[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.17-1-2-g84a58c3
Charles Plessy
plessy at debian.org
Wed Sep 7 04:16:19 UTC 2011
The following commit has been merged in the meta branch:
commit 84a58c314bc984779545b2bb3c83060fc8d823e6
Author: Charles Plessy <plessy at debian.org>
Date: Wed Sep 7 13:15:49 2011 +0900
Collected build logs for 0.1.18-1.
diff --git a/armel.log b/armel.log
index 11e0b72..7655088 100644
--- a/armel.log
+++ b/armel.log
@@ -1,67 +1,68 @@
-From buildd at ancina.debian.org Tue Jul 12 17:59:18 2011
-Return-path: <buildd at ancina.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at antheil.debian.org Tue Sep 06 09:33:50 2011
+Return-path: <buildd at antheil.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
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- by merikanto.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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-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Tue, 12 Jul 2011 17:59:10 +0000
-From: Build Daemon <buildd at ancina.debian.org>
-To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.17-1 on armel (dist=sid)
-Key-Id: A1EAA0BB
-Message-Id: <E1QghEk-0003rF-Mu at ancina.debian.org>
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+Date: Tue, 06 Sep 2011 09:33:45 +0000
+Message-Id: <E1R0s2L-00088I-Qg at antheil.debian.org>
+From: buildd on antheil <buildd at antheil.debian.org>
+To: buildd-porters at antheil.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.18-1 on armel (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on antheil.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (armel) 12 Jul 2011 17:53 ║
+║ samtools 0.1.18-1 (armel) 06 Sep 2011 09:25 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: armel
-Hit http://ftp.de.debian.org sid InRelease
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5468 kB]
Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
-Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Hit http://ftp.de.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-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
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Sources
-Get:3 http://incoming.debian.org Packages [526 kB]
-Ign http://ftp.de.debian.org sid/contrib Translation-en
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [5470 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [94.9 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armel Packages [7494 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib armel Packages [55.6 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 [53.9 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
+Get:13 http://incoming.debian.org unstable/main armel Packages [7495 kB]
+Get:14 http://incoming.debian.org unstable/contrib armel Packages [55.6 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [32.4 kB]
+Get:18 http://incoming.debian.org Packages [356 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org sid/contrib Translation-en
-Fetched 528 kB in 13s (39.8 kB/s)
+Fetched 27.0 MB in 1min 6s (405 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 0s (1007 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 1s (374 kB/s)
Download complete and in download only mode
Check arch
@@ -106,12 +107,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 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 41 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,8 +121,8 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
@@ -130,27 +131,27 @@ 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 (2.8-2)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-1)
+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 (5.12.4-1)
+perl-base: already installed (5.12.4-2)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.10)
-sysvinit: already installed (2.88dsf-13.10)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-7)
+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 (2.13-16)
gcc: 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)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -161,38 +162,66 @@ 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
+ 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 dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl procmail graphviz
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
- autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 41 not upgraded.
+Need to get 9838 kB of archives.
+After this operation, 29.2 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-3 [33.8 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-2 [990 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5+b1 [235 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5+b1 [49.4 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-4 [139 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-4 [815 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.6-1 [1535 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-4 [409 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-4 [1984 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.54-1 [27.7 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-1 [474 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 20 newly installed, 0 to remove and 15 not upgraded.
-Need to get 0 B/9391 kB of archives.
-After this operation, 28.0 MB of additional disk space will be used.
+Fetched 9838 kB in 10s (933 kB/s)
Selecting previously deselected package libpipeline1.
-(Reading database ... 11252 files and directories currently installed.)
+(Reading database ... 10542 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_armel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_armel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_armel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_armel.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_armel.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_armel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -202,15 +231,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_armel.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_armel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_armel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -220,23 +249,27 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up bsdmainutils (8.2.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -245,11 +278,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-3 gcc-4.6_4.6.1-3 libc6-dev_2.13-7 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 linux-libc-dev_2.6.39-2
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-3 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-3 gcc-4.6-base_4.6.1-3 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6_2.13-7 libc6-dev_2.13-7 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 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-3 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-2 libgomp1_4.6.1-3 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.4 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 libtasn1-3_2.9-4 libtimedate-perl_1.2000-1 libudev0_171-3 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 nullmailer_1:1.05-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.14-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 wget_1.12-3.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32 armel (armv5tel)
+Toolchain package versions: binutils_2.21.53.20110805-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-6 gcc-4.6_4.6.1-6 libc6-dev_2.13-16 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 linux-libc-dev_3.0.0-1
+Package versions: apt_0.8.15.5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110805-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-6 dash_0.5.5.1-7.4 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-6 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-7 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-6 gcc-4.6-base_4.6.1-6 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 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_1.0.5-6 libc-bin_2.13-16 libc-dev-bin_2.13-16 libc6_2.13-16 libc6-dev_2.13-16 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-6 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-5 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-16 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-2 perl-base_5.12.4-2 perl-modules_5.12.4-2 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-5 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 +293,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -281,33 +314,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -321,22 +354,22 @@ 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-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -371,15 +404,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -387,10 +420,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -411,24 +444,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -436,93 +469,63 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
+Line 2, sequence length 35 vs 8960 from CIGAR
Parse error at line 2: CIGAR and sequence length are inconsistent
make[1]: *** [ex1.bam] Aborted
make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110712-1758
+Build finished at 20110906-0933
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-5d53a889-878a-46d1-913e-aa08f7672685/build/buildd-samtools_0.1.17-1-armel-Waxu30
-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* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
- libncurses5-dev* libpipeline1* libunistring0* libxml2* man-db* po-debconf*
- quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 15 not upgraded.
-After this operation, 28.0 MB disk space will be freed.
-(Reading database ... 12647 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libncurses5-dev ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-armel-sbuild-aa205354-7d1c-41d1-92e5-305c4b07ff1d/build/buildd-samtools_0.1.18-1-armel-e_OjLd
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 6076
-Build-Time: 268
+Build-Space: 6420
+Build-Time: 304
Distribution: sid
Fail-Stage: build
-Install-Time: 31
-Job: samtools_0.1.17-1
+Install-Time: 100
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 334
-Source-Version: 0.1.17-1
-Space: 6076
+Package-Time: 505
+Source-Version: 0.1.18-1
+Space: 6420
Status: attempted
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110712-1758
-Build needed 00:05:34, 6076k disc space
+Finished at 20110906-0933
+Build needed 00:08:25, 6420k disc space
+
diff --git a/hurd-i386.log b/hurd-i386.log
index ba76113..08976e4 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,42 +1,42 @@
-From buildd at rossini.debian.net Mon Jul 11 13:19:00 2011
-Return-path: <buildd at rossini.debian.net>
-Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
+From buildd at mozart.debian.net Tue Sep 06 09:41:15 2011
+Return-path: <buildd at mozart.debian.net>
+Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1QgGO3-0002C6-U9
- for logs at buildd.debian.org; Mon, 11 Jul 2011 13:19:00 +0000
-Received: from hurd.ethz.ch ([192.33.98.55] helo=rossini.debian.net)
- by io.debian.net with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1QgGO1-000Fmu-IX; Mon, 11 Jul 2011 15:18:57 +0200
-Received: from buildd by rossini.debian.net with local (Exim 4.72)
- (envelope-from <buildd at rossini.debian.net>)
- id 1QgGO0-0000zD-UB; Mon, 11 Jul 2011 13:18:56 +0000
-Message-Id: <E1QgGO0-0000zD-UB at rossini.debian.net>
+ (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
+ id 1R0s9a-0003VY-4e
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:41:15 +0000
+Received: from mozart.debian.net ([10.1.0.1])
+ by callisto.debian.net with esmtp (Exim 4.69)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1R0s9R-00073Q-VQ; Tue, 06 Sep 2011 10:41:06 +0100
+Received: from buildd by mozart.debian.net with local (Exim 4.76)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1R0s9R-0001Ag-24; Tue, 06 Sep 2011 09:41:05 +0000
MIME-Version: 1.0
Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.78; B3.08; Q3.08)
-Date: Mon, 11 Jul 2011 13:18:56 +0000
-From: Build Daemon <buildd at rossini.debian.net>
-To: samuel.thibault at labri.fr, mbanck at gmx.net, logs at buildd.debian-ports.org,
+X-Mailer: MIME::Lite 3.027 (F2.78; A2.07; B3.08; Q3.08)
+Date: Tue, 6 Sep 2011 09:41:04 +0000
+From: Build Daemon <buildd at mozart.debian.net>
+To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.17-1 on hurd-i386 (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-1 on hurd-i386 (dist=sid)
+Message-Id: <E1R0s9R-0001Ag-24 at mozart.debian.net>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.62.3 (11 Jun 2011) on rossini.debian.net
+sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on mozart.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (hurd-i386) 11 Jul 2011 13:02 ║
+║ samtools 0.1.18-1 (hurd-i386) 06 sept. 2011 09:33 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Distribution: sid
Architecture: hurd-i386
-I: NOTICE: Log filtering will replace 'build/samtools-Bjor1m/samtools-0.1.17' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-Bjor1m' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-jFRcSJ/samtools-0.1.18' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-jFRcSJ' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'home/buildd/build/chroot-sid' with '«CHROOT»'
W: Stripped single quote from command for security:
use strict;
@@ -87,7 +87,7 @@ W: Stripped single quote from command for security:
}
}
- F->print("samtools_0.1.17-1 1424 buildd\n");
+ F->print("samtools_0.1.18-1 2503 buildd\n");
F->close();
exit 0;
@@ -97,48 +97,44 @@ W: Stripped single quote from command for security:
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Ign file: ./ InRelease
-Ign file: ./ Release.gpg
-Ign file: ./ Release
-Ign file: ./ Translation-en
-Hit http://ftp.ch.debian.org unstable InRelease
-Hit http://ftp.ch.debian.org experimental InRelease
-Hit http://ftp.fr.debian.org unstable InRelease
-Hit http://ftp.ch.debian.org unstable/main Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental InRelease
-Ign http://ftp.debian-ports.org unreleased InRelease
+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.ch.debian.org unstable/contrib Sources/DiffIndex
-Hit http://ftp.ch.debian.org unstable/non-free Sources/DiffIndex
-Hit http://ftp.ch.debian.org unstable/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
+Ign http://ftp.debian-ports.org unreleased InRelease
+Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
+Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
+Get:1 http://ftp.uk.debian.org sid/main TranslationIndex [2045 B]
+Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
+Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
Hit http://ftp.debian-ports.org unreleased Release.gpg
-Hit http://incoming.debian.org Release.gpg
-Hit http://ftp.ch.debian.org unstable/main TranslationIndex
-Hit http://ftp.ch.debian.org experimental/main Sources/DiffIndex
-Hit http://ftp.ch.debian.org experimental/contrib Sources/DiffIndex
-Hit http://ftp.ch.debian.org experimental/non-free Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
-Get:1 http://incoming.debian.org Release [1604 B]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex
Hit http://ftp.debian-ports.org unreleased Release
-Ign http://incoming.debian.org Release
-Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
-Ign http://incoming.debian.org Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
+Get:3 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Hit http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex
+Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
+Get:4 http://ftp.fr.debian.org sid/main TranslationIndex [2045 B]
+Ign http://ftp.fr.debian.org sid/non-free TranslationIndex
+Get:5 http://incoming.debian.org Sources [33.2 kB]
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Hit http://ftp.fr.debian.org unstable/main TranslationIndex
-Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
-Ign http://incoming.debian.org Packages/DiffIndex
-Hit http://incoming.debian.org Sources
+Ign http://ftp.fr.debian.org sid/contrib Translation-en
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Get:2 http://incoming.debian.org Packages [451 kB]
+Ign http://ftp.fr.debian.org sid/non-free Translation-en
+Ign http://ftp.uk.debian.org sid/contrib Translation-en
+Ign http://ftp.uk.debian.org sid/non-free Translation-en
+Get:6 http://incoming.debian.org Packages [352 kB]
Ign http://ftp.debian-ports.org unreleased/main Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 453 kB in 2min 54s (2588 B/s)
+Fetched 391 kB in 50s (7751 B/s)
Reading package lists...
-W: GPG error: http://incoming.debian.org Release: The following signatures were invalid: BADSIG 9AA38DCD55BE302B Debian Archive Automatic Signing Key (5.0/lenny) <ftpmaster at debian.org>
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -158,11 +154,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 3s (128 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 2s (145 kB/s)
Download complete and in download only mode
Check arch
@@ -170,7 +166,7 @@ Check arch
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-WI3X4y/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-JKVjjF/apt_archive/sbuild-build-depends-core-dummy.deb'.
gpg: WARNING: using insecure memory!
gpg: please see http://www.gnupg.org/faq.html for more information
OK
@@ -184,24 +180,24 @@ Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libboost-iostreams1.42.0
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 30 not upgraded.
Need to get 0 B/712 B of archives.
After this operation, 0 B of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
sbuild-build-depends-core-dummy
Authentication warning overridden.
Selecting previously deselected package sbuild-build-depends-core-dummy.
-(Reading database ... 12536 files and directories currently installed.)
+(Reading database ... 13753 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-lwozOr/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-c_dlCz/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
gpg: WARNING: using insecure memory!
gpg: please see http://www.gnupg.org/faq.html for more information
OK
@@ -215,61 +211,28 @@ Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libboost-iostreams1.42.0
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0
- libxml2 po-debconf quilt zlib1g-dev
+ cdbs diffstat libncurses5-dev quilt zlib1g-dev
Suggested packages:
- devscripts dh-make gettext-doc ncurses-doc libmail-box-perl procmail
- graphviz
+ devscripts ncurses-doc procmail graphviz
Recommended packages:
- autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0
- libxml2 po-debconf quilt sbuild-build-depends-samtools-dummy zlib1g-dev
-0 upgraded, 19 newly installed, 0 to remove and 1 not upgraded.
-Need to get 0 B/7611 kB of archives.
-After this operation, 23.3 MB of additional disk space will be used.
+ cdbs diffstat libncurses5-dev quilt sbuild-build-depends-samtools-dummy
+ zlib1g-dev
+0 upgraded, 6 newly installed, 0 to remove and 30 not upgraded.
+Need to get 0 B/1111 kB of archives.
+After this operation, 3113 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3
- libexpat1 libunistring0 gettext intltool-debian po-debconf debhelper cdbs
- diffstat libncurses5-dev quilt zlib1g-dev
+ cdbs diffstat libncurses5-dev quilt zlib1g-dev
sbuild-build-depends-samtools-dummy
Authentication warning overridden.
-Selecting previously deselected package libmagic1.
-(Reading database ... 12536 files and directories currently installed.)
-Unpacking libmagic1 (from .../libmagic1_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_hurd-i386.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_hurd-i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
-Selecting previously deselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_hurd-i386.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+(Reading database ... 13753 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -281,22 +244,7 @@ Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
Selecting previously deselected package sbuild-build-depends-samtools-dummy.
Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
Processing triggers for man-db ...
-Processing triggers for install-info ...
-Setting up libmagic1 (5.03-5+b1) ...
-Setting up file (5.03-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libexpat1 (2.0.1-7) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -308,8 +256,8 @@ Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.5_4.5.3-3 g++-4.6_4.6.1-1+hurd.1 gcc-4.4_4.4.6-6 gcc-4.5_4.5.3-3 gcc-4.6_4.6.1-1+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 hurd-dev_20110519-3 libc0.3-dev_2.13-10 libstdc++6_4.6.1-1+hurd.1 libstdc++6-4.5-dev_4.5.3-3 libstdc++6-4.6-dev_4.6.1-1+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.1 apt-utils_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-6 cpp-4.4_4.4.6-6 cpp-4.5_4.5.3-3 cpp-4.6_4.6.1-1+hurd.1 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.6-2 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.5_4.5.3-3 g++-4.6_4.6.1-1+hurd.1 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-6 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-6 gcc-4.4-base_4.4.6-6 gcc-4.5_4.5.3-3 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-1+hurd.1 gcc-4.6-base_4.6.1-1+hurd.1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran_4:4.6.0-6 gfortran-4.4_4.4.6-6 gfortran-4.6_4.6.1-1+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-6 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.10 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_1:2.4.46-2 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4+b2 libboost-iostreams1.46.1_1.46.1-6 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc0.3_2.13-10 libc0.3-dev_2.13-10 libc0.3-xen_2.13-10 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 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.6.1-1+hurd.1 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libgfortran3_4.6.1-1+hurd.1 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.4-2 libgomp1_4.6.1-1+hurd.1 libgpg-error0_1.10-0.3 libident_0.22-3 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 liblzo2-2_2.05-1 libmagic1_5.03-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libnewt0.52_0.52.11-2.1 libobjc2_4.5.3-3 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libpopt0_1.16-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libpwl5_0.11.2-3 libquadmath0_4.6.1-1+hurd.1 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-1+hurd.1 libstdc++6-4.5-dev_4.5.3-3 libstdc++6-4.6-dev_4.6.1-1+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 libunistring0_0.9.3-4 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libxml2_2.7.8.dfsg-3 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_5.9-1 netbase_4.46 netcat-traditional_1.10-39 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 quilt_0.48-7 random-egd_0.5-0+hurd.1 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-2 tzdata_2011h-3 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2.1 xz-utils_5.0.0-2 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_1.16.0.3 g++-4.5_4.5.3-8 g++-4.6_4.6.1-7+hurd.1 gcc-4.4_4.4.6-7 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-7+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 hurd-dev_20110519-3 libc0.3-dev_2.13-18 libstdc++6_4.6.1-7+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-7+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_0.4.96 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.4_4.4.6-7 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-7+hurd.1 cron_3.0pl1-119 dash_0.5.5.1-7.4 debconf_1.5.41 debfoster_2.6-2 debhelper_8.9.4 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.03-5+b1 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_4.6.1-7+hurd.1 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-2 gcc-4.4_4.4.6-7 gcc-4.4-base_4.4.6-7 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-7+hurd.1 gcc-4.6-base_4.6.1-7+hurd.1 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gfortran_4:4.6.1-2 gfortran-4.6_4.6.1-7+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110805-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-7 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-13.11 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_1.46.1-6 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc0.3_2.13-18 libc0.3-dev_2.13-18 libc0.3-xen_2.13-18 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 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libept1_1.0.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.6-2 libgcc1_1:4.6.1-7+hurd.1 libgdbm3_1.8.3-10 libgfortran3_4.6.1-7+hurd.1 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-7+hurd.1 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.03-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libobjc2_4.5.3-8 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libpwl5_0.11.2-3 libquadmath0_4.6.1-7+hurd.1 libreadline6_6.2-4 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_1.0.0d-3 libstdc++6_4.6.1-7+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-7+hurd.1 libsysfs2_2.1.0+repack-1 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libuuid1_2.19.1-5 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-4 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-16 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 netcat-traditional_1.10-39 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 quilt_0.48-7 random-egd_0.5-0+hurd.1 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-2 ttf-bitstream-vera_1.10-8 ttf-dejavu-core_2.33-1 ttf-freefont_20100919-1 type-handling_0.2.23 tzdata_2011h-3 ucf_3.0025+nmu2 util-linux_2.19.1-5 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 │
@@ -320,12 +268,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -336,6 +284,27 @@ Sufficient free space for build
User Environment
────────────────
+FAKEROOTEGID=0
+FAKEROOTEUID=0
+FAKEROOTFGID=0
+FAKEROOTFUID=0
+FAKEROOTGID=0
+FAKEROOTSGID=0
+FAKEROOTSUID=0
+FAKEROOTUID=0
+HOME=/home/buildd
+LOGNAME=buildd
+OLDPWD=/
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin
+PWD=/«PKGBUILDDIR»
+SHELL=/bin/sh
+SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env'
+SUDO_GID=105
+SUDO_UID=60000
+SUDO_USER=buildd
+TERM=rxvt-unicode
+USER=buildd
+USERNAME=root
dpkg-buildpackage
─────────────────
@@ -346,8 +315,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
@@ -362,7 +331,7 @@ make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
make[2]: Entering directory `/«PKGBUILDDIR»/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
make[1]: Leaving directory `/«PKGBUILDDIR»'
rm -f debian/stamp-makefile-check
@@ -379,8 +348,8 @@ Restoring examples/Makefile
No patches applied
rm -rf ./.pc
- debian/rules build
rm -f debian/stamp-patch*
+ debian/rules build
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
test -x debian/rules
@@ -443,7 +412,7 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
@@ -501,8 +470,20 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
@@ -514,23 +495,23 @@ touch debian/stamp-makefile-build
make[1]: Entering directory `/«PKGBUILDDIR»/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[samopen] SAM header is present: 2 sequences.
-[samopen] SAM header is present: 2 sequences.
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[bam_rmdup_core] processing reference seq1...
+[samopen] SAM header is present: 2 sequences.
+[samopen] SAM header is present: 2 sequences.
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
+[bam_rmdup_core] processing reference seq1...
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
+../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-[mpileup] 1 samples in 1 input files
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
@@ -612,20 +593,20 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_hurd-i386.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_hurd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../samtools_0.1.17-1_hurd-i386.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1317
+Build finished at 20110906-0940
Finished
────────
@@ -637,58 +618,57 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_hurd-i386.changes:
+samtools_0.1.18-1_hurd-i386.changes:
────────────────────────────────────
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 81aa66efc48ab71fcbd27710134c99b43932cbd8 600368 samtools_0.1.17-1_hurd-i386.deb
- dac894d0dfbb21af4dcd72dcd3ad1d28e30f81b6 178560 libbam-dev_0.1.17-1_hurd-i386.deb
+ 0c06c1042e7683c687458c5c6ebc0b7f9f5a41ba 533060 samtools_0.1.18-1_hurd-i386.deb
+ 6feba00b744214746124c60e3a995b91f1b0db83 160788 libbam-dev_0.1.18-1_hurd-i386.deb
Checksums-Sha256:
- b24b32eb3aa40ec743903cb4a8c1ce0bf900a546e6ddea7019bc404711a706c2 600368 samtools_0.1.17-1_hurd-i386.deb
- adfac0d7cc9eb4094f2258235e4404b69ba2819d57b9825249b73cd60b05240e 178560 libbam-dev_0.1.17-1_hurd-i386.deb
+ 48da71bb7ee2f198f5df366b262eed3264f383235a9ced77346d54c5613f13c6 533060 samtools_0.1.18-1_hurd-i386.deb
+ ac0b99fef941bb84e08a4d9ca99090d30c66d938d9e4b47a91b436324545318a 160788 libbam-dev_0.1.18-1_hurd-i386.deb
Files:
- aed65c6d5b46b486309246e007868e05 600368 science optional samtools_0.1.17-1_hurd-i386.deb
- b0623a8eea9498b01c46921569d5827c 178560 libdevel optional libbam-dev_0.1.17-1_hurd-i386.deb
+ 7cca252aad346a52f0b77fb947ada7a0 533060 science optional samtools_0.1.18-1_hurd-i386.deb
+ 0494c70de6fe467a62f6a0f129e7070c 160788 libdevel optional libbam-dev_0.1.18-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_hurd-i386.deb
+samtools_0.1.18-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 600368 bytes: control archive= 1767 bytes.
- 793 bytes, 16 lines control
+ size 533060 bytes: control archive= 1767 bytes.
+ 792 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1116
- Depends: libc0.3 (>= 2.13), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1120
+ Depends: libc0.3 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -700,31 +680,31 @@ samtools_0.1.17-1_hurd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-07-11 13:14 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-09-06 09:38 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-07-11 13:15 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-07-11 13:15 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-07-11 13:15 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-07-11 13:16 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-09-06 09:39 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-09-06 09:38 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-09-06 09:38 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -737,34 +717,34 @@ drwxr-xr-x root/root 0 2011-07-11 13:16 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-07-11 13:16 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/bin/
--rwxr-xr-x root/root 133464 2011-07-11 13:15 ./usr/bin/bcftools
--rwxr-xr-x root/root 25764 2011-07-11 13:15 ./usr/bin/razip
--rwxr-xr-x root/root 385032 2011-07-11 13:15 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/lib/samtools/
--rwxr-xr-x root/root 18224 2011-07-11 13:15 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6736 2011-07-11 13:15 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6736 2011-07-11 13:15 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10596 2011-07-11 13:15 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7424 2011-07-11 13:15 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_hurd-i386.deb
+-rwxr-xr-x root/root 5778 2011-09-06 09:39 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/bin/
+-rwxr-xr-x root/root 133848 2011-09-06 09:39 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25860 2011-09-06 09:39 ./usr/bin/razip
+-rwxr-xr-x root/root 391432 2011-09-06 09:39 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17036 2011-09-06 09:39 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6736 2011-09-06 09:39 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6736 2011-09-06 09:39 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10452 2011-09-06 09:39 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7424 2011-09-06 09:39 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-1_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 178560 bytes: control archive= 927 bytes.
+ size 160788 bytes: control archive= 931 bytes.
678 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 448
+ Installed-Size: 456
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -775,21 +755,21 @@ libbam-dev_0.1.17-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 13:16 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 13:16 ./usr/lib/
--rw-r--r-- root/root 290368 2011-07-11 13:16 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/lib/
+-rw-r--r-- root/root 293478 2011-09-06 09:39 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 09:39 ./usr/include/samtools/
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
@@ -809,73 +789,48 @@ Purging /«BUILDDIR»
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libboost-iostreams1.42.0
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libboost-iostreams1.42.0
+The following packages were automatically installed and are no longer required:
+ libpopt0 libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libcroco3* libexpat1* libglib2.0-0* libmagic1*
- libncurses5-dev* libunistring0* libxml2* po-debconf* quilt*
- sbuild-build-depends-core-dummy* sbuild-build-depends-samtools-dummy*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 1 not upgraded.
-After this operation, 23.3 MB disk space will be freed.
-(Reading database ... 13554 files and directories currently installed.)
+ cdbs* diffstat* libncurses5-dev* quilt* sbuild-build-depends-core-dummy*
+ sbuild-build-depends-samtools-dummy* zlib1g-dev*
+0 upgraded, 0 newly installed, 7 to remove and 30 not upgraded.
+After this operation, 3113 kB disk space will be freed.
+(Reading database ... 13968 files and directories currently installed.)
Removing sbuild-build-depends-samtools-dummy ...
Removing cdbs ...
-Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
Removing diffstat ...
-Removing file ...
-Purging configuration files for file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libexpat1 ...
-Purging configuration files for libexpat1 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
Removing libncurses5-dev ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
Removing sbuild-build-depends-core-dummy ...
Removing zlib1g-dev ...
Processing triggers for man-db ...
-Processing triggers for install-info ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 10120
-Build-Time: 448
+Build-Space: 10392
+Build-Time: 243
Distribution: sid
-Install-Time: 235
-Job: samtools_0.1.17-1
+Install-Time: 80
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 917
-Source-Version: 0.1.17-1
-Space: 10120
+Package-Time: 419
+Source-Version: 0.1.18-1
+Space: 10392
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1317
-Build needed 00:15:17, 10120k disc space
+Finished at 20110906-0940
+Build needed 00:06:59, 10392k disc space
diff --git a/i386.log b/i386.log
index a30f726..f45de34 100644
--- a/i386.log
+++ b/i386.log
@@ -1,68 +1,71 @@
-From buildd at biber.debian.org Mon Jul 11 12:39:57 2011
-Return-path: <buildd at biber.debian.org>
+From buildd at murphy.debian.org Tue Sep 06 09:26:25 2011
+Return-path: <buildd at murphy.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1QgFmH-0003fS-Hh
- for logs at buildd.debian.org; Mon, 11 Jul 2011 12:39:57 +0000
-Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
+ (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
+ id 1R0rvE-0000QG-PN
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:26:25 +0000
+Received: from murphy.debian.org ([70.103.162.31])
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+ CN=murphy.debian.org, EMAIL=hostmaster at murphy.debian.org (verified)
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-Date: Mon, 11 Jul 2011 12:39:55 +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 samtools_0.1.17-1 on i386 (dist=sid)
-Key-Id: 44C3EAC7
+Date: Tue, 6 Sep 2011 09:26:20 +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 samtools_0.1.18-1 on i386 (dist=sid)
+Key-Id: AC7BC9C1
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (i386) 11 Jul 2011 12:37 ║
+║ samtools 0.1.18-1 (i386) 06 Sep 2011 09:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5379 kB]
-Get:3 http://ftp.gr.debian.org unstable/contrib Sources [52.4 kB]
-Get:4 http://ftp.gr.debian.org unstable/non-free Sources [95.0 kB]
-Get:5 http://incoming.debian.org unstable InRelease [146 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7492 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [67.3 kB]
-Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.gr.debian.org unstable/contrib Translation-en
+Hit http://ftp.us.debian.org sid InRelease
+Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
Ign http://incoming.debian.org InRelease
-Get:9 http://incoming.debian.org Release.gpg [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5379 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7492 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [67.3 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.1 kB]
-Get:18 http://incoming.debian.org Packages [457 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
+Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+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
+Get:4 http://ftp.us.debian.org sid/main TranslationIndex [2045 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:5 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:6 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
+Get:9 http://incoming.debian.org sid/main i386 2011-09-06-0818.53.pdiff [2652 B]
+Get:10 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
+Get:11 http://incoming.debian.org Sources [32.4 kB]
+Ign http://ftp.us.debian.org sid/contrib Translation-en
+Get:12 http://incoming.debian.org Packages [356 kB]
+Get:13 http://incoming.debian.org sid/main i386 2011-09-06-0818.53.pdiff [2652 B]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 27.0 MB in 19s (1367 kB/s)
+Fetched 553 kB in 7s (77.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +86,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 1s (214 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 1s (298 kB/s)
Download complete and in download only mode
Check arch
@@ -101,18 +104,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -121,37 +124,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
+dash: already installed (0.5.7-1)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+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 (5.12.4-1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.19.1-2)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-10)
-gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+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 (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -176,52 +179,29 @@ The following NEW packages will be installed:
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 16 not upgraded.
-Need to get 9957 kB of archives.
-After this operation, 29.6 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 bsdmainutils i386 8.2.3 [203 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.2-1 [991 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5+b1 [233 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5+b1 [49.4 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-3 [881 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.6-1 [1503 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-4 [431 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 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 libncurses5-dev i386 5.9-1 [467 kB]
-Get:21 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9957 kB in 1s (6547 kB/s)
+0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/10.0 MB of archives.
+After this operation, 29.8 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-(Reading database ... 10694 files and directories currently installed.)
+(Reading database ... 10781 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_i386.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_i386.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -231,15 +211,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_i386.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_i386.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_i386.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -249,27 +229,27 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up bsdmainutils (8.2.3) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -278,11 +258,11 @@ 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 0 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.52.20110703-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
-Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110703-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.1-2 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libquadmath0_4.6.1-9 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -293,12 +273,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -314,33 +294,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -354,22 +334,22 @@ 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-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -404,15 +384,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -420,10 +400,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -444,24 +424,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -469,16 +449,28 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -504,7 +496,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -539,8 +531,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -566,7 +558,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -580,70 +572,69 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_i386.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.17-1_i386.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1239
+Build finished at 20110906-0926
-samtools_0.1.17-1_i386.changes:
+samtools_0.1.18-1_i386.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
+Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 567a815b439ddc12d7411c2556d66fbcc7dd0ed7 594134 samtools_0.1.17-1_i386.deb
- bfd91c2d792c346f99956b65dc0a8f4329ffa2a6 178086 libbam-dev_0.1.17-1_i386.deb
+ db4a67c1c1d94224e012f8c23cd6dd31d01a2c25 532602 samtools_0.1.18-1_i386.deb
+ f16e5e8761f0bf979e1079a037888e88fac0dc32 160330 libbam-dev_0.1.18-1_i386.deb
Checksums-Sha256:
- d4ca234ddab796eeebcbefa449beceeaedbe72d703d286951bb1408f0af48160 594134 samtools_0.1.17-1_i386.deb
- e1f454875e1bb651926b8599f319da4d8ec127d3a41307691ab437a4347ac9ec 178086 libbam-dev_0.1.17-1_i386.deb
+ 4d72eb1b950ed9bf58d022490b850c18f445e7b8e5092d0e565622f89e24cb8e 532602 samtools_0.1.18-1_i386.deb
+ 96df10e8e765e7eebe455256869db9dffc1f16c698bc15e66e160b4070691e4f 160330 libbam-dev_0.1.18-1_i386.deb
Files:
- dfd58b32a3cec1856847d0061288f2d4 594134 science optional samtools_0.1.17-1_i386.deb
- e7ecf56a73e46be1d6a5cbefa3bf4fa8 178086 libdevel optional libbam-dev_0.1.17-1_i386.deb
+ 2c0d7250db586536bc1f28a5381b5bf5 532602 science optional samtools_0.1.18-1_i386.deb
+ 16e5bc19bcad992c877c8c60dd7b0107 160330 libdevel optional libbam-dev_0.1.18-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_i386.deb
+samtools_0.1.18-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 594134 bytes: control archive= 1762 bytes.
+ size 532602 bytes: control archive= 1761 bytes.
785 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1112
+ Installed-Size: 1120
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -656,71 +647,71 @@ samtools_0.1.17-1_i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/lib/samtools/
--rwxr-xr-x root/root 7184 2011-07-11 12:39 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6576 2011-07-11 12:39 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6576 2011-07-11 12:39 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10420 2011-07-11 12:39 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 18184 2011-07-11 12:39 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/bin/
--rwxr-xr-x root/root 133368 2011-07-11 12:39 ./usr/bin/bcftools
--rwxr-xr-x root/root 24660 2011-07-11 12:39 ./usr/bin/razip
--rwxr-xr-x root/root 384136 2011-07-11 12:39 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2011-07-11 12:39 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2011-07-11 12:39 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2011-07-11 12:39 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-07-11 12:39 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/bin/
+-rwxr-xr-x root/root 133752 2011-09-06 09:26 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24676 2011-09-06 09:26 ./usr/bin/razip
+-rwxr-xr-x root/root 390696 2011-09-06 09:26 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7184 2011-09-06 09:26 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6576 2011-09-06 09:26 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 16596 2011-09-06 09:26 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 10276 2011-09-06 09:26 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6576 2011-09-06 09:26 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2011-09-06 09:26 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-09-06 09:26 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/samtools/
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-07-11 12:39 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-lrwxrwxrwx root/root 0 2011-07-11 12:39 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 5778 2011-09-06 09:26 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 126609 2011-09-06 09:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 1966 2011-09-06 09:26 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+lrwxrwxrwx root/root 0 2011-09-06 09:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.17-1_i386.deb
+libbam-dev_0.1.18-1_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 178086 bytes: control archive= 925 bytes.
+ size 160330 bytes: control archive= 926 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 448
+ Installed-Size: 456
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -731,25 +722,25 @@ libbam-dev_0.1.17-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/lib/
--rw-r--r-- root/root 289336 2011-07-11 12:39 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/include/samtools/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/lib/
+-rw-r--r-- root/root 292326 2011-09-06 09:26 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -763,26 +754,74 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-973056c3-5002-4a94-b56a-a4a10ceda557/build/buildd-samtools_0.1.17-1-i386-Ir29Dn
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-i386-sbuild-8ffc7965-4fe7-440b-a24f-af956fb3e5cb/build/buildd-samtools_0.1.18-1-i386-FaumRv
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base*
+ groff-base* html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
+ libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
+ po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded.
+After this operation, 29.8 MB disk space will be freed.
+(Reading database ... 12298 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 10108
-Build-Time: 47
+Build-Space: 10388
+Build-Time: 55
Distribution: sid
-Install-Time: 41
-Job: samtools_0.1.17-1
+Install-Time: 10
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 121
-Source-Version: 0.1.17-1
-Space: 10108
+Package-Time: 80
+Source-Version: 0.1.18-1
+Space: 10388
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1239
-Build needed 00:02:01, 10108k disc space
-Signature with key '44C3EAC7' requested:
+Finished at 20110906-0926
+Build needed 00:01:20, 10388k disc space
+Signature with key 'AC7BC9C1' requested:
diff --git a/ia64.log b/ia64.log
index 489530f..d401e5a 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,67 +1,66 @@
-From buildd at alkman.debian.org Mon Jul 11 12:43:15 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 Tue Sep 06 11:00:20 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 1QgFpT-0004J9-EX
- for logs at buildd.debian.org; Mon, 11 Jul 2011 12:43:15 +0000
-Received: from alkman.debian.org ([192.25.206.63])
+ (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
+ id 1R0tO8-0007zP-0y
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 11:00:20 +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 1QgFpS-00089h-4P
- for logs at buildd.debian.org; Mon, 11 Jul 2011 12:43:14 +0000
-Received: from buildd by alkman.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alkman.debian.org>)
- id 1QgFpP-0001ff-MY; Mon, 11 Jul 2011 12:43:11 +0000
-Date: Mon, 11 Jul 2011 12:43:11 +0000
-Message-Id: <E1QgFpP-0001ff-MY 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 samtools_0.1.17-1 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 1R0tO6-00008v-2K; Tue, 06 Sep 2011 11:00:18 +0000
+Received: from buildd by mundy.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at mundy.debian.org>)
+ id 1R0tO2-0005zD-Fi; Tue, 06 Sep 2011 11:00:14 +0000
+Date: Tue, 06 Sep 2011 11:00:14 +0000
+Message-Id: <E1R0tO2-0005zD-Fi 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 samtools_0.1.18-1 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
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (ia64) 11 Jul 2011 12:39 ║
+║ samtools 0.1.18-1 (ia64) 06 Sep 2011 10:55 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: ia64
Get:1 http://spohr.debian.org unstable InRelease [146 kB]
-Get:2 http://spohr.debian.org unstable/main Sources [5379 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
-Get:4 http://spohr.debian.org unstable/contrib Sources [52.4 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [95.0 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [7242 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://spohr.debian.org unstable/main Sources [5470 kB]
+Get:4 http://spohr.debian.org unstable/contrib Sources [53.9 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [94.9 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [7405 kB]
Ign http://incoming.debian.org InRelease
Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5379 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [54.5 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [5470 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [56.3 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 [52.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [7242 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [54.5 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [7405 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [56.3 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.1 kB]
-Get:18 http://incoming.debian.org Packages [457 kB]
+Get:17 http://incoming.debian.org Sources [32.5 kB]
+Get:18 http://incoming.debian.org Packages [331 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.4 MB in 23s (1134 kB/s)
+Fetched 26.8 MB in 17s (1539 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +81,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 0s (449 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 0s (443 kB/s)
Download complete and in download only mode
Check arch
@@ -106,18 +105,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libdb4.8
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 50 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libdb4.8
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 50 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -127,36 +120,36 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
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 (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-1)
+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 (5.12.3-7+b1)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.10)
-sysvinit: already installed (2.88dsf-13.10)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6.1-dev: already installed (2.13-7)
-gcc: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-4)
+mount: already installed (2.19.1-4)
+util-linux: already installed (2.19.1-4)
+libc6.1-dev: already installed (2.13-10)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -166,9 +159,6 @@ Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-de
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libdb4.8
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
@@ -184,52 +174,52 @@ The following NEW packages will be installed:
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 36 not upgraded.
-Need to get 12.1 MB of archives.
-After this operation, 42.3 MB of additional disk space will be used.
+0 upgraded, 22 newly installed, 0 to remove and 50 not upgraded.
+Need to get 12.0 MB of archives.
+After this operation, 45.6 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 bsdmainutils ia64 8.2.3 [238 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-1 [1122 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.04-5+b1 [263 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5+b1 [52.0 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-3 [174 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-3 [316 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-3 [1181 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 5.04-5+b1 [263 kB]
+Get:7 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5+b1 [52.0 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 html2text ia64 1.3.2a-15 [134 kB]
Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.6-1 [1973 kB]
Get:12 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
Get:13 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-4 [467 kB]
-Get:14 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-3 [2453 kB]
+Get:14 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-4 [2441 kB]
Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9 kB]
Get:20 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.9-1 [614 kB]
Get:21 http://spohr.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:22 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 12.1 MB in 1s (10.7 MB/s)
+Fetched 12.0 MB in 3s (3058 kB/s)
Selecting previously deselected package libpipeline1.
-(Reading database ... 10485 files and directories currently installed.)
+(Reading database ... 10586 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_ia64.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_ia64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_ia64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_ia64.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_ia64.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_ia64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_ia64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_ia64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -239,15 +229,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_ia64.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_ia64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_ia64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_ia64.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -257,27 +247,27 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected 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 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 (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -286,14 +276,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libdb4.8
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 50 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-6 gcc-4.4_4.4.6-6 libc6.1-dev_2.13-7 libstdc++6_4.6.0-13 libstdc++6-4.4-dev_4.4.6-6 linux-libc-dev_2.6.39-2
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-9 g++-4.4_4.4.6-6 gcc_4:4.4.5-9 gcc-4.4_4.4.6-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6-base_4.6.0-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6.1_2.13-7 libc6.1-dev_2.13-7 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-13 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-13 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-13 libstdc++6-4.4-dev_4.4.6-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7+b1 perl-base_5.12.3-7+b1 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110720-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-4 gcc-4.6_4.6.1-4 libc6.1-dev_2.13-10 libstdc++6_4.6.1-4 libstdc++6-4.6-dev_4.6.1-4 linux-libc-dev_2.6.39-3
+Package versions: apt_0.8.15.2 base-files_6.4 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110720-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-4 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-4 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-4 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-4 gcc-4.6-base_4.6.1-4 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 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_2.19.1-4 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6.1_2.13-10 libc6.1-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-4 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-4 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-4 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-4 libstdc++6-4.6-dev_4.6.1-4 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-4 libxml2_2.7.8.dfsg-4 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-4 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-4 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -304,12 +291,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -325,33 +312,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -365,23 +352,25 @@ 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-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
@@ -389,6 +378,8 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
@@ -398,16 +389,22 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -415,10 +412,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -434,27 +431,29 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -462,16 +461,20 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -497,7 +500,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -532,8 +535,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -559,7 +562,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -573,70 +576,69 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_ia64.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_ia64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.17-1_ia64.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1243
+Build finished at 20110906-1100
-samtools_0.1.17-1_ia64.changes:
+samtools_0.1.18-1_ia64.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.17-1
+Version: 0.1.18-1
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:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 53724ca4450953f26bb333732dd7bbc1e3e4f24e 736796 samtools_0.1.17-1_ia64.deb
- 27d38e521bd412d533c275bcfec6c6af09f2ddef 224840 libbam-dev_0.1.17-1_ia64.deb
+ c5702832e992687c0e3d02ff551c9572a2426926 603192 samtools_0.1.18-1_ia64.deb
+ 0f9c8981134302e058ac2cacf8a99a4041ed782a 193930 libbam-dev_0.1.18-1_ia64.deb
Checksums-Sha256:
- ac412a98f8bf0f39f72e79fc3c0f4017a5ccbfc0a782fc982f18b9dc30418823 736796 samtools_0.1.17-1_ia64.deb
- c4b4e46a0759362dae0f5f2b53284fa99e1264578e303f083e8e5858d0d3c3b0 224840 libbam-dev_0.1.17-1_ia64.deb
+ 87061f11c5437b1d82aae2be12f9a4bcafacdff5d389ec4eba240bf0a5521d4c 603192 samtools_0.1.18-1_ia64.deb
+ 28a996a7f71bebbd88d0b14214d2051a3917328ae331e496db073d7d180760d2 193930 libbam-dev_0.1.18-1_ia64.deb
Files:
- 524ee77879c61357d2eb06beaca76d49 736796 science optional samtools_0.1.17-1_ia64.deb
- fac3f60640a89682510996d03ade0939 224840 libdevel optional libbam-dev_0.1.17-1_ia64.deb
+ 4c25cf6fd0c277a9f890289958eb687a 603192 science optional samtools_0.1.18-1_ia64.deb
+ 077355a1497df7e1ebd61c30b6f69937 193930 libdevel optional libbam-dev_0.1.18-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_ia64.deb
+samtools_0.1.18-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 736796 bytes: control archive= 1760 bytes.
+ size 603192 bytes: control archive= 1760 bytes.
787 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 2032
+ Installed-Size: 1788
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -649,71 +651,71 @@ samtools_0.1.17-1_ia64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/lib/samtools/
--rwxr-xr-x root/root 30712 2011-07-11 12:42 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13360 2011-07-11 12:42 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13296 2011-07-11 12:42 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 22384 2011-07-11 12:42 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2011-07-11 12:42 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/bin/
--rwxr-xr-x root/root 298104 2011-07-11 12:42 ./usr/bin/bcftools
--rwxr-xr-x root/root 52520 2011-07-11 12:42 ./usr/bin/razip
--rwxr-xr-x root/root 777880 2011-07-11 12:42 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-07-11 12:42 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2011-09-06 10:59 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-09-06 10:59 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-09-06 10:59 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-07-11 12:42 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-07-11 12:42 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/samtools/
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-07-11 12:42 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2011-07-11 12:42 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-lrwxrwxrwx root/root 0 2011-07-11 12:42 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_ia64.deb
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2011-09-06 10:59 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-09-06 10:59 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/bin/
+-rwxr-xr-x root/root 826048 2011-09-06 10:59 ./usr/bin/samtools
+-rwxr-xr-x root/root 50704 2011-09-06 10:59 ./usr/bin/razip
+-rwxr-xr-x root/root 303872 2011-09-06 10:59 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/lib/samtools/
+-rwxr-xr-x root/root 13136 2011-09-06 10:59 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13136 2011-09-06 10:59 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 14944 2011-09-06 10:59 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 30976 2011-09-06 10:59 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 21952 2011-09-06 10:59 ./usr/lib/samtools/md5fa
+lrwxrwxrwx root/root 0 2011-09-06 10:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-1_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 224840 bytes: control archive= 922 bytes.
+ size 193930 bytes: control archive= 926 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 800
+ Installed-Size: 736
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -724,25 +726,25 @@ libbam-dev_0.1.17-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/include/samtools/
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 11:00 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/include/samtools/
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/lib/
--rw-r--r-- root/root 556858 2011-07-11 12:42 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+drwxr-xr-x root/root 0 2011-09-06 11:00 ./usr/lib/
+-rw-r--r-- root/root 581210 2011-09-06 11:00 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -756,7 +758,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-4179d541-5a60-42d5-83dc-43fa767e5f24/build/buildd-samtools_0.1.17-1-ia64-I37Jnr
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-1e7e0178-a052-4b8c-9a07-72f104b43ee6/build/buildd-samtools_0.1.18-1-ia64-u1PcjN
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -764,19 +766,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 16068
-Build-Time: 120
+Build-Space: 15608
+Build-Time: 144
Distribution: sid
-Install-Time: 64
-Job: samtools_0.1.17-1
+Install-Time: 62
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 235
-Source-Version: 0.1.17-1
-Space: 16068
+Package-Time: 254
+Source-Version: 0.1.18-1
+Space: 15608
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1243
-Build needed 00:03:55, 16068k disc space
-Signature with key '591AB71E' requested:
+Finished at 20110906-1100
+Build needed 00:04:14, 15608k disc space
+Signature with key '96FA48F4' requested:
diff --git a/info b/info
index e06e6cb..2b270f0 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-i386~1310388004~sid~successful
-powerpc~1310388092~sid~successful
-ia64~1310388196~sid~successful
-kfreebsd-i386~1310388443~sid~successful
-sparc~1310388463~sid~failed
-mips~1310389257~sid~successful
-hurd-i386~1310390340~sid~successful
-kfreebsd-amd64~1310395607~sid~successful
-s390~1310412477~sid~successful
-mipsel~1310455676~sid~successful
-armel~1310493558~sid~failed
+i386~1315301186~sid~successful
+kfreebsd-i386~1315301530~sid~successful
+powerpc~1315301629~sid~successful
+armel~1315301631~sid~failed
+kfreebsd-amd64~1315301956~sid~successful
+hurd-i386~1315302076~sid~successful
+mipsel~1315302340~sid~successful
+mips~1315302649~sid~successful
+ia64~1315306820~sid~successful
+s390~1315308404~sid~successful
+sparc~1315333538~sid~failed
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 1e7c15b..5ba88e4 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,81 +1,77 @@
-From buildd at fasch.debian.org Mon Jul 11 14:46:46 2011
+From buildd at fasch.debian.org Tue Sep 06 09:39:15 2011
Return-path: <buildd at fasch.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 fasch.debian.org>)
- id 1QgHl0-0007Jz-7N
- for logs at buildd.debian.org; Mon, 11 Jul 2011 14:46:46 +0000
+ id 1R0s7f-0002vM-5V
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:39:15 +0000
Received: from fasch.debian.org ([194.177.211.201])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=fasch.debian.org, EMAIL=hostmaster at fasch.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 fasch.debian.org>)
- id 1QgHky-0002td-Os; Mon, 11 Jul 2011 14:46:45 +0000
+ id 1R0s7c-0001aF-Fz; Tue, 06 Sep 2011 09:39:12 +0000
Received: from buildd by fasch.debian.org with local (Exim 4.72)
(envelope-from <buildd at fasch.debian.org>)
- id 1QgHkx-0004bK-Mx; Mon, 11 Jul 2011 14:46:43 +0000
-Message-Id: <E1QgHkx-0004bK-Mx at fasch.debian.org>
+ id 1R0s7b-0004VG-KM; Tue, 06 Sep 2011 09:39:11 +0000
+Message-Id: <E1R0s7b-0004VG-KM at fasch.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Mon, 11 Jul 2011 14:46:43 +0000
+Date: Tue, 6 Sep 2011 09:39:11 +0000
From: buildd on fasch <buildd at fasch.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.17-1 on kfreebsd-amd64
+Subject: Log for successful build of samtools_0.1.18-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 516A3A7B
+Key-Id: 56BAE008
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (kfreebsd-amd64) 11 Jul 2011 14:43 ║
+║ samtools 0.1.18-1 (kfreebsd-amd64) 06 Sep 2011 09:36 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: kfreebsd-amd64
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]
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
Hit http://ftp.gr.debian.org sid/main kfreebsd-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
+Get:1 http://ftp.gr.debian.org sid/main TranslationIndex [2045 B]
Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
+Get:2 http://incoming.debian.org Release.gpg [836 B]
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/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:4 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:5 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:6 http://incoming.debian.org Release [1604 B]
-Get:7 http://incoming.debian.org sid/main 2011-07-11-1412.48.pdiff [8897 B]
-Get:8 http://incoming.debian.org sid/main kfreebsd-amd64 2011-07-11-1412.48.pdiff [14.6 kB]
-Get:9 http://incoming.debian.org sid/main 2011-07-11-1412.48.pdiff [8897 B]
-Get:10 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [82.8 kB]
-Hit http://incoming.debian.org Sources
-Get:11 http://incoming.debian.org Packages [435 kB]
-Get:12 http://incoming.debian.org sid/main kfreebsd-amd64 2011-07-11-1412.48.pdiff [14.6 kB]
+Get:3 http://incoming.debian.org Release [1604 B]
+Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
+Get:4 http://incoming.debian.org Sources [33.2 kB]
+Get:5 http://incoming.debian.org Packages [352 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 696 kB in 5s (121 kB/s)
+Fetched 389 kB in 4s (81.7 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,11 +92,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/debian/ sid/main samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/debian/ sid/main samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/debian/ sid/main samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 2s (187 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 2s (182 kB/s)
Download complete and in download only mode
Check arch
@@ -114,7 +110,7 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+fakeroot: already installed (1.17-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
@@ -134,130 +130,61 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
+dash: already installed (0.5.7-1)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.2+ds2-1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+freebsd-utils: already installed (8.2+ds2-5)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
+bsdutils: already installed (1:2.19.1-5)
+util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 8.9.0
+debhelper: already installed (8.9.6 >= 8 is satisfied)
cdbs: missing
-quilt: missing
+quilt: already installed (0.48-7)
libncurses5-dev: missing
-zlib1g-dev: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: cdbs libncurses5-dev
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 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
Suggested packages:
- devscripts dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl procmail graphviz
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ devscripts ncurses-doc
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+ cdbs libncurses5-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/10.1 MB of archives.
-After this operation, 28.4 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 12157 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-amd64.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-amd64.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/579 kB of archives.
+After this operation, 2003 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
-Selecting previously deselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-amd64.deb) ...
+(Reading database ... 17857 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_kfreebsd-amd64.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected 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 man-db (2.6.0.2-1) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
-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 (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
-Setting up diffstat (1.54-1) ...
+Processing triggers for man-db ...
+Setting up cdbs (0.4.96) ...
Setting up libncurses5-dev (5.9-1) ...
-Setting up quilt (0.48-7) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -265,8 +192,8 @@ Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-3 gcc-4.6_4.6.1-3 kfreebsd-kernel-headers_0.56 libc0.1-dev_2.13-10 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3
-Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.1-1 cpp-4.6_4.6.1-3 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-1 g++_4:4.6.1-1 g++-4.6_4.6.1-3 gcc_4:4.6.1-1 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-3 gcc-4.6-base_4.6.1-3 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.56 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.17.2-9.1 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc0.1_2.13-10 libc0.1-dev_2.13-10 libcam0_8.2+ds1-3 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-3 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-3 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-2 libgomp1_4.6.1-3 libgpg-error0_1.10-0.3 libkiconv4_8.2+ds1-3 libkvm0_8.2+ds1-3 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.1-3 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libsbuf0_8.2+ds1-3 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 libtasn1-3_2.9-4 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 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_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 type-handling_0.2.23 tzdata_2011h-3 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 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 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-10 g++-4.6_4.6.1-9 gcc-4.4_4.4.6-10 gcc-4.6_4.6.1-9 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.4-dev_4.4.6-10 libstdc++6-4.6-dev_4.6.1-9
+Package versions: apt_0.8.15.6 autoconf_2.68-1 autoconf2.64_2.64-3 autogen_1:5.12-0.1 automake_1:1.11.1-1 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 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_0.4.96 chrpath_0.13-2 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 dejagnu_1.5-2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 expect_5.45-1 fakeroot_1.17-1 file_5.04-5+b1 findutils_4.4.2-1 flex_2.5.35-10 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.4_4.4.6-10 g++-4.6_4.6.1-9 g++-4.6-multilib_4.6.1-9 g++-multilib_4:4.6.1-2 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-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gcc-4.6-multilib_4.6.1-9 gcc-multilib_4:4.6.1-2 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 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 guile-1.8-libs_1.8.8+1-6 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 lib32gcc1_1:4.6.1-9 lib32gomp1_4.6.1-9 lib32quadmath0_4.6.1-9 lib32stdc++6_4.6.1-9 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_2.13-18 libc-dev-bin_2.13-18 libc0.1_2.13-18 libc0.1-dev_2.13-18 libc0.1-dev-i386_2.13-18 libc0.1-i386_2.13-18 libcam0_8.2+ds1-4 libcloog-ppl-dev_0.15.9-3 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libelfg0-dev_0.8.13-3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp-dev_2:5.0.2+dfsg-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 libltdl7_2.4-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmpc-dev_0.9-3 libmpc2_0.9-3 libmpfr-dev_3.0.1-6 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libopts25_1:5.12-0.1 libopts25-dev_1:5.12-0.1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libppl-c4_0.11.2-4 libppl0.11-dev_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-9 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 libsigsegv2_2.9-4 libslang2_2.2.4-3 libsqlite3-0_3.7.7-2 libss2_1.42~WIP-2011-07-02-1 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-9 libstdc++6-4.4-dev_4.4.6-10 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 libtool_2.4-4 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 locales_2.13-18 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lsb-release_3.2-28 lzma_4.43-14 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 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 patchutils_0.3.2-1 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 python_2.6.7-3 python-minimal_2.6.7-3 python-support_1.0.14 python2.6_2.6.7-4 python2.6-minimal_2.6.7-4 quilt_0.48-7 readline-common_6.2-4 realpath_1.15 sed_4.2.1-9 sensible-utils_0.0.6 sharutils_1:4.11-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tcl8.5_8.5.10-1 texinfo_4.13a.dfsg.1-8 type-handling_0.2.23 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -277,12 +204,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -298,33 +225,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -338,22 +265,22 @@ 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-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -382,15 +309,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -398,10 +325,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -422,24 +349,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -447,16 +374,20 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -482,7 +413,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -517,8 +448,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -544,7 +475,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -558,28 +489,28 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_kfreebsd-amd64.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_kfreebsd-amd64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../samtools_0.1.17-1_kfreebsd-amd64.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1445
+Build finished at 20110906-0938
-samtools_0.1.17-1_kfreebsd-amd64.changes:
+samtools_0.1.18-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
@@ -588,40 +519,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 0f8061d716d9b73d056557e924f44b11f4188b3f 594980 samtools_0.1.17-1_kfreebsd-amd64.deb
- 928599643e76e0ceb2dada8d4b6609dbe19309e4 170180 libbam-dev_0.1.17-1_kfreebsd-amd64.deb
+ 8a39f128e0ac110ee1d45084e8243951ce3cf6aa 527722 samtools_0.1.18-1_kfreebsd-amd64.deb
+ 9b59a326c91d5e85fce7e846c7d990059c6bddd5 153840 libbam-dev_0.1.18-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 40b708b18d43aa4217b69c2355f074ea657aa953fdccbb453da134ba2ef9b350 594980 samtools_0.1.17-1_kfreebsd-amd64.deb
- 5b3d670c56f99a8bdd5f1b246c846fae99ca16652f6a390eb7ca1a2a8dfb0736 170180 libbam-dev_0.1.17-1_kfreebsd-amd64.deb
+ bf6c3f4fd9084f11801119ee989e4bf7d173a3bb2c57a79ad7f7ee9413623d57 527722 samtools_0.1.18-1_kfreebsd-amd64.deb
+ 2dca0e928fb2c3f451ae07a518b083c06fc6a21fea40713b9944627bdb845ff8 153840 libbam-dev_0.1.18-1_kfreebsd-amd64.deb
Files:
- 7183a76d762a07a74723ea4061a87a6d 594980 science optional samtools_0.1.17-1_kfreebsd-amd64.deb
- da8422ad9630e4d5abfaaeb0091bc0e0 170180 libdevel optional libbam-dev_0.1.17-1_kfreebsd-amd64.deb
+ 8b5fc39f2c2a24d1d455126ac50a801f 527722 science optional samtools_0.1.18-1_kfreebsd-amd64.deb
+ 4fa210cfabefb9fcd39c5abb0c2dc303 153840 libdevel optional libbam-dev_0.1.18-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_kfreebsd-amd64.deb
+samtools_0.1.18-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 594980 bytes: control archive= 1764 bytes.
+ size 527722 bytes: control archive= 1766 bytes.
797 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1022
+ Installed-Size: 1036
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -634,31 +564,31 @@ samtools_0.1.17-1_kfreebsd-amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-07-11 14:45 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-09-06 09:38 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-07-11 14:45 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-07-11 14:45 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-07-11 14:45 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-09-06 09:38 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-09-06 09:38 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-09-06 09:38 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -671,34 +601,34 @@ drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-07-11 14:45 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/bin/
--rwxr-xr-x root/root 130528 2011-07-11 14:45 ./usr/bin/bcftools
--rwxr-xr-x root/root 24448 2011-07-11 14:45 ./usr/bin/razip
--rwxr-xr-x root/root 356920 2011-07-11 14:45 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/lib/samtools/
--rwxr-xr-x root/root 19288 2011-07-11 14:45 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8208 2011-07-11 14:45 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8144 2011-07-11 14:45 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11992 2011-07-11 14:45 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8736 2011-07-11 14:45 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2011-09-06 09:38 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/bin/
+-rwxr-xr-x root/root 130528 2011-09-06 09:38 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24536 2011-09-06 09:38 ./usr/bin/razip
+-rwxr-xr-x root/root 363832 2011-09-06 09:38 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18000 2011-09-06 09:38 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8208 2011-09-06 09:38 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8144 2011-09-06 09:38 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11864 2011-09-06 09:38 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8736 2011-09-06 09:38 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-1_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 170180 bytes: control archive= 932 bytes.
+ size 153840 bytes: control archive= 928 bytes.
683 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 464
+ Installed-Size: 466
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -709,21 +639,21 @@ libbam-dev_0.1.17-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/lib/
--rw-r--r-- root/root 320058 2011-07-11 14:45 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/
+-rw-r--r-- root/root 323274 2011-09-06 09:38 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/include/samtools/
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
@@ -741,7 +671,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1310395393-15518/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1315301795-15293/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE
Reading package lists...
Building dependency tree...
Reading state information...
@@ -750,63 +680,31 @@ 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*
- libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
- po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 21 to remove and 0 not upgraded.
-After this operation, 28.4 MB disk space will be freed.
-(Reading database ... 13567 files and directories currently installed.)
+ cdbs* libncurses5-dev*
+0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded.
+After this operation, 2003 kB disk space will be freed.
+(Reading database ... 17948 files and directories currently installed.)
Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 11694
-Build-Time: 57
+Build-Space: 12178
+Build-Time: 60
Distribution: sid
-Install-Time: 81
-Job: samtools_0.1.17-1
+Install-Time: 35
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 161
-Source-Version: 0.1.17-1
-Space: 11694
+Package-Time: 127
+Source-Version: 0.1.18-1
+Space: 12178
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1445
-Build needed 00:02:41, 11694k disc space
-Signature with key '516A3A7B' requested:
+Finished at 20110906-0938
+Build needed 00:02:07, 12178k disc space
+Signature with key '56BAE008' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 512c33b..c1bb53a 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,75 +1,83 @@
-From buildd at field.debian.org Mon Jul 11 12:47:23 2011
-Return-path: <buildd at field.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at finzi.debian.org Tue Sep 06 09:32:10 2011
+Return-path: <buildd at finzi.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- 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 1QgFtS-0004mp-Nx
- for logs at buildd.debian.org; Mon, 11 Jul 2011 12:47:22 +0000
-Received: from field.debian.org ([194.177.211.210])
+ (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
+ id 1R0s0n-0001sW-MP
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:32:10 +0000
+Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1QgFtQ-0000DQ-Mp; Mon, 11 Jul 2011 12:47:20 +0000
-Received: from buildd by field.debian.org with local (Exim 4.72)
- (envelope-from <buildd at field.debian.org>)
- id 1QgFtO-0000VJ-Vd; Mon, 11 Jul 2011 12:47:19 +0000
-Message-Id: <E1QgFtO-0000VJ-Vd at field.debian.org>
+ CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
+ id 1R0s0k-0001KV-DO; Tue, 06 Sep 2011 09:32:06 +0000
+Received: from buildd by finzi.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at finzi.debian.org>)
+ id 1R0s0i-000EQw-17; Tue, 06 Sep 2011 09:32:04 +0000
+Message-Id: <E1R0s0i-000EQw-17 at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Mon, 11 Jul 2011 12:47:18 +0000
-From: buildd on field <buildd at field.debian.org>
+Date: Tue, 6 Sep 2011 09:32:03 +0000
+From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.17-1 on kfreebsd-i386
+Subject: Log for successful build of samtools_0.1.18-1 on kfreebsd-i386
(dist=sid)
-Key-Id: 22C61858
+Key-Id: C1A6480B
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (kfreebsd-i386) 11 Jul 2011 12:43 ║
+║ samtools 0.1.18-1 (kfreebsd-i386) 06 Sep 2011 09:29 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: kfreebsd-i386
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org sid InRelease [146 kB]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.gr.debian.org sid/main TranslationIndex
-Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Ign http://ftp.gr.debian.org sid/contrib Translation-en
-Ign http://ftp.gr.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
+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
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Get:4 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
+Get:5 http://incoming.debian.org sid/main TranslationIndex [2045 B]
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [36.1 kB]
-Get:4 http://incoming.debian.org Packages [457 kB]
+Get:6 http://mirror-ubc.debian.org sid InRelease [146 kB]
+Get:7 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:8 http://incoming.debian.org Release [1604 B]
+Get:9 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
+Get:10 http://incoming.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
+Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
+Get:11 http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
+Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
+Get:12 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
+Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
+Get:13 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
+Get:14 http://mirror-ubc.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
+Get:15 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
+Get:16 http://incoming.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
+Ign http://mirror-ubc.debian.org sid/contrib Translation-en
+Ign http://mirror-ubc.debian.org sid/non-free Translation-en
+Get:17 http://incoming.debian.org Sources [32.4 kB]
+Get:18 http://incoming.debian.org Packages [356 kB]
+Get:19 http://mirror-ubc.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 496 kB in 5s (85.1 kB/s)
+Get:20 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
+Fetched 712 kB in 9s (72.5 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,11 +98,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 1s (213 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 0s (397 kB/s)
Download complete and in download only mode
Check arch
@@ -108,18 +116,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+fakeroot: already installed (1.17-1)
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 0 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 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -128,37 +136,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
+dash: already installed (0.5.7-1)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.2+ds1-2)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+freebsd-utils: already installed (8.2+ds2-5)
+grep: already installed (2.9-2)
+gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
+bsdutils: already installed (1:2.19.1-5)
+util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -169,40 +177,38 @@ 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 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ diffstat file gettext gettext-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
- devscripts dh-make gettext-doc groff ncurses-doc less www-browser
+ devscripts dh-make gettext-doc ncurses-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
+ 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 libncurses5-dev libpcre3
- 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 libncurses5-dev libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 16 not upgraded.
-Need to get 0 B/9683 kB of archives.
-After this operation, 27.0 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/8631 kB of archives.
+After this operation, 24.1 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-(Reading database ... 12215 files and directories currently installed.)
+(Reading database ... 12381 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-i386.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_kfreebsd-i386.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -212,15 +218,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-i386.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -230,24 +236,23 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -256,11 +261,11 @@ 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 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 kfreebsd-kernel-headers_0.56 libc0.1-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2
-Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.2+ds1-2 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.56 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.17.2-9.1 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc0.1_2.13-10 libc0.1-dev_2.13-10 libcam0_8.2+ds1-3 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-3 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-2 libgomp1_4.6.1-2 libgpg-error0_1.10-0.3 libkiconv4_8.2+ds1-3 libkvm0_8.2+ds1-3 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.1-2 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libsbuf0_8.2+ds1-3 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtasn1-3_2.9-4 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 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_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 type-handling_0.2.23 tzdata_2011h-3 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 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 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9
+Package versions: apt_0.8.15.6 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.17-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 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_2.13-18 libc-dev-bin_2.13-18 libc0.1_2.13-18 libc0.1-dev_2.13-18 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 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_4.6.1-9 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_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-9 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -271,12 +276,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -292,33 +297,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -332,22 +337,22 @@ 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-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -382,15 +387,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -398,10 +403,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -422,24 +427,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -447,16 +452,28 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -482,7 +499,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -517,8 +534,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -544,7 +561,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -558,67 +575,66 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_kfreebsd-i386.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_kfreebsd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.17-1_kfreebsd-i386.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1246
+Build finished at 20110906-0931
-samtools_0.1.17-1_kfreebsd-i386.changes:
+samtools_0.1.18-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 079b9aad31db2a2c636198f0eb90bb2b49f51e66 599780 samtools_0.1.17-1_kfreebsd-i386.deb
- 9f4e107f6de963aaef4e5dbe500cdda6336d8324 178550 libbam-dev_0.1.17-1_kfreebsd-i386.deb
+ cb33cc7329b1278127faff60292add2734416ffc 532642 samtools_0.1.18-1_kfreebsd-i386.deb
+ 10b014005110e5fc17890bd96bfe206df1153ff4 160694 libbam-dev_0.1.18-1_kfreebsd-i386.deb
Checksums-Sha256:
- 62064c9bc162cb6aa58400a5b8564e6f12002468ba9d69e5ec20e64c948f45a3 599780 samtools_0.1.17-1_kfreebsd-i386.deb
- fe092366bc2af8f5a5ab9d7aa793ecb6d80eb7dc195a448cf908aa3126f59332 178550 libbam-dev_0.1.17-1_kfreebsd-i386.deb
+ 6270482bbac85ed3cb7300cdb1d516aaab254846a84dfbd036c2908ec4e69534 532642 samtools_0.1.18-1_kfreebsd-i386.deb
+ 1f972e4fb50e21be809430edadadfdf744fce92591a28bdd2e5c35dfe8303191 160694 libbam-dev_0.1.18-1_kfreebsd-i386.deb
Files:
- 873c09ed27b4dc6158a49ac405bd5a1c 599780 science optional samtools_0.1.17-1_kfreebsd-i386.deb
- 8389c9a0977c09e4de6c4af887f9bbba 178550 libdevel optional libbam-dev_0.1.17-1_kfreebsd-i386.deb
+ 717849b0b349a09f57b0a384e0bb90d2 532642 science optional samtools_0.1.18-1_kfreebsd-i386.deb
+ 53394320ca5f013d7be58c182b0f8504 160694 libdevel optional libbam-dev_0.1.18-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_kfreebsd-i386.deb
+samtools_0.1.18-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 599780 bytes: control archive= 1763 bytes.
+ size 532642 bytes: control archive= 1761 bytes.
796 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 1054
@@ -634,31 +650,31 @@ samtools_0.1.17-1_kfreebsd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-07-11 12:46 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-09-06 09:31 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-07-11 12:46 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-07-11 12:46 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-07-11 12:46 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-09-06 09:31 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-09-06 09:31 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-09-06 09:31 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -671,34 +687,34 @@ drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-07-11 12:46 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/bin/
--rwxr-xr-x root/root 133368 2011-07-11 12:46 ./usr/bin/bcftools
--rwxr-xr-x root/root 25588 2011-07-11 12:46 ./usr/bin/razip
--rwxr-xr-x root/root 385000 2011-07-11 12:46 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/lib/samtools/
--rwxr-xr-x root/root 18184 2011-07-11 12:46 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6560 2011-07-11 12:46 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6560 2011-07-11 12:46 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10388 2011-07-11 12:46 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7136 2011-07-11 12:46 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2011-09-06 09:31 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/bin/
+-rwxr-xr-x root/root 133656 2011-09-06 09:31 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25684 2011-09-06 09:31 ./usr/bin/razip
+-rwxr-xr-x root/root 391400 2011-09-06 09:31 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/lib/samtools/
+-rwxr-xr-x root/root 16748 2011-09-06 09:31 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6560 2011-09-06 09:31 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6560 2011-09-06 09:31 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10244 2011-09-06 09:31 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7136 2011-09-06 09:31 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-1_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 178550 bytes: control archive= 926 bytes.
+ size 160694 bytes: control archive= 929 bytes.
682 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 432
+ Installed-Size: 434
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -709,21 +725,21 @@ libbam-dev_0.1.17-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/lib/
--rw-r--r-- root/root 290308 2011-07-11 12:46 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/lib/
+-rw-r--r-- root/root 293418 2011-09-06 09:31 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/include/samtools/
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
@@ -741,22 +757,22 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1310388232-99437/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1315301373-52721/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm
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 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
- libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
- po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 21 to remove and 16 not upgraded.
-After this operation, 27.0 MB disk space will be freed.
-(Reading database ... 13625 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
+ libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 20 to remove and 0 not upgraded.
+After this operation, 24.1 MB disk space will be freed.
+(Reading database ... 13608 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -767,10 +783,6 @@ 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 ...
@@ -782,6 +794,8 @@ Purging configuration files for libmagic1 ...
Removing libncurses5-dev ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
+Removing man-db ...
+Purging configuration files for man-db ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
@@ -795,18 +809,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 9806
-Build-Time: 56
+Build-Space: 10056
+Build-Time: 67
Distribution: sid
-Install-Time: 78
-Job: samtools_0.1.17-1
+Install-Time: 41
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 156
-Source-Version: 0.1.17-1
-Space: 9806
+Package-Time: 129
+Source-Version: 0.1.18-1
+Space: 10056
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1246
-Build needed 00:02:36, 9806k disc space
-Signature with key '22C61858' requested:
+Finished at 20110906-0931
+Build needed 00:02:09, 10056k disc space
+Signature with key 'C1A6480B' requested:
diff --git a/mips.log b/mips.log
index 04aa6ac..eb49adf 100644
--- a/mips.log
+++ b/mips.log
@@ -1,67 +1,67 @@
-From buildd2 at corelli.debian.org Mon Jul 11 13:00:57 2011
+From buildd2 at corelli.debian.org Tue Sep 06 09:50:49 2011
Return-path: <buildd2 at corelli.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 <buildd2 at corelli.debian.org>)
- id 1QgG6a-0007JP-Ng
- for logs at buildd.debian.org; Mon, 11 Jul 2011 13:00:57 +0000
+ id 1R0sIq-0005Hf-N7
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:50:49 +0000
Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=corelli.debian.org, EMAIL=hostmaster at corelli.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 <buildd2 at corelli.debian.org>)
- id 1QgG6Y-0000ZY-Js
- for logs at buildd.debian.org; Mon, 11 Jul 2011 13:00:55 +0000
+ id 1R0sIn-0002DM-QB
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:50:46 +0000
Received: from buildd2 by corelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd2 at corelli.debian.org>) id 1QgG6V-0007c9-U4
- for logs at buildd.debian.org; Mon, 11 Jul 2011 13:00:52 +0000
+ (envelope-from <buildd2 at corelli.debian.org>) id 1R0sIl-0005Rp-Hc
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:50:43 +0000
From: buildd on corelli <buildd2 at corelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.17-1 on mips (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QgG6V-0007c9-U4 at corelli.debian.org>
-Date: Mon, 11 Jul 2011 13:00:51 +0000
+Message-Id: <E1R0sIl-0005Rp-Hc at corelli.debian.org>
+Date: Tue, 06 Sep 2011 09:50:43 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on corelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (mips) 11 Jul 2011 12:38 ║
+║ samtools 0.1.18-1 (mips) 06 Sep 2011 09:27 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: mips
Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5379 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5470 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 [5379 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [52.4 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [95.0 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7297 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [54.4 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5470 kB]
+Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [94.9 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7462 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [56.2 kB]
Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7297 kB]
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [54.4 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7462 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [56.2 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 [36.1 kB]
-Get:18 http://incoming.debian.org Packages [457 kB]
+Get:17 http://incoming.debian.org Sources [32.4 kB]
+Get:18 http://incoming.debian.org Packages [356 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.5 MB in 1min 10s (375 kB/s)
+Fetched 27.0 MB in 1min 12s (372 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 1s (285 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 0s (432 kB/s)
Download complete and in download only mode
Check arch
@@ -100,18 +100,24 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 21 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,37 +126,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
+dash: already installed (0.5.7-1)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+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 (5.12.4-1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.19.1-2)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-8)
-gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+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 (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -160,6 +166,9 @@ Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-de
Reading package lists...
Building dependency tree...
Reading state information...
+The following packages were automatically installed and are no longer required:
+ libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
@@ -175,52 +184,52 @@ The following NEW packages will be installed:
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 21 not upgraded.
-Need to get 10.1 MB of archives.
-After this operation, 31.8 MB of additional disk space will be used.
+0 upgraded, 22 newly installed, 0 to remove and 13 not upgraded.
+Need to get 10.0 MB of archives.
+After this operation, 31.5 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 bsdmainutils mips 8.2.3 [206 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-1 [1005 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5+b1 [239 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5+b1 [49.9 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-3 [859 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 5.04-5+b1 [239 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5+b1 [49.9 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 html2text mips 1.3.2a-15 [103 kB]
Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.6-1 [1509 kB]
Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-4 [415 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-4 [2025 kB]
Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 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 libncurses5-dev mips 5.9-1 [509 kB]
Get:21 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:22 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.1 MB in 1s (6138 kB/s)
+Fetched 10.0 MB in 1s (5927 kB/s)
Selecting previously deselected package libpipeline1.
-(Reading database ... 10644 files and directories currently installed.)
+(Reading database ... 10686 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mips.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mips.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_mips.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_mips.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mips.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_mips.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_mips.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mips.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -230,15 +239,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mips.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_mips.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_mips.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mips.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -248,27 +257,27 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected 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 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 (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -277,11 +286,14 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-1 gcc-4.6_4.6.1-1 libc6-dev_2.13-8 libstdc++6_4.6.1-1 libstdc++6-4.6-dev_4.6.1-1 linux-libc-dev_2.6.39-2
-Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-1 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-1 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-1 gcc-4.6-base_4.6.1-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-1 libattr1_1:2.4.46-1 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-8 libc-dev-bin_2.13-8 libc6_2.13-8 libc6-dev_2.13-8 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-1 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-1 libstdc++6-4.6-dev_4.6.1-1 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-8 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-2 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-8 gcc-4.6_4.6.1-8 libc6-dev_2.13-18 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.52.20110606-2 binutils-dev_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-8 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-8 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-8 gcc-4.6-base_4.6.1-8 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_1.0.5-6 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-8 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_4.6.1-8 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-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 │
@@ -292,12 +304,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -313,33 +325,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -353,22 +365,22 @@ 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-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -403,15 +415,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -419,10 +431,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -443,24 +455,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -468,16 +480,28 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -503,7 +527,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -538,8 +562,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -565,7 +589,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -579,28 +603,28 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_mips.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_mips.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../samtools_0.1.17-1_mips.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1300
+Build finished at 20110906-0950
-samtools_0.1.17-1_mips.changes:
+samtools_0.1.18-1_mips.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org>
@@ -609,40 +633,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 8a62b3bfaaa332229c07c073ec06ba0ef5a05b95 627090 samtools_0.1.17-1_mips.deb
- cd135ea4f4380d05f4212639e5065f8cadc3711c 199160 libbam-dev_0.1.17-1_mips.deb
+ 0556db815f6ab9c75d000c38d220bcd6e51d6ff2 524810 samtools_0.1.18-1_mips.deb
+ 0cbc630a407d999d3d18b06334ded7f86c8f8a73 163634 libbam-dev_0.1.18-1_mips.deb
Checksums-Sha256:
- 0eea617858da545210ba046879e222886aae48b13c9dc5a230c74807a86c0186 627090 samtools_0.1.17-1_mips.deb
- 12c2f5042c024a06a28272f137cae7ac3b949a6206d446306afc246000d7363e 199160 libbam-dev_0.1.17-1_mips.deb
+ 1db408c1fe42dfeaea2128756b51366a2817e6a17c1ed94cf3457908a1188d2d 524810 samtools_0.1.18-1_mips.deb
+ a20ffd308f29f865fa66d0a17d7940b5083c7bb767dac8f082b35536b219d69c 163634 libbam-dev_0.1.18-1_mips.deb
Files:
- 52bed6f44e522cd92d9d1ba9816a443a 627090 science optional samtools_0.1.17-1_mips.deb
- 77be420c35e3c9ef7baeb5e5025d5bf2 199160 libdevel optional libbam-dev_0.1.17-1_mips.deb
+ 1db4db366036e5ce0a5ef3881d36a986 524810 science optional samtools_0.1.18-1_mips.deb
+ b88be612247af99b9f5af291ad89566b 163634 libdevel optional libbam-dev_0.1.18-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_mips.deb
+samtools_0.1.18-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 627090 bytes: control archive= 1767 bytes.
+ size 524810 bytes: control archive= 1769 bytes.
785 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1188
+ Installed-Size: 1200
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -655,71 +678,22 @@ samtools_0.1.17-1_mips.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/samtools/
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5778 2011-07-11 12:59 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-07-11 12:59 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-07-11 12:59 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2011-07-11 12:48 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2011-07-11 12:59 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/lib/samtools/
--rwxr-xr-x root/root 12512 2011-07-11 12:59 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2011-07-11 12:59 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2011-07-11 12:59 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9252 2011-07-11 12:59 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 18660 2011-07-11 12:59 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/bin/
--rwxr-xr-x root/root 151072 2011-07-11 12:59 ./usr/bin/bcftools
--rwxr-xr-x root/root 432004 2011-07-11 12:59 ./usr/bin/samtools
--rwxr-xr-x root/root 29296 2011-07-11 12:59 ./usr/bin/razip
-lrwxrwxrwx root/root 0 2011-07-11 12:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_mips.deb
+dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-380d3c0f-13d1-414c-ac3d-217f99a29cfc/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools_0.1.18-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
+
+
+libbam-dev_0.1.18-1_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 199160 bytes: control archive= 924 bytes.
+ size 163634 bytes: control archive= 930 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 492
+ Installed-Size: 496
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -730,25 +704,7 @@ libbam-dev_0.1.17-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/include/samtools/
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/lib/
--rw-r--r-- root/root 332126 2011-07-11 12:59 ./usr/lib/libbam.a
+dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-380d3c0f-13d1-414c-ac3d-217f99a29cfc/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/libbam-dev_0.1.18-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -762,7 +718,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-60a27d1f-4720-45f9-a7e3-7e3bfa63d2a9/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z
+Purging /var/lib/schroot/mount/sid-mips-sbuild-380d3c0f-13d1-414c-ac3d-217f99a29cfc/build/buildd2-samtools_0.1.18-1-mips-etBaIQ
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
@@ -772,86 +728,83 @@ Can't open average space db /var/lib/sbuild/avg-build-space
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 10672
-Build-Time: 1157
+Build-Space: 10920
+Build-Time: 1176
Distribution: sid
-Install-Time: 78
-Job: samtools_0.1.17-1
+Install-Time: 75
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 1351
-Source-Version: 0.1.17-1
-Space: 10672
+Package-Time: 1366
+Source-Version: 0.1.18-1
+Space: 10920
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1300
-Build needed 00:22:31, 10672k disc space
-Signature with key '865BEAD2' requested:
+Finished at 20110906-0950
+Build needed 00:22:46, 10920k disc space
+Signature with key '4D9CC026' requested:
-From buildd at rem.debian.org Tue Jul 12 07:27:55 2011
-Return-path: <buildd at rem.debian.org>
+From buildd at mayer.debian.org Tue Sep 06 09:45:40 2011
+Return-path: <buildd at mayer.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
- id 1QgXNq-0002WS-GT
- for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:55 +0000
-Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1R0sDr-0004bB-Fy
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:40 +0000
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from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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+ 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 rem.debian.org>)
- id 1QgXNp-0003oU-KU
- for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:53 +0000
-Received: from buildd by rem.debian.org with local (Exim 4.72)
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- for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:52 +0000
-Date: Tue, 12 Jul 2011 07:27:52 +0000
-Message-Id: <E1QgXNo-0004sl-AG at rem.debian.org>
-From: buildd on rem <buildd at rem.debian.org>
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1R0sDo-0001wh-HQ
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:37 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>) id 1R0sDk-00042i-2R
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:32 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.17-1 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1R0sDk-00042i-2R at mayer.debian.org>
+Date: Tue, 06 Sep 2011 09:45:32 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (mipsel) 12 Jul 2011 07:20 ║
+║ samtools 0.1.18-1 (mipsel) 06 Sep 2011 09:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: mipsel
-Get:1 http://mirror.ayous.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror.ayous.org unstable/main Sources [5385 kB]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5385 kB]
-Get:7 http://mirror.ayous.org unstable/contrib Sources [52.4 kB]
-Get:8 http://mirror.ayous.org unstable/non-free Sources [96.0 kB]
-Get:9 http://mirror.ayous.org unstable/main mipsel Packages [7308 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
-Get:11 http://mirror.ayous.org unstable/contrib mipsel Packages [54.7 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:12 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
-Get:13 http://incoming.debian.org unstable/non-free Sources [96.0 kB]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/main mipsel Packages [7308 kB]
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [54.7 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [40.4 kB]
-Get:18 http://incoming.debian.org Packages [530 kB]
+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
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 26.7 MB in 1min 1s (436 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -872,11 +825,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 0s (1256 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 0s (467 kB/s)
Download complete and in download only mode
Check arch
@@ -890,18 +843,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -910,37 +863,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
+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 (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+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 (5.12.3-7+b1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.19.1-2)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-7)
-gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+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 (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -951,66 +904,40 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz
+ devscripts dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 40 not upgraded.
-Need to get 10.1 MB of archives.
-After this operation, 31.8 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 bsdmainutils mipsel 8.2.3 [208 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-1 [1008 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5+b1 [238 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5+b1 [49.9 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-3 [858 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.94 [75.5 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 libncurses5-dev mipsel 5.9-1 [506 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.1 MB in 1s (5938 kB/s)
+0 upgraded, 21 newly installed, 0 to remove and 4 not upgraded.
+Need to get 0 B/9778 kB of archives.
+After this operation, 30.7 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-(Reading database ... 10621 files and directories currently installed.)
+(Reading database ... 11131 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_mipsel.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_mipsel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -1020,15 +947,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -1038,27 +965,24 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
-Setting up 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 libpcre3 (8.12-4) ...
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -1067,11 +991,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-13 gcc-4.6_4.6.0-13 libc6-dev_2.13-7 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 linux-libc-dev_2.6.39-2
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.0-13 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.0-13 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.6_4.6.0-13 gcc-4.6-base_4.6.0-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6_2.13-7 libc6-dev_2.13-7 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-13 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-13 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7+b1 perl-base_5.12.3-7+b1 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011g-1 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-7 gcc-4.6_4.6.1-7 libc6-dev_2.13-18 libstdc++6_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.52.20110606-2 binutils-dev_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-7 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-7 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-8 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-7 gcc-4.6-base_4.6.1-7 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-7 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_4.6.1-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 libtimedate-perl_1.2000-1 libudev0_172-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1082,12 +1006,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -1103,33 +1027,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -1143,22 +1067,22 @@ 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-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -1193,15 +1117,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -1209,10 +1133,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -1233,24 +1157,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -1258,16 +1182,28 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1293,7 +1229,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -1328,8 +1264,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1355,7 +1291,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -1369,70 +1305,69 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_mipsel.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.17-1_mipsel.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110712-0727
+Build finished at 20110906-0945
-samtools_0.1.17-1_mipsel.changes:
+samtools_0.1.18-1_mipsel.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 9d262fdb8603b5ad735afc967cc4f3e313727d9f 638486 samtools_0.1.17-1_mipsel.deb
- f0c56bb4a5193d8f00d91a43d1e914427a168929 200426 libbam-dev_0.1.17-1_mipsel.deb
+ 246b8af54b8e4f52d6d4dc8a408a431878aef7c7 527834 samtools_0.1.18-1_mipsel.deb
+ c3a6dab5622d5c2fd0578f13e2b4149a801b3ead 165668 libbam-dev_0.1.18-1_mipsel.deb
Checksums-Sha256:
- 2339081f1fd713f4c6740bdf17a6f1a74fbd9765c8f6d7e75189652acac650e9 638486 samtools_0.1.17-1_mipsel.deb
- 2d9f9ef295f21fe7412a7b54c6e25a25e342ce9dc794f51c795a121d4f78aede 200426 libbam-dev_0.1.17-1_mipsel.deb
+ ef734da95a9d183c7603141f20ce78dfe1c036044704f648e6c48e0b38e88840 527834 samtools_0.1.18-1_mipsel.deb
+ a49d72fe4def41845d68a5e769800c8eb0bb06162e8f1d6a33d1061257e4dd32 165668 libbam-dev_0.1.18-1_mipsel.deb
Files:
- d84eee56a2dafb7caa64ab0ed036e223 638486 science optional samtools_0.1.17-1_mipsel.deb
- 21ee4145a9ac304c18c1ab47f54b1d22 200426 libdevel optional libbam-dev_0.1.17-1_mipsel.deb
+ 4deeb6454e957327454c23815fba395d 527834 science optional samtools_0.1.18-1_mipsel.deb
+ 34d65a3d9781feaa3681e21a80b13191 165668 libdevel optional libbam-dev_0.1.18-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_mipsel.deb
+samtools_0.1.18-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 638486 bytes: control archive= 1761 bytes.
+ size 527834 bytes: control archive= 1766 bytes.
787 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1188
+ Installed-Size: 1200
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -1445,71 +1380,22 @@ samtools_0.1.17-1_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/samtools/
--rwxr-xr-x root/root 9252 2011-07-12 07:27 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 18660 2011-07-12 07:27 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 12512 2011-07-12 07:27 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-07-12 07:27 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-07-12 07:27 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-07-12 07:27 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2011-07-12 07:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 1966 2011-07-12 07:27 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/bin/
--rwxr-xr-x root/root 432788 2011-07-12 07:27 ./usr/bin/samtools
--rwxr-xr-x root/root 151072 2011-07-12 07:27 ./usr/bin/bcftools
--rwxr-xr-x root/root 29152 2011-07-12 07:27 ./usr/bin/razip
-lrwxrwxrwx root/root 0 2011-07-12 07:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_mipsel.deb
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+
+
+libbam-dev_0.1.18-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 200426 bytes: control archive= 926 bytes.
+ size 165668 bytes: control archive= 923 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 492
+ Installed-Size: 496
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -1520,25 +1406,7 @@ libbam-dev_0.1.17-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/samtools/
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
--rw-r--r-- root/root 334126 2011-07-12 07:27 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/libbam-dev_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1552,27 +1420,73 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-9e208add-8fa5-4149-8d78-337bd94eed0f/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 4 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*
+ libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
+ po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 21 to remove and 4 not upgraded.
+After this operation, 30.7 MB disk space will be freed.
+(Reading database ... 12540 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10676
-Build-Time: 274
+Build-Space: 10932
+Build-Time: 290
Distribution: sid
-Install-Time: 77
-Job: samtools_0.1.17-1
+Install-Time: 46
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 452
-Source-Version: 0.1.17-1
-Space: 10676
+Package-Time: 351
+Source-Version: 0.1.18-1
+Space: 10932
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110712-0727
-Build needed 00:07:32, 10676k disc space
-Signature with key '21BDEC11' requested:
+Finished at 20110906-0945
+Build needed 00:05:51, 10932k disc space
+Signature with key 'A5633F94' requested:
diff --git a/mipsel.log b/mipsel.log
index c113b50..b40c66a 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,67 +1,64 @@
-From buildd at rem.debian.org Tue Jul 12 07:27:55 2011
-Return-path: <buildd at rem.debian.org>
+From buildd at mayer.debian.org Tue Sep 06 09:45:40 2011
+Return-path: <buildd at mayer.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
- id 1QgXNq-0002WS-GT
- for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:55 +0000
-Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1R0sDr-0004bB-Fy
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:40 +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=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
+ 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 rem.debian.org>)
- id 1QgXNp-0003oU-KU
- for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:53 +0000
-Received: from buildd by rem.debian.org with local (Exim 4.72)
- (envelope-from <buildd at rem.debian.org>) id 1QgXNo-0004sl-AG
- for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:52 +0000
-Date: Tue, 12 Jul 2011 07:27:52 +0000
-Message-Id: <E1QgXNo-0004sl-AG at rem.debian.org>
-From: buildd on rem <buildd at rem.debian.org>
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1R0sDo-0001wh-HQ
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:37 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>) id 1R0sDk-00042i-2R
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:32 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.17-1 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1R0sDk-00042i-2R at mayer.debian.org>
+Date: Tue, 06 Sep 2011 09:45:32 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (mipsel) 12 Jul 2011 07:20 ║
+║ samtools 0.1.18-1 (mipsel) 06 Sep 2011 09:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: mipsel
-Get:1 http://mirror.ayous.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror.ayous.org unstable/main Sources [5385 kB]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5385 kB]
-Get:7 http://mirror.ayous.org unstable/contrib Sources [52.4 kB]
-Get:8 http://mirror.ayous.org unstable/non-free Sources [96.0 kB]
-Get:9 http://mirror.ayous.org unstable/main mipsel Packages [7308 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
-Get:11 http://mirror.ayous.org unstable/contrib mipsel Packages [54.7 kB]
-Ign http://mirror.ayous.org unstable/contrib TranslationIndex
-Get:12 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
-Get:13 http://incoming.debian.org unstable/non-free Sources [96.0 kB]
-Ign http://mirror.ayous.org unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/main mipsel Packages [7308 kB]
-Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [54.7 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [40.4 kB]
-Get:18 http://incoming.debian.org Packages [530 kB]
+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
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 26.7 MB in 1min 1s (436 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +79,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 0s (1256 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 0s (467 kB/s)
Download complete and in download only mode
Check arch
@@ -100,18 +97,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,37 +117,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
+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 (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+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 (5.12.3-7+b1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.19.1-2)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-7)
-gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+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 (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -161,66 +158,40 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz
+ devscripts dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 40 not upgraded.
-Need to get 10.1 MB of archives.
-After this operation, 31.8 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 bsdmainutils mipsel 8.2.3 [208 kB]
-Get:3 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
-Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-1 [1008 kB]
-Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5+b1 [238 kB]
-Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5+b1 [49.9 kB]
-Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
-Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
-Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-3 [858 kB]
-Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
-Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
-Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
-Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
-Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
-Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.94 [75.5 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 libncurses5-dev mipsel 5.9-1 [506 kB]
-Get:21 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.1 MB in 1s (5938 kB/s)
+0 upgraded, 21 newly installed, 0 to remove and 4 not upgraded.
+Need to get 0 B/9778 kB of archives.
+After this operation, 30.7 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-(Reading database ... 10621 files and directories currently installed.)
+(Reading database ... 11131 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_mipsel.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_mipsel.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_mipsel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -230,15 +201,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -248,27 +219,24 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
Setting up libpipeline1 (1.2.0-3) ...
-Setting up 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 libpcre3 (8.12-4) ...
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -277,11 +245,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-13 gcc-4.6_4.6.0-13 libc6-dev_2.13-7 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 linux-libc-dev_2.6.39-2
-Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.0-13 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.0-13 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.6_4.6.0-13 gcc-4.6-base_4.6.0-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6_2.13-7 libc6-dev_2.13-7 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-13 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-13 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7+b1 perl-base_5.12.3-7+b1 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011g-1 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-7 gcc-4.6_4.6.1-7 libc6-dev_2.13-18 libstdc++6_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.52.20110606-2 binutils-dev_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-7 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.65-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-7 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-8 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-7 gcc-4.6-base_4.6.1-7 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-7 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_4.6.1-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 libtimedate-perl_1.2000-1 libudev0_172-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -292,12 +260,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -313,33 +281,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -353,22 +321,22 @@ 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-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -403,15 +371,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -419,10 +387,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -443,24 +411,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -468,16 +436,28 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -503,7 +483,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -538,8 +518,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -565,7 +545,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -579,70 +559,69 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_mipsel.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.17-1_mipsel.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110712-0727
+Build finished at 20110906-0945
-samtools_0.1.17-1_mipsel.changes:
+samtools_0.1.18-1_mipsel.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 9d262fdb8603b5ad735afc967cc4f3e313727d9f 638486 samtools_0.1.17-1_mipsel.deb
- f0c56bb4a5193d8f00d91a43d1e914427a168929 200426 libbam-dev_0.1.17-1_mipsel.deb
+ 246b8af54b8e4f52d6d4dc8a408a431878aef7c7 527834 samtools_0.1.18-1_mipsel.deb
+ c3a6dab5622d5c2fd0578f13e2b4149a801b3ead 165668 libbam-dev_0.1.18-1_mipsel.deb
Checksums-Sha256:
- 2339081f1fd713f4c6740bdf17a6f1a74fbd9765c8f6d7e75189652acac650e9 638486 samtools_0.1.17-1_mipsel.deb
- 2d9f9ef295f21fe7412a7b54c6e25a25e342ce9dc794f51c795a121d4f78aede 200426 libbam-dev_0.1.17-1_mipsel.deb
+ ef734da95a9d183c7603141f20ce78dfe1c036044704f648e6c48e0b38e88840 527834 samtools_0.1.18-1_mipsel.deb
+ a49d72fe4def41845d68a5e769800c8eb0bb06162e8f1d6a33d1061257e4dd32 165668 libbam-dev_0.1.18-1_mipsel.deb
Files:
- d84eee56a2dafb7caa64ab0ed036e223 638486 science optional samtools_0.1.17-1_mipsel.deb
- 21ee4145a9ac304c18c1ab47f54b1d22 200426 libdevel optional libbam-dev_0.1.17-1_mipsel.deb
+ 4deeb6454e957327454c23815fba395d 527834 science optional samtools_0.1.18-1_mipsel.deb
+ 34d65a3d9781feaa3681e21a80b13191 165668 libdevel optional libbam-dev_0.1.18-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_mipsel.deb
+samtools_0.1.18-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 638486 bytes: control archive= 1761 bytes.
+ size 527834 bytes: control archive= 1766 bytes.
787 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1188
+ Installed-Size: 1200
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -655,71 +634,22 @@ samtools_0.1.17-1_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/samtools/
--rwxr-xr-x root/root 9252 2011-07-12 07:27 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 18660 2011-07-12 07:27 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 12512 2011-07-12 07:27 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-07-12 07:27 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-07-12 07:27 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-07-12 07:27 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2011-07-12 07:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 1966 2011-07-12 07:27 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/bin/
--rwxr-xr-x root/root 432788 2011-07-12 07:27 ./usr/bin/samtools
--rwxr-xr-x root/root 151072 2011-07-12 07:27 ./usr/bin/bcftools
--rwxr-xr-x root/root 29152 2011-07-12 07:27 ./usr/bin/razip
-lrwxrwxrwx root/root 0 2011-07-12 07:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_mipsel.deb
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+
+
+libbam-dev_0.1.18-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 200426 bytes: control archive= 926 bytes.
+ size 165668 bytes: control archive= 923 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 492
+ Installed-Size: 496
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -730,25 +660,7 @@ libbam-dev_0.1.17-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/samtools/
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
--rw-r--r-- root/root 334126 2011-07-12 07:27 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/libbam-dev_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -762,27 +674,73 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-9e208add-8fa5-4149-8d78-337bd94eed0f/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 4 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*
+ libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
+ po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 21 to remove and 4 not upgraded.
+After this operation, 30.7 MB disk space will be freed.
+(Reading database ... 12540 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10676
-Build-Time: 274
+Build-Space: 10932
+Build-Time: 290
Distribution: sid
-Install-Time: 77
-Job: samtools_0.1.17-1
+Install-Time: 46
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 452
-Source-Version: 0.1.17-1
-Space: 10676
+Package-Time: 351
+Source-Version: 0.1.18-1
+Space: 10932
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110712-0727
-Build needed 00:07:32, 10676k disc space
-Signature with key '21BDEC11' requested:
+Finished at 20110906-0945
+Build needed 00:05:51, 10932k disc space
+Signature with key 'A5633F94' requested:
diff --git a/powerpc.log b/powerpc.log
index 0aeec27..0f8bfb4 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,69 @@
-From buildd at porpora.debian.org Mon Jul 11 12:41:31 2011
-Return-path: <buildd at porpora.debian.org>
+From buildd at poulenc.debian.org Tue Sep 06 09:33:42 2011
+Return-path: <buildd at poulenc.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 1QgFnn-0003zI-7F
- for logs at buildd.debian.org; Mon, 11 Jul 2011 12:41:31 +0000
-Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
- helo=porpora.debian.org)
+ (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
+ id 1R0s2H-00024n-Fg
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 09:33:41 +0000
+Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
+ helo=poulenc.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=poulenc.debian.org, EMAIL=hostmaster at poulenc.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 1QgFnm-00087a-F0; Mon, 11 Jul 2011 12:41:30 +0000
-Received: from buildd by porpora.debian.org with local (Exim 4.72)
- (envelope-from <buildd at porpora.debian.org>)
- id 1QgFnl-0006tU-VM; Mon, 11 Jul 2011 12:41:30 +0000
-Message-Id: <E1QgFnl-0006tU-VM at porpora.debian.org>
+ (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
+ id 1R0s2E-0001LO-Vh; Tue, 06 Sep 2011 09:33:39 +0000
+Received: from buildd by poulenc.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at poulenc.debian.org>)
+ id 1R0s2E-0006DP-Ik; Tue, 06 Sep 2011 09:33:38 +0000
+Message-Id: <E1R0s2E-0006DP-Ik at poulenc.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Mon, 11 Jul 2011 12:41:29 +0000
-From: buildd on porpora <buildd at porpora.debian.org>
+Date: Tue, 6 Sep 2011 09:33:38 +0000
+From: buildd on poulenc <buildd at poulenc.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.17-1 on powerpc (dist=sid)
-Key-Id: CDFA0A89
+Subject: Log for successful build of samtools_0.1.18-1 on powerpc (dist=sid)
+Key-Id: 779E1DD6
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 poulenc.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (powerpc) 11 Jul 2011 12:38 ║
+║ samtools 0.1.18-1 (powerpc) 06 Sep 2011 09:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
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 [5379 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5468 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 [5379 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [52.4 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [95.0 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7392 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [54.0 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5470 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [94.9 kB]
+Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7561 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
+Get:11 http://incoming.debian.org unstable/main powerpc Packages [7562 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.8 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Get:13 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 [52.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7392 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [54.0 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.1 kB]
-Get:18 http://incoming.debian.org Packages [457 kB]
+Get:17 http://incoming.debian.org Sources [32.4 kB]
+Get:18 http://incoming.debian.org Packages [356 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.7 MB in 24s (1077 kB/s)
+Fetched 27.2 MB in 23s (1177 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 1s (351 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 1s (362 kB/s)
Download complete and in download only mode
Check arch
@@ -102,7 +102,7 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+fakeroot: already installed (1.18-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
@@ -122,37 +122,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
+dash: already installed (0.5.7-1)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+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 (5.12.4-1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.19.1-2)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-10)
-gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+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 (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -179,50 +179,50 @@ The following NEW packages will be installed:
zlib1g-dev
0 upgraded, 22 newly installed, 0 to remove and 12 not upgraded.
Need to get 10.2 MB of archives.
-After this operation, 31.0 MB of additional disk space will be used.
+After this operation, 30.9 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 bsdmainutils powerpc 8.2.3 [207 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-1 [1020 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5+b1 [240 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5+b1 [49.9 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-3 [258 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-3 [837 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 5.04-5+b1 [240 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5+b1 [49.9 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 html2text powerpc 1.3.2a-15 [105 kB]
Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.6-1 [1611 kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-4 [422 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-4 [2032 kB]
Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 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 libncurses5-dev powerpc 5.9-1 [489 kB]
Get:21 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.2 MB in 2s (3787 kB/s)
+Fetched 10.2 MB in 2s (3391 kB/s)
Selecting previously deselected package libpipeline1.
-(Reading database ... 10789 files and directories currently installed.)
+(Reading database ... 10610 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_powerpc.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_powerpc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_powerpc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_powerpc.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_powerpc.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_powerpc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_powerpc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_powerpc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -232,15 +232,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_powerpc.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_powerpc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_powerpc.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_powerpc.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -250,27 +250,27 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected 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 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 (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -282,8 +282,8 @@ 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-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.52.20110703-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
-Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110703-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-i18n_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblocale-gettext-perl_1.05-6+b2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtext-charwidth-perl_0.04-6+b3 libtext-iconv-perl_1.7-2+b2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 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 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-8 gcc-4.6_4.6.1-8 libc6-dev_2.13-18 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-8 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-8 gcc_4:4.6.1-2 gcc-4.6_4.6.1-8 gcc-4.6-base_4.6.1-8 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_1.0.5-6 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-8 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-8 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011h-4 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 │
@@ -294,12 +294,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -315,33 +315,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -355,22 +355,22 @@ 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-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -405,15 +405,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -421,10 +421,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -445,24 +445,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -470,16 +470,28 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -505,7 +517,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -540,8 +552,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -567,7 +579,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -581,70 +593,69 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_powerpc.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_powerpc.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.17-1_powerpc.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1241
+Build finished at 20110906-0933
-samtools_0.1.17-1_powerpc.changes:
+samtools_0.1.18-1_powerpc.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
+Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 26bfabbc96a9796352ad07507c503099668dff55 601652 samtools_0.1.17-1_powerpc.deb
- ae1d4ef1b47efbf57d8071146ce74c74da50d996 176310 libbam-dev_0.1.17-1_powerpc.deb
+ f7ed545f582aa2efadee0d55422588213ad4d5db 512292 samtools_0.1.18-1_powerpc.deb
+ 2c43474da868b56256ca0acc5a5080e01f5d9579 149584 libbam-dev_0.1.18-1_powerpc.deb
Checksums-Sha256:
- 8a6be5d436e0eac96f8a674c30c23645bbf66f2188739bd9286e1f9ec751b95a 601652 samtools_0.1.17-1_powerpc.deb
- 0f39f874f69623b9879ceb16a1768459a3c8c6d25874bf63c37ce88b00132574 176310 libbam-dev_0.1.17-1_powerpc.deb
+ c48b3ca656154208361b4d13fb6897eeff47a6189e1f197cc3bc36c01c280143 512292 samtools_0.1.18-1_powerpc.deb
+ e204784b09aa88f9f999d5e0364d134ac7c682230099168bd868149ad7b3386d 149584 libbam-dev_0.1.18-1_powerpc.deb
Files:
- 3ab0ca69226f2b6c7e8cb7914a700742 601652 science optional samtools_0.1.17-1_powerpc.deb
- 63edbea9ae7e3c6e550ca0148bbae691 176310 libdevel optional libbam-dev_0.1.17-1_powerpc.deb
+ 338eb3e991fcdea95207ba74a922fade 512292 science optional samtools_0.1.18-1_powerpc.deb
+ 8d976b9703d653b65f3e75bcad81b7d4 149584 libdevel optional libbam-dev_0.1.18-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_powerpc.deb
+samtools_0.1.18-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 601652 bytes: control archive= 1759 bytes.
+ size 512292 bytes: control archive= 1767 bytes.
788 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1092
+ Installed-Size: 1100
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -657,71 +668,71 @@ samtools_0.1.17-1_powerpc.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/bin/
--rwxr-xr-x root/root 129480 2011-07-11 12:41 ./usr/bin/bcftools
--rwxr-xr-x root/root 366980 2011-07-11 12:41 ./usr/bin/samtools
--rwxr-xr-x root/root 25296 2011-07-11 12:41 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/samtools/
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2011-09-06 09:33 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-09-06 09:33 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/samtools/
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 5778 2011-09-06 09:33 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5778 2011-07-11 12:41 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2011-07-11 12:41 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-07-11 12:41 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/samtools/
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/samtools/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1966 2011-09-06 09:33 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-07-11 12:41 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 126609 2011-09-06 09:33 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2011-07-11 12:41 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/lib/samtools/
--rwxr-xr-x root/root 18892 2011-07-11 12:41 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7832 2011-07-11 12:41 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7112 2011-07-11 12:41 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7128 2011-07-11 12:41 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10956 2011-07-11 12:41 ./usr/lib/samtools/md5fa
-lrwxrwxrwx root/root 0 2011-07-11 12:41 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.17-1_powerpc.deb
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7168 2011-09-06 09:33 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10916 2011-09-06 09:33 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7872 2011-09-06 09:33 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7152 2011-09-06 09:33 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 18528 2011-09-06 09:33 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/bin/
+-rwxr-xr-x root/root 373860 2011-09-06 09:33 ./usr/bin/samtools
+-rwxr-xr-x root/root 25336 2011-09-06 09:33 ./usr/bin/razip
+-rwxr-xr-x root/root 130168 2011-09-06 09:33 ./usr/bin/bcftools
+lrwxrwxrwx root/root 0 2011-09-06 09:33 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-1_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 176310 bytes: control archive= 925 bytes.
+ size 149584 bytes: control archive= 927 bytes.
676 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 432
+ Installed-Size: 440
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -732,25 +743,25 @@ libbam-dev_0.1.17-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/include/samtools/
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/include/samtools/
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/lib/
--rw-r--r-- root/root 272578 2011-07-11 12:41 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/lib/
+-rw-r--r-- root/root 275254 2011-09-06 09:33 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -764,7 +775,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-048f7e08-ffb0-4f12-82a5-b134ec7f4b61/build/buildd-samtools_0.1.17-1-powerpc-oStMKO
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-d8c0c76c-2697-4d52-b93a-866cdd0ed93f/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -772,18 +783,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 10180
-Build-Time: 85
+Build-Space: 10444
+Build-Time: 76
Distribution: sid
-Install-Time: 45
-Job: samtools_0.1.17-1
+Install-Time: 46
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 169
-Source-Version: 0.1.17-1
-Space: 10180
+Package-Time: 159
+Source-Version: 0.1.18-1
+Space: 10444
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1241
-Build needed 00:02:49, 10180k disc space
-Signature with key 'CDFA0A89' requested:
+Finished at 20110906-0933
+Build needed 00:02:39, 10444k disc space
+Signature with key '779E1DD6' requested:
diff --git a/s390.log b/s390.log
index 970da2d..57e298e 100644
--- a/s390.log
+++ b/s390.log
@@ -1,69 +1,69 @@
-From buildd at zandonai.debian.org Mon Jul 11 19:27:56 2011
+From buildd at zandonai.debian.org Tue Sep 06 11:26:39 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 1QgM96-0004WV-Ly
- for logs at buildd.debian.org; Mon, 11 Jul 2011 19:27:56 +0000
+ id 1R0tnb-0002G0-8u
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 11:26:39 +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 1QgM95-0001Jo-GA; Mon, 11 Jul 2011 19:27:55 +0000
+ id 1R0tnY-0006rD-Ou; Tue, 06 Sep 2011 11:26:36 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1QgM95-0002SX-1c; Mon, 11 Jul 2011 19:27:55 +0000
-Message-Id: <E1QgM95-0002SX-1c at zandonai.debian.org>
+ id 1R0tnY-0007wU-Df; Tue, 06 Sep 2011 11:26:36 +0000
+Message-Id: <E1R0tnY-0007wU-Df 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: Mon, 11 Jul 2011 19:27:55 +0000
+Date: Tue, 6 Sep 2011 11:26:36 +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 samtools_0.1.17-1 on s390 (dist=sid)
-Key-Id: 9BD94C88
+Subject: Log for successful build of samtools_0.1.18-1 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
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (s390) 11 Jul 2011 19:26 ║
+║ samtools 0.1.18-1 (s390) 06 Sep 2011 11:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: s390
Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.de.debian.org unstable/main Sources [5381 kB]
+Get:2 http://ftp.de.debian.org unstable/main Sources [5470 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 [5381 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [52.4 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [95.0 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7306 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [53.1 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5470 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [53.9 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [94.9 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7467 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.8 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 [52.4 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7306 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [53.1 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7467 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [34.7 kB]
-Get:18 http://incoming.debian.org Packages [337 kB]
+Get:17 http://incoming.debian.org Sources [34.4 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 26.4 MB in 30s (867 kB/s)
+Fetched 26.9 MB in 27s (982 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 0s (1651 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 1s (311 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,8 +122,8 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+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 (0.5.5.1-7.4)
@@ -132,27 +132,27 @@ 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 (2.8-2)
-gzip: already installed (1.3.12-9)
+grep: already installed (2.9-1)
+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 (5.12.4-1)
+perl-base: already installed (5.12.4-2)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.10)
-sysvinit: already installed (2.88dsf-13.10)
+sysvinit-utils: already installed (2.88dsf-13.11)
+sysvinit: already installed (2.88dsf-13.11)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.19.1-2)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-10)
-gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+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 (2.13-15)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -177,52 +177,52 @@ The following NEW packages will be installed:
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 22 newly installed, 0 to remove and 41 not upgraded.
Need to get 10.3 MB of archives.
After this operation, 30.8 MB of additional disk space will be used.
Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-3 [39.0 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-1 [1017 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5+b1 [243 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5+b1 [50.1 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-3 [881 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 5.04-5+b1 [243 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5+b1 [50.1 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 html2text s390 1.3.2a-15 [101 kB]
Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.6-1 [1639 kB]
Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-4 [431 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-4 [2073 kB]
Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4 kB]
Get:20 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-1 [504 kB]
Get:21 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
Get:22 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 10.3 MB in 2s (3494 kB/s)
+Fetched 10.3 MB in 4s (2199 kB/s)
Selecting previously deselected package libpipeline1.
-(Reading database ... 10570 files and directories currently installed.)
+(Reading database ... 10583 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_s390.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_s390.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_s390.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_s390.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_s390.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_s390.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_s390.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_s390.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_s390.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -232,15 +232,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_s390.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_s390.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_s390.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_s390.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -250,27 +250,27 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected 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 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 (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -279,11 +279,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.52.20110703-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
-Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110703-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110805-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-6 gcc-4.6_4.6.1-6 libc6-dev_2.13-15 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 linux-libc-dev_3.0.0-1
+Package versions: apt_0.8.15.5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110805-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-6 dash_0.5.5.1-7.4 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-6 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-7 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-6 gcc-4.6-base_4.6.1-6 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 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_1.0.5-6 libc-bin_2.13-15 libc-dev-bin_2.13-15 libc6_2.13-15 libc6-dev_2.13-15 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-6 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-5 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-2 perl-base_5.12.4-2 perl-modules_5.12.4-2 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-5 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -294,12 +294,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -315,33 +315,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -355,22 +355,22 @@ 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-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -399,15 +399,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -415,10 +415,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -439,24 +439,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -464,16 +464,20 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -499,7 +503,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -534,8 +538,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -561,7 +565,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -575,28 +579,28 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_s390.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_s390.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.17-1_s390.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.18-1_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 samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1927
+Build finished at 20110906-1126
-samtools_0.1.17-1_s390.changes:
+samtools_0.1.18-1_s390.changes:
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -605,40 +609,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * New upstream release 0.1.17 (6 July, 2011).
- * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
- * Patched the example makefile to not use samtools pileup, deprecated.
- (debian/control, debian/rules, debian/patches/series,
- debian/patches/no-pileup-tests.patch)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 967a23a0149ba52edd46b0d9a433e094c4137d5c 603632 samtools_0.1.17-1_s390.deb
- fcb8f9dee9a1388fefd969f369fca88427be147e 180332 libbam-dev_0.1.17-1_s390.deb
+ ad01740b1f0b6eeb8ae20d3bfc6d1715d235dff2 528480 samtools_0.1.18-1_s390.deb
+ daff8ba29c9e4dc4a474bb75b0574028503e6541 156202 libbam-dev_0.1.18-1_s390.deb
Checksums-Sha256:
- 645db24cae75df25daa1902c214feb9e210752820fd6fd0bd0616d37936c0e35 603632 samtools_0.1.17-1_s390.deb
- 18a469606c7e0859291d03f4388f168655cdb24c02e7a67c7fdca1d0a2840be5 180332 libbam-dev_0.1.17-1_s390.deb
+ 7b524fc82bf4a5bed7567ae0fcb2d309bf4796452dd57fb6b48a0e162101d1f5 528480 samtools_0.1.18-1_s390.deb
+ c8f9a97601fbf99c8c3bbab4408e077eacdb6e9c09aad60165c847c0f3075cc3 156202 libbam-dev_0.1.18-1_s390.deb
Files:
- 293df49ac670e99a49b826eb038a3329 603632 science optional samtools_0.1.17-1_s390.deb
- f31a692d919fc0b2c58824670ca92621 180332 libdevel optional libbam-dev_0.1.17-1_s390.deb
+ bf41bbb8305379ab1d388bb9f3253210 528480 science optional samtools_0.1.18-1_s390.deb
+ 8fc2b46e29bbd9fd20cd994b200765f6 156202 libdevel optional libbam-dev_0.1.18-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_s390.deb
+samtools_0.1.18-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 603632 bytes: control archive= 1753 bytes.
+ size 528480 bytes: control archive= 1759 bytes.
785 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1148
+ Installed-Size: 1156
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -651,25 +654,25 @@ samtools_0.1.17-1_s390.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/bin/
--rwxr-xr-x root/root 141448 2011-07-11 19:27 ./usr/bin/bcftools
--rwxr-xr-x root/root 409316 2011-07-11 19:27 ./usr/bin/samtools
--rwxr-xr-x root/root 27452 2011-07-11 19:27 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/lib/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/lib/samtools/
--rwxr-xr-x root/root 11536 2011-07-11 19:27 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7416 2011-07-11 19:27 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7416 2011-07-11 19:27 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8276 2011-07-11 19:27 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 18692 2011-07-11 19:27 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2011-07-11 19:27 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-07-11 19:27 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/bin/
+-rwxr-xr-x root/root 141448 2011-09-06 11:26 ./usr/bin/bcftools
+-rwxr-xr-x root/root 415908 2011-09-06 11:26 ./usr/bin/samtools
+-rwxr-xr-x root/root 27452 2011-09-06 11:26 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11364 2011-09-06 11:26 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7416 2011-09-06 11:26 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7416 2011-09-06 11:26 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8276 2011-09-06 11:26 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 17340 2011-09-06 11:26 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2011-09-06 11:26 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-09-06 11:26 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/samtools/
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
@@ -679,43 +682,43 @@ drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/samtools/
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2011-07-11 19:27 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-09-06 11:26 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/samtools/
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2011-07-11 19:27 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2011-09-06 11:26 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-07-11 19:27 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-09-06 11:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-lrwxrwxrwx root/root 0 2011-07-11 19:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+lrwxrwxrwx root/root 0 2011-09-06 11:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.17-1_s390.deb
+libbam-dev_0.1.18-1_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 180332 bytes: control archive= 922 bytes.
+ size 156202 bytes: control archive= 922 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 444
+ Installed-Size: 452
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -726,25 +729,25 @@ libbam-dev_0.1.17-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/include/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/include/samtools/
+-rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/lib/
--rw-r--r-- root/root 285766 2011-07-11 19:27 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/lib/
+-rw-r--r-- root/root 288314 2011-09-06 11:26 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -758,7 +761,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-d38d2160-eff9-4944-8614-e527240226bd/build/buildd-samtools_0.1.17-1-s390-A4DcW9
+Purging /var/lib/schroot/mount/sid-s390-sbuild-9c6ebf4f-c0d8-40a3-b578-aee78824964f/build/buildd-samtools_0.1.18-1-s390-u0rVt9
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -766,18 +769,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 10896
-Build-Time: 45
+Build-Space: 11232
+Build-Time: 66
Distribution: sid
-Install-Time: 15
-Job: samtools_0.1.17-1
+Install-Time: 14
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 96
-Source-Version: 0.1.17-1
-Space: 10896
+Package-Time: 123
+Source-Version: 0.1.18-1
+Space: 11232
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1927
-Build needed 00:01:36, 10896k disc space
-Signature with key '9BD94C88' requested:
+Finished at 20110906-1126
+Build needed 00:02:03, 11232k disc space
+Signature with key '2D941D26' requested:
diff --git a/sparc.log b/sparc.log
index 041b107..c54bdaf 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,70 @@
-From buildd at schroeder.debian.org Mon Jul 11 12:47:43 2011
-Return-path: <buildd at schroeder.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at spontini.debian.org Tue Sep 06 18:25:37 2011
+Return-path: <buildd at spontini.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1QgFtn-0004sF-9R
- for logs at buildd.debian.org; Mon, 11 Jul 2011 12:47:43 +0000
-Received: from schroeder.debian.org ([193.198.184.11])
+ (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
+ id 1R10L3-0004DW-5z
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 18:25:37 +0000
+Received: from spontini.debian.org ([2607:f8f0:610:4000:a00:20ff:fea0:918b])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=schroeder.debian.org,
- EMAIL=hostmaster at schroeder.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1QgFtl-0000Dc-Vr
- for logs at buildd.debian.org; Mon, 11 Jul 2011 12:47:42 +0000
-Received: from buildd by schroeder.debian.org with local (Exim 4.72)
- (envelope-from <buildd at schroeder.debian.org>)
- id 1QgFtj-0001WZ-Q7; Mon, 11 Jul 2011 12:47:39 +0000
-Message-Id: <E1QgFtj-0001WZ-Q7 at schroeder.debian.org>
+ CN=spontini.debian.org,
+ EMAIL=hostmaster at spontini.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
+ id 1R10Kr-0003Ih-Dv
+ for logs at buildd.debian.org; Tue, 06 Sep 2011 18:25:25 +0000
+Received: from buildd by spontini.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at spontini.debian.org>)
+ id 1R10Ke-0006ZI-U6; Tue, 06 Sep 2011 18:25:13 +0000
+Message-Id: <E1R10Ke-0006ZI-U6 at spontini.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Mon, 11 Jul 2011 12:47:39 +0000
-From: buildd on schroeder <buildd at schroeder.debian.org>
-To: logs at buildd.debian.org,buildd-admin at schroeder.debian.org
-Subject: Log for attempted build of samtools_0.1.17-1 on sparc (dist=sid)
-Key-Id: 9BBB678A
+Date: Tue, 6 Sep 2011 18:25:12 +0000
+From: buildd on spontini <buildd at spontini.debian.org>
+To: logs at buildd.debian.org,buildd-admin at spontini.debian.org
+Subject: Log for attempted build of samtools_0.1.18-1 on sparc (dist=sid)
+Key-Id: 4B280692
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on spontini.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (sparc) 11 Jul 2011 12:43 ║
+║ samtools 0.1.18-1 (sparc) 06 Sep 2011 18:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Architecture: sparc
-Get:1 http://ftp.carnet.hr unstable InRelease [146 kB]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.carnet.hr unstable/main Sources [5379 kB]
-Get:4 http://ftp.carnet.hr unstable/contrib Sources [52.4 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5481 kB]
Ign http://incoming.debian.org InRelease
-Get:5 http://ftp.carnet.hr unstable/non-free Sources [95.0 kB]
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://incoming.debian.org Release [1604 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5379 kB]
-Get:9 http://ftp.carnet.hr unstable/main sparc Packages [7336 kB]
-Get:10 http://ftp.carnet.hr unstable/contrib sparc Packages [54.1 kB]
-Ign http://ftp.carnet.hr unstable/contrib TranslationIndex
-Get:11 http://ftp.carnet.hr unstable/main TranslationIndex [2045 B]
-Get:12 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
-Get:14 http://incoming.debian.org unstable/main sparc Packages [7336 kB]
-Get:15 http://incoming.debian.org unstable/contrib sparc Packages [54.1 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org Release [1604 B]
+Get:6 http://incoming.debian.org unstable/main Sources [5481 kB]
+Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
+Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [95.2 kB]
+Get:9 http://mirror-ubc.debian.org unstable/main sparc Packages [7513 kB]
+Get:10 http://mirror-ubc.debian.org unstable/contrib sparc Packages [55.8 kB]
+Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
+Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
+Get:12 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [95.2 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7513 kB]
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [36.1 kB]
-Get:18 http://incoming.debian.org Packages [457 kB]
-Ign http://ftp.carnet.hr unstable/contrib Translation-en
+Get:17 http://incoming.debian.org Sources [53.9 kB]
+Get:18 http://incoming.debian.org Packages [387 kB]
Ign http://incoming.debian.org Translation-en
Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 26.6 MB in 27s (954 kB/s)
+Fetched 27.1 MB in 1min 1s (443 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,11 +85,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 384 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
-Fetched 384 kB in 1s (305 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.18-1 (dsc) [1946 B]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.18-1 (tar) [379 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.18-1 (diff) [7593 B]
+Fetched 389 kB in 0s (898 kB/s)
Download complete and in download only mode
Check arch
@@ -103,18 +103,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,38 +123,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22+b1)
+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 (0.5.5.1-7.4)
+dash: already installed (0.5.7-1)
debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b2)
-grep: already installed (2.8-2)
-gzip: already installed (1.3.12-9)
+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 (5.12.4-1)
+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-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-2)
-mount: already installed (2.19.1-2)
-util-linux: already installed (2.19.1-2)
-libc6-dev: already installed (2.13-10)
-libc6-dev-sparc64: already installed (2.13-10)
-gcc: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
+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 (2.13-18)
+libc6-dev-sparc64: already installed (2.13-18)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.0
+Using default version 8.9.6
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -179,52 +179,52 @@ The following NEW packages will be installed:
html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 11 not upgraded.
-Need to get 10.1 MB of archives.
-After this operation, 30.6 MB of additional disk space will be used.
-Get:1 http://ftp.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
-Get:2 http://ftp.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:3 http://ftp.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:4 http://ftp.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-1 [1013 kB]
-Get:5 http://ftp.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5+b1 [239 kB]
-Get:6 http://ftp.carnet.hr/debian/ unstable/main file sparc 5.04-5+b1 [49.6 kB]
-Get:7 http://ftp.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
-Get:8 http://ftp.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
-Get:9 http://ftp.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-3 [841 kB]
-Get:10 http://ftp.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:11 http://ftp.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
-Get:12 http://ftp.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:13 http://ftp.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
-Get:14 http://ftp.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
-Get:15 http://ftp.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.carnet.hr/debian/ unstable/main debhelper all 8.9.0 [559 kB]
-Get:18 http://ftp.carnet.hr/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
-Get:19 http://ftp.carnet.hr/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
-Get:20 http://ftp.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 kB]
-Get:21 http://ftp.carnet.hr/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://ftp.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+0 upgraded, 22 newly installed, 0 to remove and 9 not upgraded.
+Need to get 9998 kB of archives.
+After this operation, 30.4 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 sparc 5.04-5+b1 [239 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main file sparc 5.04-5+b1 [49.6 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-4 [132 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-4 [816 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-4 [1985 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.1 MB in 8s (1189 kB/s)
+Fetched 9998 kB in 3s (3005 kB/s)
Selecting previously deselected package libpipeline1.
-(Reading database ... 10906 files and directories currently installed.)
+(Reading database ... 10977 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_sparc.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
Selecting previously deselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_sparc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-1_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_sparc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_sparc.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_sparc.deb) ...
Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_sparc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_sparc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -234,15 +234,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_sparc.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_sparc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_sparc.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_sparc.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -252,27 +252,27 @@ Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected 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 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 (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
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 (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -281,11 +281,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
-Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.1-1 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b2 g++_4:4.6.1-1 g++-4.6_4.6.1-2 gcc_4:4.6.1-1 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libc6-dev-sparc64_2.13-10 libc6-sparc64_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15+b1 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 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 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-8 gcc-4.6_4.6.1-8 libc6-dev_2.13-18 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-8 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b2 g++_4:4.6.1-2 g++-4.6_4.6.1-8 gcc_4:4.6.1-2 gcc-4.6_4.6.1-8 gcc-4.6-base_4.6.1-8 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libc6-dev-sparc64_2.13-18 libc6-sparc64_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-8 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-8 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15+b1 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-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 │
@@ -296,12 +296,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Jul 11 12:10:24 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.17
-dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -317,33 +317,33 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.17-1
- dpkg-source --before-build samtools-0.1.17
+dpkg-buildpackage: source version 0.1.18-1
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -357,22 +357,22 @@ 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-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
Now at patch no-pileup-tests.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -407,15 +407,15 @@ kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
@@ -423,10 +423,10 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
@@ -447,24 +447,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -472,29 +472,41 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_famask':
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
make[1]: *** [ex1.bam] Bus error
make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-1247
+Build finished at 20110906-1825
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-761f2948-8f46-47c3-8963-ec2b01392c87/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-9fa16328-83bf-4bcd-9f01-67b63bcd622e/build/buildd-samtools_0.1.18-1-sparc-NEkTE7
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -502,18 +514,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 6412
-Build-Time: 125
+Build-Space: 6748
+Build-Time: 334
Distribution: sid
Fail-Stage: build
-Install-Time: 53
-Job: samtools_0.1.17-1
+Install-Time: 82
+Job: samtools_0.1.18-1
Package: samtools
-Package-Time: 226
-Source-Version: 0.1.17-1
-Space: 6412
+Package-Time: 519
+Source-Version: 0.1.18-1
+Space: 6748
Status: attempted
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-1247
-Build needed 00:03:46, 6412k disc space
+Finished at 20110906-1825
+Build needed 00:08:39, 6748k disc space
--
Processing of sequence alignments in SAM and BAM formats.
More information about the debian-med-commit
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