x root/root 114968 2011-10-05 10:37 ./usr/bin/flankBed
--rwxr-xr-x root/root 88452 2011-10-05 10:37 ./usr/bin/overlap
--rwxr-xr-x root/root 231568 2011-10-05 10:37 ./usr/bin/bamToBed
--rwxr-xr-x root/root 109648 2011-10-05 10:37 ./usr/bin/complementBed
--rwxr-xr-x root/root 305448 2011-10-05 10:37 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 112724 2011-10-05 10:37 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 145548 2011-10-05 10:37 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 63832 2011-10-05 10:37 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 371160 2011-10-05 10:37 ./usr/bin/pairToBed
--rwxr-xr-x root/root 235752 2011-10-05 10:37 ./usr/bin/bedToBam
--rwxr-xr-x root/root 97464 2011-10-05 10:37 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 109200 2011-10-05 10:37 ./usr/bin/mergeBed
--rwxr-xr-x root/root 122076 2011-10-05 10:37 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 176448 2011-10-05 10:37 ./usr/bin/pairToPair
--rwxr-xr-x root/root 104464 2011-10-05 10:37 ./usr/bin/annotateBed
--rwxr-xr-x root/root 133196 2011-10-05 10:37 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 145560 2011-10-05 10:37 ./usr/bin/nucBed
--rwxr-xr-x root/root 120916 2011-10-05 10:37 ./usr/bin/closestBed
--rwxr-xr-x root/root 309532 2011-10-05 10:37 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 358696 2011-10-05 10:37 ./usr/bin/intersectBed
--rwxr-xr-x root/root 145728 2011-10-05 10:37 ./usr/bin/sortBed
--rwxr-xr-x root/root 107056 2011-10-05 10:37 ./usr/bin/slopBed
-drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 10:34 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
-drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 10:37 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
+drwxr-xr-x root/root 0 2011-10-29 04:48 ./
+drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/bin/
+-rwxr-xr-x root/root 289044 2011-10-29 04:48 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 105796 2011-10-29 04:48 ./usr/bin/linksBed
+-rwxr-xr-x root/root 293148 2011-10-29 04:48 ./usr/bin/windowBed
+-rwxr-xr-x root/root 113560 2011-10-29 04:48 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 280868 2011-10-29 04:48 ./usr/bin/tagBam
+-rwxr-xr-x root/root 114968 2011-10-29 04:48 ./usr/bin/flankBed
+-rwxr-xr-x root/root 88452 2011-10-29 04:48 ./usr/bin/overlap
+-rwxr-xr-x root/root 232524 2011-10-29 04:48 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 109648 2011-10-29 04:48 ./usr/bin/complementBed
+-rwxr-xr-x root/root 305560 2011-10-29 04:48 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 112724 2011-10-29 04:48 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 145548 2011-10-29 04:48 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 63832 2011-10-29 04:48 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 371160 2011-10-29 04:48 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 235752 2011-10-29 04:48 ./usr/bin/bedToBam
+-rwxr-xr-x root/root 97464 2011-10-29 04:48 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 109200 2011-10-29 04:48 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 122076 2011-10-29 04:48 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 176448 2011-10-29 04:48 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 104464 2011-10-29 04:48 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 133196 2011-10-29 04:48 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 145560 2011-10-29 04:48 ./usr/bin/nucBed
+-rwxr-xr-x root/root 122384 2011-10-29 04:48 ./usr/bin/closestBed
+-rwxr-xr-x root/root 309532 2011-10-29 04:48 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 358696 2011-10-29 04:48 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 145728 2011-10-29 04:48 ./usr/bin/sortBed
+-rwxr-xr-x root/root 107056 2011-10-29 04:48 ./usr/bin/slopBed
+drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 04:45 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 04:48 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -769,7 +770,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-f49330f7-0046-47af-b265-29c81e0dd95e/build/buildd-bedtools_2.13.3-1-s390-oUtfeu
+Purging /var/lib/schroot/mount/sid-s390-sbuild-5f182113-afe0-4fd0-9912-c4017f9968c8/build/buildd-bedtools_2.13.4-1-s390-7mfGTR
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -777,18 +778,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 109228
-Build-Time: 191
+Build-Space: 109412
+Build-Time: 170
Distribution: sid
-Install-Time: 13
-Job: bedtools_2.13.3-1
+Install-Time: 10
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 247
-Source-Version: 2.13.3-1
-Space: 109228
+Package-Time: 218
+Source-Version: 2.13.4-1
+Space: 109412
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-1037
-Build needed 00:04:07, 109228k disc space
+Finished at 20111029-0448
+Build needed 00:03:38, 109412k disc space
Signature with key '2D941D26' requested:
diff --git a/sparc.log b/sparc.log
index fe8347d..bfe1c94 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,4 +1,4 @@
-From buildd at lebrun.debian.org Wed Oct 05 10:14:25 2011
+From buildd at lebrun.debian.org Sat Oct 29 04:42:32 2011
Return-path: <buildd at lebrun.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -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 lebrun.debian.org>)
- id 1RBOUb-0005VT-1V
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:14:25 +0000
+ id 1RK0ka-0006LI-DL
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 04:42:32 +0000
Received: from lebrun.debian.org ([193.198.184.10])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1RBOUa-0003N0-4k
- for logs at buildd.debian.org; Wed, 05 Oct 2011 10:14:24 +0000
+ id 1RK0kZ-0002sp-J8
+ for logs at buildd.debian.org; Sat, 29 Oct 2011 04:42:31 +0000
Received: from buildd by lebrun.debian.org with local (Exim 4.72)
(envelope-from <buildd at lebrun.debian.org>)
- id 1RBOUY-0002Ie-7R; Wed, 05 Oct 2011 10:14:22 +0000
-Message-Id: <E1RBOUY-0002Ie-7R at lebrun.debian.org>
+ id 1RK0kX-0006eR-IR; Sat, 29 Oct 2011 04:42:29 +0000
+Message-Id: <E1RK0kX-0006eR-IR at lebrun.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 5 Oct 2011 10:14:21 +0000
+Date: Sat, 29 Oct 2011 04:42:29 +0000
From: buildd on lebrun <buildd at lebrun.debian.org>
To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
-Subject: Log for successful build of bedtools_2.13.3-1 on sparc (dist=sid)
+Subject: Log for successful build of bedtools_2.13.4-1 on sparc (dist=sid)
Key-Id: 632E3DB6
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bedtools 2.13.3-1 (sparc) 05 Oct 2011 10:01 ║
+║ bedtools 2.13.4-1 (sparc) 29 Oct 2011 04:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bedtools
-Version: 2.13.3-1
-Source Version: 2.13.3-1
+Version: 2.13.4-1
+Source Version: 2.13.4-1
Architecture: sparc
Get:1 http://debian.carnet.hr unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://debian.carnet.hr unstable/main Sources [5816 kB]
-Get:4 http://debian.carnet.hr unstable/contrib Sources [57.1 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [5874 kB]
+Get:4 http://debian.carnet.hr unstable/contrib Sources [56.5 kB]
+Get:5 http://debian.carnet.hr unstable/non-free Sources [104 kB]
+Get:6 http://debian.carnet.hr unstable/main sparc Packages [7644 kB]
Ign http://incoming.debian.org InRelease
-Get:5 http://debian.carnet.hr unstable/non-free Sources [103 kB]
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://incoming.debian.org Release [1604 B]
-Get:8 http://debian.carnet.hr unstable/main sparc Packages [7604 kB]
-Get:9 http://incoming.debian.org unstable/main Sources [5816 kB]
-Get:10 http://debian.carnet.hr unstable/contrib sparc Packages [55.0 kB]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org Release [1604 B]
+Get:9 http://incoming.debian.org unstable/main Sources [5874 kB]
+Get:10 http://debian.carnet.hr unstable/contrib sparc Packages [55.3 kB]
Ign http://debian.carnet.hr unstable/contrib TranslationIndex
Get:11 http://debian.carnet.hr unstable/main TranslationIndex [2045 B]
-Get:12 http://incoming.debian.org unstable/contrib Sources [57.1 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:14 http://incoming.debian.org unstable/main sparc Packages [7604 kB]
Ign http://debian.carnet.hr unstable/contrib Translation-en
-Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.0 kB]
+Get:12 http://incoming.debian.org unstable/contrib Sources [56.5 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [104 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7644 kB]
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.3 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [37.0 kB]
-Get:18 http://incoming.debian.org Packages [266 kB]
+Get:17 http://incoming.debian.org Sources [36.6 kB]
+Get:18 http://incoming.debian.org Packages [333 kB]
Ign http://incoming.debian.org Translation-en
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 27.9 MB in 29s (945 kB/s)
+Fetched 28.1 MB in 29s (945 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bedtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/git/debian-med/bedtools.git
-Need to get 666 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (dsc) [1967 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (tar) [660 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.3-1 (diff) [4282 B]
-Fetched 666 kB in 1s (404 kB/s)
+Need to get 922 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (dsc) [1967 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (tar) [916 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bedtools 2.13.4-1 (diff) [4231 B]
+Fetched 922 kB in 2s (389 kB/s)
Download complete and in download only mode
Check arch
@@ -102,18 +102,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.1-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 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 23 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -125,23 +125,23 @@ Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
-coreutils: already installed (8.13-2)
+coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
-debianutils: already installed (4.0.2)
+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-2011-07-02-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
findutils: already installed (4.4.2-1+b2)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
+ncurses-base: already installed (5.9-2)
+ncurses-bin: already installed (5.9-2)
+perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
+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)
@@ -151,7 +151,7 @@ libc6-dev-sparc64: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
cdbs: missing
debhelper: missing
Using default version 8.9.8
@@ -176,24 +176,24 @@ 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 9519 kB of archives.
-After this operation, 28.4 MB of additional disk space will be used.
+0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.
+Need to get 9455 kB of archives.
+After this operation, 27.2 MB of additional disk space will be used.
Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
Get:2 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:3 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:4 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:5 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
-Get:6 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.08-1 [246 kB]
-Get:7 http://debian.carnet.hr/debian/ unstable/main file sparc 5.08-1 [51.0 kB]
-Get:8 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-4 [132 kB]
-Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-4 [816 kB]
-Get:10 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
-Get:11 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:12 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
-Get:13 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:14 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
-Get:15 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-4 [1985 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.99 [77.1 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
Get:16 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:17 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
Get:18 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.9.8 [552 kB]
@@ -201,12 +201,20 @@ Get:19 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.54-1 [28.3
Get:20 http://debian.carnet.hr/debian/ unstable/main quilt all 0.48-8 [357 kB]
Get:21 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9519 kB in 8s (1121 kB/s)
+Fetched 9455 kB in 8s (1135 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10902 files and directories currently installed.)
+(Reading database ... 10908 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_sparc.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_sparc.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_sparc.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_sparc.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_sparc.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_sparc.deb) ...
Selecting previously unselected package groff-base.
@@ -214,25 +222,17 @@ Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-2_sparc.deb) ...
Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.08-1_sparc.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.09-2_sparc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.08-1_sparc.deb) ...
+Unpacking file (from .../archives/file_5.09-2_sparc.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_sparc.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_sparc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_sparc.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_sparc.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_sparc.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_sparc.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_sparc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-5_sparc.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
@@ -247,23 +247,23 @@ Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
Setting up libpcre3 (8.12-4) ...
+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 (5.08-1) ...
-Setting up file (5.08-1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+Setting up 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up 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) ...
@@ -274,11 +274,11 @@ 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 23 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.53.20110922-1 dpkg-dev_1.16.1 g++-4.6_4.6.1-13 gcc-4.6_4.6.1-13 libc6-dev_2.13-21 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 linux-libc-dev_3.0.0-4
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110922-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.99 coreutils_8.13-2 cpp_4:4.6.1-3 cpp-4.6_4.6.1-13 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.08-1 findutils_4.4.2-1+b2 g++_4:4.6.1-3 g++-4.6_4.6.1-13 gcc_4:4.6.1-3 gcc-4.6_4.6.1-13 gcc-4.6-base_4.6.1-13 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-dev-sparc64_2.13-21 libc6-sparc64_2.13-21 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-13 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-13 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-13 libstdc++6-4.6-dev_4.6.1-13 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15+b1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-8 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011k-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+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 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+b2 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-13.12 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-2011-10-09-1 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 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_1.2.0-3 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 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+b1 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -289,12 +289,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Oct 5 08:41:27 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Sat Oct 29 02:18:35 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bedtools_2.13.3-1.dsc
-dpkg-source: info: extracting bedtools in bedtools-2.13.3
-dpkg-source: info: unpacking bedtools_2.13.3.orig.tar.xz
-dpkg-source: info: unpacking bedtools_2.13.3-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bedtools_2.13.4-1.dsc
+dpkg-source: info: extracting bedtools in bedtools-2.13.4
+dpkg-source: info: unpacking bedtools_2.13.4.orig.tar.gz
+dpkg-source: info: unpacking bedtools_2.13.4-1.debian.tar.gz
dpkg-source: info: applying gzstream.h.patch
Check disc space
@@ -304,30 +304,25 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bedtools
-dpkg-buildpackage: source version 2.13.3-1
- dpkg-source --before-build bedtools-2.13.3
+dpkg-buildpackage: source version 2.13.4-1
+ dpkg-source --before-build bedtools-2.13.4
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 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+/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_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
Cleaning up.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch gzstream.h.patch
Restoring src/utils/gzstream/gzstream.C
@@ -340,21 +335,21 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
-cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+cd . && QUILT_PATCHES=/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch gzstream.h.patch
patching file src/utils/gzstream/gzstream.C
Now at patch gzstream.h.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+make[1]: Entering directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall" CPPFLAGS="" LDFLAGS=""
-make[1]: Entering directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
+/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_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building BEDTools:
@@ -372,7 +367,7 @@ Building BEDTools:
* compiling chromsweep.cpp
- Building in src/utils/gzstream
-g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
+g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -c -o ../../../obj//gzstream.o gzstream.C -I.
- Building in src/utils/fileType
* compiling fileType.cpp
@@ -432,10 +427,6 @@ Fasta.cpp: In member function 'void FastaIndexEntry::clear()':
Fasta.cpp:28:14: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:31:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
Fasta.cpp:32:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null]
-Fasta.cpp: In member function 'std::string FastaReference::getSubSequence(std::string, int, int)':
-Fasta.cpp:308:55: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
-Fasta.cpp: In member function 'std::string FastaReference::getSequence(std::string)':
-Fasta.cpp:266:47: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
* compiling split.cpp
- Building in src/utils/genomeFile
@@ -605,7 +596,7 @@ unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-
* compiling windowBed.cpp
* linking windowBed
-make[1]: Leaving directory `/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv/bedtools-2.13.3'
+make[1]: Leaving directory `/build/buildd-bedtools_2.13.4-1-sparc-1fdoun/bedtools-2.13.4'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary-arch
@@ -650,22 +641,22 @@ dh_shlibdeps -pbedtools
dh_gencontrol -pbedtools
dh_md5sums -pbedtools
dh_builddeb -pbedtools -- -Z xz
-dpkg-deb: building package `bedtools' in `../bedtools_2.13.3-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.13.3-1_sparc.changes
+dpkg-deb: building package `bedtools' in `../bedtools_2.13.4-1_sparc.deb'.
+ dpkg-genchanges -B -msparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org> >../bedtools_2.13.4-1_sparc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build bedtools-2.13.3
+ dpkg-source --after-build bedtools-2.13.4
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111005-1014
+Build finished at 20111029-0442
-bedtools_2.13.3-1_sparc.changes:
+bedtools_2.13.4-1_sparc.changes:
Format: 1.8
-Date: Wed, 05 Oct 2011 17:18:15 +0900
+Date: Sat, 29 Oct 2011 11:08:02 +0900
Source: bedtools
Binary: bedtools
Architecture: sparc
-Version: 2.13.3-1
+Version: 2.13.4-1
Distribution: sid
Urgency: low
Maintainer: sparc Build Daemon (lebrun) <buildd_sparc-lebrun at buildd.debian.org>
@@ -673,33 +664,34 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
bedtools - suite of utilities for comparing genomic features
Changes:
- bedtools (2.13.3-1) unstable; urgency=low
+ bedtools (2.13.4-1) unstable; urgency=low
.
- [ea1c596] New upstream release.
+ [e553c37] New upstream release.
Checksums-Sha1:
- 6927d20756e9f5d81b86436d7eae3b0888737003 565030 bedtools_2.13.3-1_sparc.deb
+ 13a45b7ece651e91bd674aaf50200938d5550af4 566770 bedtools_2.13.4-1_sparc.deb
Checksums-Sha256:
- 55ba5ad7a2549281440a0856edf3255be799946ccc493208fc8630d61dd558ad 565030 bedtools_2.13.3-1_sparc.deb
+ 5d69b4719e0747483606d8cef7f20c0830f6fbffa3b0b11c318a0754c237ca03 566770 bedtools_2.13.4-1_sparc.deb
Files:
- 072e8e8f3aa5694db71114ca8731de99 565030 science optional bedtools_2.13.3-1_sparc.deb
+ 22f3cca102d26fa103651de3acc9a083 566770 science optional bedtools_2.13.4-1_sparc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bedtools_2.13.3-1_sparc.deb
+bedtools_2.13.4-1_sparc.deb
───────────────────────────
new debian package, version 2.0.
- size 565030 bytes: control archive= 1722 bytes.
- 835 bytes, 18 lines control
+ size 566770 bytes: control archive= 1729 bytes.
+ 865 bytes, 19 lines control
2025 bytes, 35 lines md5sums
Package: bedtools
- Version: 2.13.3-1
+ Version: 2.13.4-1
Architecture: sparc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 4590
+ Installed-Size: 4594
+ 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
Section: science
@@ -714,49 +706,49 @@ bedtools_2.13.3-1_sparc.deb
.
The groupBy utility is distribued in the filo package.
-drwxr-xr-x root/root 0 2011-10-05 10:13 ./
-drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/
-drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/bin/
--rwxr-xr-x root/root 298604 2011-10-05 10:13 ./usr/bin/multiBamCov
--rwxr-xr-x root/root 291176 2011-10-05 10:13 ./usr/bin/genomeCoverageBed
--rwxr-xr-x root/root 103476 2011-10-05 10:13 ./usr/bin/complementBed
--rwxr-xr-x root/root 175004 2011-10-05 10:13 ./usr/bin/pairToPair
--rwxr-xr-x root/root 274036 2011-10-05 10:13 ./usr/bin/tagBam
--rwxr-xr-x root/root 142564 2011-10-05 10:13 ./usr/bin/nucBed
--rwxr-xr-x root/root 282188 2011-10-05 10:13 ./usr/bin/windowBed
--rwxr-xr-x root/root 142528 2011-10-05 10:13 ./usr/bin/fastaFromBed
--rwxr-xr-x root/root 109568 2011-10-05 10:13 ./usr/bin/maskFastaFromBed
--rwxr-xr-x root/root 60340 2011-10-05 10:13 ./usr/bin/unionBedGraphs
--rwxr-xr-x root/root 347776 2011-10-05 10:13 ./usr/bin/intersectBed
--rwxr-xr-x root/root 102904 2011-10-05 10:13 ./usr/bin/slopBed
--rwxr-xr-x root/root 110472 2011-10-05 10:13 ./usr/bin/subtractBed
--rwxr-xr-x root/root 118112 2011-10-05 10:13 ./usr/bin/closestBed
--rwxr-xr-x root/root 106176 2011-10-05 10:13 ./usr/bin/mergeBed
--rwxr-xr-x root/root 117984 2011-10-05 10:13 ./usr/bin/bedToIgv
--rwxr-xr-x root/root 364188 2011-10-05 10:13 ./usr/bin/pairToBed
--rwxr-xr-x root/root 94224 2011-10-05 10:13 ./usr/bin/bed12ToBed6
--rwxr-xr-x root/root 127696 2011-10-05 10:13 ./usr/bin/shuffleBed
--rwxr-xr-x root/root 104252 2011-10-05 10:13 ./usr/bin/linksBed
--rwxr-xr-x root/root 84868 2011-10-05 10:13 ./usr/bin/overlap
--rwxr-xr-x root/root 276352 2011-10-05 10:13 ./usr/bin/coverageBed
--rwxr-xr-x root/root 144596 2011-10-05 10:13 ./usr/bin/sortBed
--rwxr-xr-x root/root 224460 2011-10-05 10:13 ./usr/bin/bamToBed
--rwxr-xr-x root/root 101772 2011-10-05 10:13 ./usr/bin/annotateBed
--rwxr-xr-x root/root 110908 2011-10-05 10:13 ./usr/bin/flankBed
--rwxr-xr-x root/root 224712 2011-10-05 10:13 ./usr/bin/bedToBam
-drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/
-drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/bedtools/
-drwxr-xr-x root/root 0 2011-10-05 10:03 ./usr/share/bedtools/genomes/
--rwxr-xr-x root/root 585 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm9.genome
--rwxr-xr-x root/root 1972 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg19.genome
--rwxr-xr-x root/root 856 2011-09-30 19:42 ./usr/share/bedtools/genomes/human.hg18.genome
--rwxr-xr-x root/root 565 2011-09-30 19:42 ./usr/share/bedtools/genomes/mouse.mm8.genome
-drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-10-05 10:13 ./usr/share/doc/bedtools/
--rw-r--r-- root/root 1442 2011-09-30 19:42 ./usr/share/doc/bedtools/README.rst
--rw-r--r-- root/root 4611 2011-10-03 04:37 ./usr/share/doc/bedtools/copyright
--rw-r--r-- root/root 11213 2011-09-30 19:42 ./usr/share/doc/bedtools/changelog.gz
--rw-r--r-- root/root 440 2011-10-05 08:18 ./usr/share/doc/bedtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-10-29 04:41 ./
+drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/
+drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/bin/
+-rwxr-xr-x root/root 298604 2011-10-29 04:41 ./usr/bin/multiBamCov
+-rwxr-xr-x root/root 293484 2011-10-29 04:41 ./usr/bin/genomeCoverageBed
+-rwxr-xr-x root/root 103412 2011-10-29 04:41 ./usr/bin/complementBed
+-rwxr-xr-x root/root 175004 2011-10-29 04:41 ./usr/bin/pairToPair
+-rwxr-xr-x root/root 274036 2011-10-29 04:41 ./usr/bin/tagBam
+-rwxr-xr-x root/root 142564 2011-10-29 04:41 ./usr/bin/nucBed
+-rwxr-xr-x root/root 282188 2011-10-29 04:41 ./usr/bin/windowBed
+-rwxr-xr-x root/root 142528 2011-10-29 04:41 ./usr/bin/fastaFromBed
+-rwxr-xr-x root/root 109568 2011-10-29 04:41 ./usr/bin/maskFastaFromBed
+-rwxr-xr-x root/root 60340 2011-10-29 04:41 ./usr/bin/unionBedGraphs
+-rwxr-xr-x root/root 347776 2011-10-29 04:41 ./usr/bin/intersectBed
+-rwxr-xr-x root/root 102840 2011-10-29 04:41 ./usr/bin/slopBed
+-rwxr-xr-x root/root 110056 2011-10-29 04:41 ./usr/bin/subtractBed
+-rwxr-xr-x root/root 119044 2011-10-29 04:41 ./usr/bin/closestBed
+-rwxr-xr-x root/root 106176 2011-10-29 04:41 ./usr/bin/mergeBed
+-rwxr-xr-x root/root 117984 2011-10-29 04:41 ./usr/bin/bedToIgv
+-rwxr-xr-x root/root 364188 2011-10-29 04:41 ./usr/bin/pairToBed
+-rwxr-xr-x root/root 94192 2011-10-29 04:41 ./usr/bin/bed12ToBed6
+-rwxr-xr-x root/root 127536 2011-10-29 04:41 ./usr/bin/shuffleBed
+-rwxr-xr-x root/root 104252 2011-10-29 04:41 ./usr/bin/linksBed
+-rwxr-xr-x root/root 84868 2011-10-29 04:41 ./usr/bin/overlap
+-rwxr-xr-x root/root 278172 2011-10-29 04:41 ./usr/bin/coverageBed
+-rwxr-xr-x root/root 144116 2011-10-29 04:41 ./usr/bin/sortBed
+-rwxr-xr-x root/root 224720 2011-10-29 04:41 ./usr/bin/bamToBed
+-rwxr-xr-x root/root 101708 2011-10-29 04:41 ./usr/bin/annotateBed
+-rwxr-xr-x root/root 110716 2011-10-29 04:41 ./usr/bin/flankBed
+-rwxr-xr-x root/root 224712 2011-10-29 04:41 ./usr/bin/bedToBam
+drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/
+drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/bedtools/
+drwxr-xr-x root/root 0 2011-10-29 04:32 ./usr/share/bedtools/genomes/
+-rwxr-xr-x root/root 585 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm9.genome
+-rwxr-xr-x root/root 1972 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg19.genome
+-rwxr-xr-x root/root 856 2011-10-26 11:47 ./usr/share/bedtools/genomes/human.hg18.genome
+-rwxr-xr-x root/root 565 2011-10-26 11:47 ./usr/share/bedtools/genomes/mouse.mm8.genome
+drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-10-29 04:41 ./usr/share/doc/bedtools/
+-rw-r--r-- root/root 1442 2011-10-26 11:47 ./usr/share/doc/bedtools/README.rst
+-rw-r--r-- root/root 4611 2011-10-29 01:54 ./usr/share/doc/bedtools/copyright
+-rw-r--r-- root/root 11515 2011-10-26 11:47 ./usr/share/doc/bedtools/changelog.gz
+-rw-r--r-- root/root 584 2011-10-29 02:09 ./usr/share/doc/bedtools/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -770,7 +762,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-988ad83e-08e6-4653-9744-f669e0870e35/build/buildd-bedtools_2.13.3-1-sparc-dYiwkv
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-91ac1074-8b93-44eb-820f-cfc94961ab24/build/buildd-bedtools_2.13.4-1-sparc-1fdoun
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -778,18 +770,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 102048
-Build-Time: 622
+Build-Space: 101744
+Build-Time: 615
Distribution: sid
-Install-Time: 66
-Job: bedtools_2.13.3-1
+Install-Time: 65
+Job: bedtools_2.13.4-1
Package: bedtools
-Package-Time: 740
-Source-Version: 2.13.3-1
-Space: 102048
+Package-Time: 735
+Source-Version: 2.13.4-1
+Space: 101744
Status: successful
-Version: 2.13.3-1
+Version: 2.13.4-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111005-1014
-Build needed 00:12:20, 102048k disc space
+Finished at 20111029-0442
+Build needed 00:12:15, 101744k disc space
Signature with key '632E3DB6' requested:
--
Suite of utilities for comparing genomic features.
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