[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. 0c660b51cd5581b8c1b0c72d7012b8d9a8219f97
Charles Plessy
plessy at debian.org
Fri Nov 26 11:56:23 UTC 2010
The following commit has been merged in the meta branch:
commit 0c660b51cd5581b8c1b0c72d7012b8d9a8219f97
Author: Charles Plessy <plessy at debian.org>
Date: Fri Nov 26 15:22:24 2010 +0900
# Collected build logs for version 0.1.10-1
diff --git a/alpha.build b/alpha.build
index ddb819e..6ca0787 100644
--- a/alpha.build
+++ b/alpha.build
@@ -1,36 +1,91 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/alpha received Tue Nov 2 08:15:26 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=alpha">alpha</a> >> Tue Nov 2 08:15:26 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goedel.debian.org
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/alpha received Wed Nov 17 12:01:42 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=alpha">alpha</a> >> Wed Nov 17 12:01:42 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goetz.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (alpha) 02 Nov 2010 08:05 ║
+║ samtools 0.1.10-1 (alpha) 17 Nov 2010 11:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: alpha
-Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-34703713-5fd1-4394-9d01-2e772f189780/build/buildd-samtools_0.1.9-1-alpha-5dIPqs
-Start Time: 20101102-0805
-Hit http://ftp.de.debian.org sid Release.gpg
-Ign http://ftp.de.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.de.debian.org/debian/ sid/main Translation-en
-Hit http://ftp.de.debian.org sid Release
-Hit http://ftp.de.debian.org sid/main alpha Packages/DiffIndex
-Hit http://incoming.debian.org sid Release.gpg
+Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-df690562-3900-4ca4-8c9d-9feec1b9b390/build/buildd-samtools_0.1.10-1-alpha-o4KeS3
+Start Time: 20101117-1153
+Get:1 http://ftp.uk.debian.org sid Release.gpg [835 B]
+Ign http://ftp.uk.debian.org/debian/ sid/contrib Translation-en
+Ign http://ftp.uk.debian.org/debian/ sid/main Translation-en
+Get:2 http://ftp.uk.debian.org sid Release [104 kB]
+Get:3 http://incoming.debian.org sid Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Hit http://incoming.debian.org Release.gpg
+Get:4 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:5 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://ftp.de.debian.org sid/contrib alpha Packages/DiffIndex
-Hit http://incoming.debian.org sid Release
-Hit http://incoming.debian.org Release
-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 alpha Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib alpha Packages/DiffIndex
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+Get:6 http://incoming.debian.org sid Release [104 kB]
+Get:7 http://ftp.uk.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:8 http://ftp.uk.debian.org sid/main alpha Packages/DiffIndex [2038 B]
+Get:9 http://ftp.uk.debian.org sid/contrib alpha Packages/DiffIndex [2023 B]
+Get:10 http://incoming.debian.org Release [1604 B]
+Get:11 http://ftp.uk.debian.org sid/main Sources [4061 kB]
+Get:12 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:13 http://ftp.uk.debian.org sid/contrib 2010-11-09-0809.31.pdiff [588 B]
+Get:14 http://ftp.uk.debian.org sid/main alpha Packages [6720 kB]
+Get:15 http://ftp.uk.debian.org sid/contrib 2010-11-09-0809.31.pdiff [588 B]
+Get:16 http://ftp.uk.debian.org sid/contrib 2010-11-09-0809.31.pdiff [588 B]
+Get:17 http://incoming.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:18 http://incoming.debian.org sid/main alpha Packages/DiffIndex [2038 B]
+Get:19 http://incoming.debian.org sid/contrib alpha Packages/DiffIndex [2023 B]
+Get:20 http://ftp.uk.debian.org sid/contrib alpha 2010-11-07-2008.09.pdiff [535 B]
+Get:21 http://incoming.debian.org Sources [15.1 kB]
+Get:22 http://incoming.debian.org Packages [227 kB]
+Get:23 http://incoming.debian.org sid/main Sources [4061 kB]
+Get:24 http://ftp.uk.debian.org sid/contrib alpha 2010-11-07-2008.09.pdiff [535 B]
+Get:25 http://ftp.uk.debian.org sid/contrib alpha 2010-11-07-2008.09.pdiff [535 B]
+Get:26 http://ftp.uk.debian.org sid/contrib 2010-11-11-0208.43.pdiff [339 B]
+Get:27 http://ftp.uk.debian.org sid/contrib 2010-11-11-0208.43.pdiff [339 B]
+Get:28 http://ftp.uk.debian.org sid/contrib 2010-11-11-0208.43.pdiff [339 B]
+Get:29 http://ftp.uk.debian.org sid/contrib alpha 2010-11-09-0208.55.pdiff [29 B]
+Get:30 http://ftp.uk.debian.org sid/contrib alpha 2010-11-09-0208.55.pdiff [29 B]
+Get:31 http://ftp.uk.debian.org sid/contrib alpha 2010-11-09-0208.55.pdiff [29 B]
+Get:32 http://incoming.debian.org sid/contrib 2010-11-09-0809.31.pdiff [588 B]
+Get:33 http://incoming.debian.org sid/contrib 2010-11-09-0809.31.pdiff [588 B]
+Get:34 http://incoming.debian.org sid/main alpha Packages [6720 kB]
+Get:35 http://incoming.debian.org sid/contrib 2010-11-09-0809.31.pdiff [588 B]
+Get:36 http://ftp.uk.debian.org sid/contrib 2010-11-12-0209.29.pdiff [730 B]
+Get:37 http://ftp.uk.debian.org sid/contrib 2010-11-12-0209.29.pdiff [730 B]
+Get:38 http://ftp.uk.debian.org sid/contrib 2010-11-12-0209.29.pdiff [730 B]
+Get:39 http://ftp.uk.debian.org sid/contrib alpha 2010-11-09-1433.27.pdiff [376 B]
+Get:40 http://ftp.uk.debian.org sid/contrib alpha 2010-11-09-1433.27.pdiff [376 B]
+Get:41 http://ftp.uk.debian.org sid/contrib alpha 2010-11-09-1433.27.pdiff [376 B]
+Get:42 http://ftp.uk.debian.org sid/contrib 2010-11-14-0210.10.pdiff [31 B]
+Get:43 http://ftp.uk.debian.org sid/contrib 2010-11-14-0210.10.pdiff [31 B]
+Get:44 http://ftp.uk.debian.org sid/contrib 2010-11-14-0210.10.pdiff [31 B]
+Get:45 http://ftp.uk.debian.org sid/contrib alpha 2010-11-11-0208.43.pdiff [237 B]
+Get:46 http://ftp.uk.debian.org sid/contrib alpha 2010-11-11-0208.43.pdiff [237 B]
+Get:47 http://ftp.uk.debian.org sid/contrib alpha 2010-11-11-0208.43.pdiff [237 B]
+Get:48 http://incoming.debian.org sid/contrib alpha 2010-11-07-2008.09.pdiff [535 B]
+Get:49 http://incoming.debian.org sid/contrib alpha 2010-11-07-2008.09.pdiff [535 B]
+Get:50 http://incoming.debian.org sid/contrib alpha 2010-11-07-2008.09.pdiff [535 B]
+Get:51 http://incoming.debian.org sid/contrib 2010-11-11-0208.43.pdiff [339 B]
+Get:52 http://incoming.debian.org sid/contrib 2010-11-11-0208.43.pdiff [339 B]
+Get:53 http://incoming.debian.org sid/contrib 2010-11-11-0208.43.pdiff [339 B]
+Get:54 http://incoming.debian.org sid/contrib alpha 2010-11-09-0208.55.pdiff [29 B]
+Get:55 http://incoming.debian.org sid/contrib alpha 2010-11-09-0208.55.pdiff [29 B]
+Get:56 http://incoming.debian.org sid/contrib alpha 2010-11-09-0208.55.pdiff [29 B]
+Get:57 http://incoming.debian.org sid/contrib 2010-11-12-0209.29.pdiff [730 B]
+Get:58 http://incoming.debian.org sid/contrib 2010-11-12-0209.29.pdiff [730 B]
+Get:59 http://incoming.debian.org sid/contrib 2010-11-12-0209.29.pdiff [730 B]
+Get:60 http://incoming.debian.org sid/contrib alpha 2010-11-09-1433.27.pdiff [376 B]
+Get:61 http://incoming.debian.org sid/contrib alpha 2010-11-09-1433.27.pdiff [376 B]
+Get:62 http://incoming.debian.org sid/contrib alpha 2010-11-09-1433.27.pdiff [376 B]
+Get:63 http://incoming.debian.org sid/contrib 2010-11-14-0210.10.pdiff [31 B]
+Get:64 http://incoming.debian.org sid/contrib 2010-11-14-0210.10.pdiff [31 B]
+Get:65 http://incoming.debian.org sid/contrib 2010-11-14-0210.10.pdiff [31 B]
+Get:66 http://incoming.debian.org sid/contrib alpha 2010-11-11-0208.43.pdiff [237 B]
+Get:67 http://incoming.debian.org sid/contrib alpha 2010-11-11-0208.43.pdiff [237 B]
+Get:68 http://incoming.debian.org sid/contrib alpha 2010-11-11-0208.43.pdiff [237 B]
+Fetched 22.0 MB in 36s (609 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -51,11 +106,11 @@ 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 358 kB of source archives.
-Get:1 http://incoming.debian.org/debian/ sid/main samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://incoming.debian.org/debian/ sid/main samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://incoming.debian.org/debian/ sid/main samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 1s (327 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 5s (60.6 kB/s)
Download complete and in download only mode
Check arch
@@ -69,41 +124,120 @@ Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: already installed (8.0.0 >= 7 is satisfied)
+debhelper: missing
+Using default version 8.0.0
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following extra packages will be installed:
+ bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
- devscripts doc-base
+ wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
+ groff less www-browser libmail-box-perl
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev zlib1g-dev
+ bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 19 newly installed, 0 to remove and 21 not upgraded.
+Need to get 12.6 MB of archives.
+After this operation, 39.1 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ sid/main bsdmainutils alpha 8.0.16 [212 kB]
+Get:2 http://ftp.uk.debian.org/debian/ sid/main groff-base alpha 1.20.1-10 [1210 kB]
+Get:3 http://ftp.uk.debian.org/debian/ sid/main man-db alpha 2.5.7-6 [1624 kB]
+Get:4 http://ftp.uk.debian.org/debian/ sid/main libmagic1 alpha 5.04-5 [243 kB]
+Get:5 http://ftp.uk.debian.org/debian/ sid/main file alpha 5.04-5 [50.2 kB]
+Get:6 http://ftp.uk.debian.org/debian/ sid/main gettext-base alpha 0.18.1.1-3 [160 kB]
+Get:7 http://ftp.uk.debian.org/debian/ sid/main libpcre3 alpha 8.02-1.1 [250 kB]
+Get:8 http://ftp.uk.debian.org/debian/ sid/main libxml2 alpha 2.7.8.dfsg-1 [900 kB]
+Get:9 http://ftp.uk.debian.org/debian/ sid/main html2text alpha 1.3.2a-15 [111 kB]
+Get:10 http://ftp.uk.debian.org/debian/ sid/main libglib2.0-0 alpha 2.24.2-1 [1168 kB]
+Get:11 http://ftp.uk.debian.org/debian/ sid/main libcroco3 alpha 0.6.2-1 [128 kB]
+Get:12 http://ftp.uk.debian.org/debian/ sid/main libunistring0 alpha 0.9.3-3 [447 kB]
+Get:13 http://ftp.uk.debian.org/debian/ sid/main gettext alpha 0.18.1.1-3 [2218 kB]
+Get:14 http://ftp.uk.debian.org/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://ftp.uk.debian.org/debian/ sid/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://ftp.uk.debian.org/debian/ sid/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.uk.debian.org/debian/ sid/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.uk.debian.org/debian/ sid/main libncurses5-dev alpha 5.7+20100313-4 [1675 kB]
+Get:19 http://ftp.uk.debian.org/debian/ sid/main zlib1g-dev alpha 1:1.2.3.4.dfsg-3 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 3 newly installed, 0 to remove and 39 not upgraded.
-Need to get 0 B/3121 kB of archives.
-After this operation, 9556 kB of additional disk space will be used.
+Fetched 12.6 MB in 7s (1692 kB/s)
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10068 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_alpha.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_alpha.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-6_alpha.deb) ...
+Selecting previously deselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.04-5_alpha.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../archives/file_5.04-5_alpha.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_alpha.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_alpha.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_alpha.deb) ...
+Selecting previously deselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_alpha.deb) ...
+Selecting previously deselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_alpha.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_alpha.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_alpha.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_alpha.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_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 13752 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_alpha.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_alpha.deb) ...
-Processing triggers for man-db ...
+Setting up bsdmainutils (8.0.16) ...
+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 (1.20.1-10) ...
+Setting up man-db (2.5.7-6) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libpcre3 (8.02-1.1) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libunistring0 (0.9.3-3) ...
+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 (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: Linux 2.6.26-2-alpha-generic alpha (alpha)
-Toolchain package versions: libc6.1-dev_2.11.2-6 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-22 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libstdc++6_4.4.5-6
-Package versions: apt_0.8.7 asciidoc_8.5.2-1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 binutils-dev_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.3_4.3.5-3 cpp-4.4_4.4.5-6 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.4 diffutils_1:3.0-1 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.3_4.3.5-3 gcc-4.3-base_4.3.5-3 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-2 gettext-base_0.18.1.1-2 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6.1_2.11.2-6 libc6.1-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.4 libelf-dev_0.148-1 libelf1_0.148-1 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-6 libgpg-error0_1.6-1 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libssl0.9.8_0.9.8o-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 libxml2-utils_2.7.7.dfsg-4 libxslt1.1_1.1.26-6 linux-libc-dev_2.6.32-22 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 module-init-tools_3.12-1 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 python_2.6.6-3+squeeze1 python-minimal_2.6.6-3+squeeze1 python2.6_2.6.6-6 python2.6-minimal_2.6.6-6 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 sgml-data_2.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2.1 tzdata_2010o-1 util-linux_2.17.2-3.1 xml-core_0.13 xmlto_0.0.23-2 xsltproc_1.1.26-6 xz-utils_4.999.9beta+20100713-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-bpo.5-alpha-generic alpha (alpha)
+Toolchain package versions: libc6.1-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libstdc++6_4.4.5-6
+Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 dash_0.5.5.1-7.2 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6.1_2.11.2-7 libc6.1-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-27 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.43 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010o-1 util-linux_2.17.2-3.3 vim-common_2:7.3.035+hg~8fdc12103333-1 vim-tiny_2:7.3.035+hg~8fdc12103333-1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -115,12 +249,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -135,34 +269,34 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture alpha
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/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_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/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_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
- 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
+ debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -180,9 +314,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -193,10 +328,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -209,27 +344,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -239,14 +375,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-alpha-5dIPqs/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -259,8 +395,8 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtool
[samopen] SAM header is present: 2 sequences.
(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 seq1...
[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'
@@ -268,15 +404,16 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtool
[bam_rmdupse_core] 4666 / 6542 = 0.7132 in library 'ex1'
[bam_rmdupse_core] 1395 / 3271 = 0.4265 in library 'ex1b'
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-[mpileup] 1 samples in 1 input files
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/examples'
- /usr/bin/fakeroot debian/rules binary-arch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
+ /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -306,8 +443,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -331,7 +468,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-alpha-5dIPqs/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -346,71 +483,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_alpha.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_alpha.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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_alpha.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_alpha.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101102-0815
+Build finished at 20101117-1201
-samtools_0.1.9-1_alpha.changes:
+samtools_0.1.10-1_alpha.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: alpha
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: Debian Build Daemon <buildd_alpha-goedel at buildd...>
+Maintainer: alpha Build Daemon (goetz) <buildd_alpha-goetz at buildd...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- e4219c813040b0f44c6217a582c2a7f7d58d6c87 587334 samtools_0.1.9-1_alpha.deb
- ad05a90b1e5c20fc759457ef563883741fba313a 199422 libbam-dev_0.1.9-1_alpha.deb
+ a1e51ad4045a416cdea105b8f4bda5335a97aba5 605070 samtools_0.1.10-1_alpha.deb
+ 289158da20b96f15c5179e69a62b660494c7a34a 207186 libbam-dev_0.1.10-1_alpha.deb
Checksums-Sha256:
- 5d723fc5e63f035a0854cefbfe4dbe88fe71d3ca3855606a15989889b3e363e1 587334 samtools_0.1.9-1_alpha.deb
- 3b961f753ee5f36adf7c43ddd38d7bcf58cfbe4c3c89945ffa0796248ce50891 199422 libbam-dev_0.1.9-1_alpha.deb
+ 2faa4d1455551181538b101b40c86539a286e6385e7d837c51fddddba7df5224 605070 samtools_0.1.10-1_alpha.deb
+ d936b2faf2ea800c0b3d249392e328f2de9321e6b7acdb6527daeafcc902df12 207186 libbam-dev_0.1.10-1_alpha.deb
Files:
- cef23fe836e78cd60a70ec78de547eac 587334 science optional samtools_0.1.9-1_alpha.deb
- 47b3c805bd8df7e58bf27abbe05c7c92 199422 libdevel optional libbam-dev_0.1.9-1_alpha.deb
+ 70f64ae69b1eb44108a3b6c5da0bad9a 605070 science optional samtools_0.1.10-1_alpha.deb
+ e5c671c45e8bbb25726bd396010b1bd1 207186 libdevel optional libbam-dev_0.1.10-1_alpha.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_alpha.deb
-──────────────────────────
+samtools_0.1.10-1_alpha.deb
+───────────────────────────
new debian package, version 2.0.
- size 587334 bytes: control archive= 1793 bytes.
- 793 bytes, 16 lines control
+ size 605070 bytes: control archive= 1796 bytes.
+ 794 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: alpha
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1104
+ Installed-Size: 1128
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -423,72 +554,72 @@ samtools_0.1.9-1_alpha.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 2010-11-02 08:14 ./
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-02 08:07 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-11-02 08:14 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-02 08:14 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-02 08:14 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/samtools/
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2010-11-02 08:14 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/bin/
--rwxr-xr-x root/root 111048 2010-11-02 08:14 ./usr/bin/bcftools
--rwxr-xr-x root/root 31536 2010-11-02 08:14 ./usr/bin/razip
--rwxr-xr-x root/root 385360 2010-11-02 08:14 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/lib/samtools/
--rwxr-xr-x root/root 22296 2010-11-02 08:14 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9728 2010-11-02 08:14 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9728 2010-11-02 08:14 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 15320 2010-11-02 08:14 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 11136 2010-11-02 08:14 ./usr/lib/samtools/md5sum-lite
-lrwxrwxrwx root/root 0 2010-11-02 08:14 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_alpha.deb
-────────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/lib/samtools/
+-rwxr-xr-x root/root 22296 2010-11-17 12:01 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 11136 2010-11-17 12:01 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 15320 2010-11-17 12:01 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9728 2010-11-17 12:01 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9728 2010-11-17 12:01 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/bin/
+-rwxr-xr-x root/root 31536 2010-11-17 12:01 ./usr/bin/razip
+-rwxr-xr-x root/root 410312 2010-11-17 12:01 ./usr/bin/samtools
+-rwxr-xr-x root/root 111048 2010-11-17 12:01 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-17 12:01 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./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 2010-11-17 11:56 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-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 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 12:01 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 12:01 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/samtools/
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.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 5778 2010-11-17 12:01 ./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 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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+lrwxrwxrwx root/root 0 2010-11-17 12:01 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_alpha.deb
+─────────────────────────────
new debian package, version 2.0.
- size 199422 bytes: control archive= 897 bytes.
- 673 bytes, 15 lines control
+ size 207186 bytes: control archive= 894 bytes.
+ 674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: alpha
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 596
+ Installed-Size: 616
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -499,23 +630,23 @@ libbam-dev_0.1.9-1_alpha.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/lib/
--rw-r--r-- root/root 462396 2010-11-02 08:14 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/include/
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/include/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/lib/
+-rw-r--r-- root/root 475334 2010-11-17 12:01 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -524,14 +655,10 @@ drwxr-xr-x root/root 0 2010-11-02 08:14 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-alpha-sbuild-34703713-5fd1-4394-9d01-2e772f189780/build/buildd-samtools_0.1.9-1-alpha-5dIPqs
-(Reading database ... 14885 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing cdbs ...
-Removing zlib1g-dev ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-alpha-sbuild-df690562-3900-4ca4-8c9d-9feec1b9b390/build/buildd-samtools_0.1.10-1-alpha-o4KeS3
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101102-0815
-Build needed 00:09:49, 11040k disc space
+Finished at 20101117-1201
+Build needed 00:08:01, 11400k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/armel.build b/armel.build
index 4c5e4ec..daf806c 100644
--- a/armel.build
+++ b/armel.build
@@ -1,41 +1,41 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/armel received Mon Nov 1 11:28:28 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=armel">armel</a> >> Mon Nov 1 11:28:28 2010<pre>
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/armel received Wed Nov 17 11:58:47 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=armel">armel</a> >> Wed Nov 17 11:58:47 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on antheil.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (armel) 01 Nov 2010 11:22 ║
+║ samtools 0.1.10-1 (armel) 17 Nov 2010 11:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: armel
-Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-288e114f-4684-4567-9345-244658328abb/build/buildd-samtools_0.1.9-1-armel-8inJsJ
-Start Time: 20101101-1122
+Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-3065dfec-037e-4cdb-a2aa-531dc5b60773/build/buildd-samtools_0.1.10-1-armel-EP8FwK
+Start Time: 20101117-1152
Get:1 http://ftp.uk.debian.org unstable Release.gpg [835B]
Ign http://ftp.uk.debian.org/debian/ unstable/contrib Translation-en
Ign http://ftp.uk.debian.org/debian/ unstable/main Translation-en
Get:2 http://ftp.uk.debian.org unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [4061kB]
+Get:4 http://incoming.debian.org unstable Release.gpg [835B]
Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://ftp.uk.debian.org unstable/main Sources [4011kB]
Get:5 http://incoming.debian.org Release.gpg [835B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
Get:6 http://incoming.debian.org unstable Release [104kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4011kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib Sources [38.7kB]
-Get:10 http://ftp.uk.debian.org unstable/non-free Sources [81.3kB]
-Get:11 http://ftp.uk.debian.org unstable/main armel Packages [6680kB]
-Get:12 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [81.3kB]
-Get:14 http://incoming.debian.org unstable/main armel Packages [6680kB]
-Get:15 http://ftp.uk.debian.org unstable/contrib armel Packages [49.7kB]
+Get:8 http://incoming.debian.org unstable/main Sources [4061kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib Sources [39.0kB]
+Get:10 http://ftp.uk.debian.org unstable/non-free Sources [83.1kB]
+Get:11 http://ftp.uk.debian.org unstable/main armel Packages [6747kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [49.7kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [39.0kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.1kB]
+Get:15 http://incoming.debian.org unstable/main armel Packages [6747kB]
Get:16 http://incoming.debian.org unstable/contrib armel Packages [49.7kB]
-Get:17 http://incoming.debian.org Sources [11.5kB]
-Get:18 http://incoming.debian.org Packages [200kB]
-Fetched 22.1MB in 50s (441kB/s)
+Get:17 http://incoming.debian.org Sources [15.1kB]
+Get:18 http://incoming.debian.org Packages [227kB]
+Fetched 22.4MB in 50s (448kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -56,11 +56,11 @@ 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 358kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264B]
-Fetched 358kB in 1s (281kB/s)
+Need to get 361kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332B]
+Fetched 361kB in 1s (307kB/s)
Download complete and in download only mode
Check arch
@@ -100,32 +100,32 @@ The following NEW packages will be installed:
libunistring0 libxml2 man-db po-debconf zlib1g-dev
The following packages will be upgraded:
libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 32 not upgraded.
+2 upgraded, 19 newly installed, 0 to remove and 49 not upgraded.
Need to get 12.0MB of archives.
-After this operation, 34.1MB of additional disk space will be used.
+After this operation, 34.3MB of additional disk space will be used.
Get:1 http://ftp.uk.debian.org/debian/ unstable/main ncurses-bin armel 5.7+20100313-4 [319kB]
Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 armel 5.7+20100313-4 [344kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.0.13 [202kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.0.16 [204kB]
Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.20.1-10 [1038kB]
Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.5.7-6 [1222kB]
Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5 [237kB]
Get:7 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4kB]
Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-3 [129kB]
Get:9 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.02-1.1 [234kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.7.dfsg-4 [816kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-1 [817kB]
Get:11 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.24.2-1 [1050kB]
Get:13 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113kB]
Get:14 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410kB]
Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981kB]
Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16 [224kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.0.0 [454kB]
Get:19 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240kB]
Get:20 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.7+20100313-4 [1603kB]
Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.0MB in 7s (1691kB/s)
+Fetched 12.0MB in 3s (3606kB/s)
(Reading database ... 10006 files and directories currently installed.)
Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-4_armel.deb) ...
Unpacking replacement ncurses-bin ...
@@ -136,7 +136,7 @@ Unpacking replacement libncurses5 ...
Setting up libncurses5 (5.7+20100313-4) ...
Selecting previously deselected package bsdmainutils.
(Reading database ... 10006 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_armel.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_armel.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_armel.deb) ...
Selecting previously deselected package man-db.
@@ -150,7 +150,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_armel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -164,7 +164,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -173,7 +173,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_armel.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.0.16) ...
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 (1.20.1-10) ...
@@ -183,14 +183,14 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
@@ -199,7 +199,7 @@ Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.4-17 g++-4.4_4.4.4-17 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-17 libstdc++6_4.4.4-17
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-17 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-17 gcc_4:4.4.4-2 gcc-4.4_4.4.4-17 gcc-4.4-base_4.4.4-17 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-17 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-17 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-17 libstdc++6-4.4-dev_4.4.4-17 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-3 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-17 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-17 gcc_4:4.4.4-2 gcc-4.4_4.4.4-17 gcc-4.4-base_4.4.4-17 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-17 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-17 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-17 libstdc++6-4.4-dev_4.4.4-17 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-3 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -211,12 +211,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -231,25 +231,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture armel
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/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_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/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_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -257,8 +257,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -282,9 +282,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -295,10 +296,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -311,27 +312,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -341,31 +343,31 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-armel-8inJsJ/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-armel-8inJsJ/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
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_0.1.9-1-armel-8inJsJ/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1128
+Build finished at 20101117-1158
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-288e114f-4684-4567-9345-244658328abb/build/buildd-samtools_0.1.9-1-armel-8inJsJ
+Purging /var/lib/schroot/mount/sid-armel-sbuild-3065dfec-037e-4cdb-a2aa-531dc5b60773/build/buildd-samtools_0.1.10-1-armel-EP8FwK
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1128
-Build needed 00:06:00, 4756k disc space
+Finished at 20101117-1158
+Build needed 00:06:04, 4960k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/armhf.build b/armhf.build
index 06775c5..9c9359c 100644
--- a/armhf.build
+++ b/armhf.build
@@ -1,17 +1,17 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>File `log' in samtools_0.1.9-1_armhf (Nov 1 16:35)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
-<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.9-1_armhf (Nov 1 16:35)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=armhf">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=armhf">0.1.9-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=armhf&stamp=1288629355">Nov 1 16:35</a> >> log</td></tr></table><p><pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on efikamx05.lan
+<html><head><title>File `log' in samtools_0.1.10-1_armhf (Nov 17 16:04)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
+<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.10-1_armhf (Nov 17 16:04)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=armhf">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.10-1&arch=armhf">0.1.10-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.10-1&arch=armhf&stamp=1290009874">Nov 17 16:04</a> >> log</td></tr></table><p><pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on efikamx01.lan
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (armhf) 01 Nov 2010 19:35 ║
+║ samtools 0.1.10-1 (armhf) 17 Nov 2010 19:03 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: armhf
-Chroot Build Dir: /var/lib/schroot/mount/sid-armhf-sbuild-07ca07e8-81ea-4792-9d39-51f27d8050b5/build/buildd-samtools_0.1.9-1-armhf-WeJDhX
-Start Time: 20101101-1935
+Chroot Build Dir: /var/lib/schroot/mount/sid-armhf-sbuild-ae55037d-2fca-4bcb-92dd-9b7bd9142996/build/buildd-samtools_0.1.10-1-armhf-XV65Zs
+Start Time: 20101117-1903
W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
I: This option will be removed in the future; please update your configuration
W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
@@ -24,31 +24,27 @@ W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
I: This option will be removed in the future; please update your configuration
W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
I: This option will be removed in the future; please update your configuration
-Get:1 http://ftp.gr.debian.org unstable Release.gpg [835 B]
-Get:2 http://ftp.gr.debian.org unstable Release [104 kB]
+Hit http://ftp.gr.debian.org unstable Release.gpg
+Hit http://ftp.gr.debian.org unstable Release
+Hit http://www.freevec.org unstable Release.gpg
+Hit http://incoming.debian-ports.org unstable Release.gpg
+Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
Hit http://ftp.debian-ports.org unreleased Release.gpg
Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-Get:3 http://incoming.debian-ports.org unstable Release.gpg [835 B]
-Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
+Ign http://www.freevec.org/repository/ unstable/main Translation-en
+Hit http://ftp.gr.debian.org unstable/main Sources/DiffIndex
Hit http://ftp.debian-ports.org unstable Release.gpg
Ign http://ftp.debian-ports.org/debian/ unstable/main Translation-en
Hit http://ftp.debian-ports.org unreleased Release
-Hit http://www.freevec.org unstable Release.gpg
-Get:4 http://incoming.debian-ports.org unstable Release [8817 B]
-Ign http://www.freevec.org/repository/ unstable/main Translation-en
-Hit http://ftp.debian-ports.org unstable Release
-Get:5 http://ftp.gr.debian.org unstable/main Sources/DiffIndex [2038 B]
-Hit http://ftp.debian-ports.org unreleased/main armhf Packages
Hit http://www.freevec.org unstable Release
-Get:6 http://ftp.gr.debian.org unstable/main 2010-11-01-1409.21.pdiff [3126 B]
-Get:7 http://ftp.gr.debian.org unstable/main 2010-11-01-1409.21.pdiff [3126 B]
-Hit http://ftp.debian-ports.org unstable/main armhf Packages
-Hit http://incoming.debian-ports.org unstable/main Sources
-Get:8 http://ftp.gr.debian.org unstable/main 2010-11-01-1409.21.pdiff [3126 B]
+Hit http://incoming.debian-ports.org unstable Release
+Hit http://ftp.debian-ports.org unstable Release
Ign http://www.freevec.org unstable/main armhf Packages
-Get:9 http://incoming.debian-ports.org unstable/main armhf Packages [16.7 kB]
+Hit http://incoming.debian-ports.org unstable/main Sources
+Hit http://ftp.debian-ports.org unreleased/main armhf Packages
+Hit http://incoming.debian-ports.org unstable/main armhf Packages
Hit http://www.freevec.org unstable/main armhf Packages
-Fetched 136 kB in 4s (27.9 kB/s)
+Hit http://ftp.debian-ports.org unstable/main armhf Packages
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,11 +77,11 @@ 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 358 kB of source archives.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 0s (561 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 0s (736 kB/s)
Download complete and in download only mode
Check arch
@@ -150,28 +146,29 @@ I: This option will be removed in the future; please update your configuration
W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
I: This option will be removed in the future; please update your configuration
Kernel: Linux 2.6.31.14-efikamx armhf (armv7l)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.4+armhf linux-libc-dev_2.6.35~rc6-1+armhf~experimental.2 gcc-4.4_4.4.5-5+armhf g++-4.4_4.4.5-5+armhf binutils_2.20.51.20101009-1+armhf libstdc++6-4.4-dev_4.4.5-5+armhf libstdc++6_4.4.5-5+armhf
-Package versions: adduser_3.112+nmu1 apt_0.8.7 autoconf_2.67-2 autoconf-archive_20090426-1 automake_1:1.11.1-1 automake1.4_1:1.4-p6-13.1 automake1.7_1.7.9-9.1 automake1.9_1.9.6+nogfdl-3.1 automoc_1.0~version-0.9.88-4 autotools-dev_20100122.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 bc_1.06.95-2 binutils_2.20.51.20101009-1+armhf bison_1:2.4.1.dfsg-3 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1+armhf build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 ccache_3.0.1-1 cdbs_0.4.89 chrpath_0.13-2 cmake_2.8.2-2 cmake-data_2.8.2-2 comerr-dev_2.1-1.41.12-2 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.5-5+armhf ctn_3.0.6-13 ctn-dev_3.0.6-13 dash_0.5.5.1-7.2 dbus_1.2.24-3 dbus-x11_1.2.24-3 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2010.06.16 debiandoc-sgml_1.2.15 debianutils_3.4.1 defoma_0.11.11 desktop-file-utils_0.15-2 devscripts_2.10.69 dh-buildinfo_0.9 diffstat_1.53-1 diffutils_1:3.0
- -1 dmsetup_2:1.02.48-3 docbook_4.5-4 docbook-dsssl_1.79-6 docbook-to-man_1:2.0.0-28 docbook-utils_0.6.14-1.1 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 doxygen_1.7.1-2 dpatch_2.0.31 dpkg_1.15.8.4+armhf dpkg-dev_1.15.8.4+armhf dssi-dev_1.0.0-1 e2fslibs_1.41.12-2 e2fslibs-dev_1.41.12-2 e2fsprogs_1.41.12-2 ed_1.4-3 emacsen-common_1.4.19 esound-common_0.2.41-7 fakeroot_1.14.4-1 fftw-dev_2.1.3-22 fftw2_2.1.3-22 file_5.04-5 findutils_4.4.2-1 flex_2.5.35-10 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 freeglut3_2.6.0-1 freeglut3-dev_2.6.0-1 g++_4:4.4.4-2 g++-4.4_4.4.5-5+armhf gcc_4:4.4.4-2 gcc-4.4_4.4.5-5+armhf gcc-4.4-base_4.4.5-5+armhf gconf2_2.28.1-5 gconf2-common_2.28.1-5 gettext_0.18.1.1-1+armhf gettext-base_0.18.1.1-1+armhf ghostscript_8.71~dfsg2-6 gnome-mime-data_2.18.0-1 gnome-pkg-tools_0.16.3 gnupg_1.4.10-4 gpgv_1.4.10-4 graphviz_2.26.3-5 grep_2.6.3-3 groff-base_1.20.1-10 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gvfs_1.6.4-2 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15
- imagemagick_8:6.6.0.4-2.2 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool_0.41.1-1 intltool-debian_0.35.0+20060710.1 jadetex_3.13-12 kde-sc-dev-latest_4:4.4.5+5.64 kdelibs-bin_4:4.4.5-1 kdelibs5-dev_4:4.4.5-1 kdoctools_4:4.4.5-1 krb5-multidev_1.8.3+dfsg-2 ladspa-sdk_1.13-1 lesstif2_1:0.95.2-1 lesstif2-dev_1:0.95.2-1 libaa1_1.4p5-38 libaa1-dev_1.4p5-38 libacl1_2.2.49-4 libacl1-dev_2.2.49-4 libarchive-dev_2.8.4-1 libarchive1_2.8.4-1 libart-2.0-2_2.3.21-1 libart-2.0-dev_2.3.21-1 libartsc0_1.5.9-3 libartsc0-dev_1.5.9-3 libasound2_1.0.23-1+armhf libasound2-dev_1.0.23-1+armhf libasyncns0_0.3-1 libatasmart4_0.17+git20100219-2 libatk1.0-0_1.30.0-1 libatk1.0-dev_1.30.0-1 libatomic-ops-dev_7.2~alpha5+cvs20100919-1 libattica0_0.1.4-1 libattr1_1:2.4.44-2 libattr1-dev_1:2.4.44-2 libaudio-dev_1.9.2-3 libaudio2_1.9.2-3 libaudiofile-dev_0.2.6-8 libaudiofile0_0.2.6-8 libautobox-core-perl_1.2-1 libautobox-dump-perl_20090426.1746-1 libautobox-list-util-perl_20090629-1 libautobox-perl_2.71-1
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- 1:2.19-3 libcdt4_2.26.3-5 libcelt-dev_0.7.1-1 libcelt0-0_0.7.1-1 libcgraph5_2.26.3-5 libchm-dev_2:0.40-3 libchm1_2:0.40-3 libclalsadrv-dev_2.0.0-3 libclalsadrv2_2.0.0-3 libclass-perl_1.00-1 libclass-singleton-perl_1.4-1 libclucene0ldbl_0.9.21b-2 libcomerr2_1.41.12-2 libcppunit-1.12-1_1.12.1-1 libcppunit-dev_1.12.1-1 libcroco3_0.6.2-1 libcups2_1.4.4-6 libcupsimage2_1.4.4-6 libcurl3_7.21.2-1 libcurl3-gnutls_7.21.2-1 libcurl4-gnutls-dev_7.21.2-1 libdata-optlist-perl_0.104-1 libdate-iso8601-perl_0.003-1 libdate-jd-perl_0.003-1 libdatetime-format-epoch-perl_0.11-1 libdatetime-locale-perl_1:0.45-1 libdatetime-perl_2:0.6500-1 libdatetime-timezone-perl_1:1.23-1+2010n libdatetime-timezone-systemv-perl_0.003-1 libdatetime-timezone-tzfile-perl_0.002-1 libdatrie1_0.2.4-1 libdb-dev_4.8 libdb4.7_4.7.25-9+armhf libdb4.8_4.8.30-2+armhf libdb4.8-dev_4.8.30-2+armhf libdbus-1-3_1.2.24-3 libdbus-1-dev_1.2.24-3 libdbus-glib-1-2_0.88-2 libdbus-glib-1-dev_0.88-2 libdevmapper1.02.1_2:1.02.48-3 libd
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+ ibwnck22_2.30.4-2 libwrap0_7.6.q-19 libwww-perl_5.837-1 libwxbase2.8-0_2.8.10.1-3 libwxbase2.8-dev_2.8.10.1-3 libwxgtk2.8-0_2.8.10.1-3 libwxgtk2.8-dev_2.8.10.1-3 libx11-6_2:1.3.3-3 libx11-data_2:1.3.3-3 libx11-dev_2:1.3.3-3 libxapian-dev_1.2.3-2 libxapian22_1.2.3-2 libxau-dev_1:1.0.6-1 libxau6_1:1.0.6-1 libxaw7_2:1.0.8-2 libxaw7-dev_2:1.0.8-2 libxcb-atom1_0.3.6-1 libxcb-aux0_0.3.6-1 libxcb-event1_0.3.6-1 libxcb-render-util0_0.3.6-1 libxcb-render-util0-dev_0.3.6-1 libxcb-render0_1.6-1 libxcb-render0-dev_1.6-1 libxcb1_1.6-1 libxcb1-dev_1.6-1 libxcomposite-dev_1:0.4.3-1 libxcomposite1_1:0.4.3-1 libxcursor-dev_1:1.1.11-1 libxcursor1_1:1.1.11-1 libxdamage-dev_1:1.1.3-1 libxdamage1_1:1.1.3-1 libxdmcp-dev_1:1.0.3-2 libxdmcp6_1:1.0.3-2 libxdot4_2.26.3-5 libxerces-c2-dev_2.8.0+deb1-2 libxerces-c28_2.8.0+deb1-2 libxext-dev_2:1.1.2-1 libxext6_2:1.1.2-1 libxfixes-dev_1:4.0.5-1 libxfixes3_1:4.0.5-1 libxfont1_1:1.4.1-2 libxft-dev_2.1.14-2 libxft2_2.1.14-2 libxi-dev_2:1.3-4 libxi6_2:1.3-4
+ libxinerama-dev_2:1.1-3 libxinerama1_2:1.1-3 libxkbfile1_1:1.0.6-2 libxml-parser-perl_2.36-1.1 libxml2_2.7.8.dfsg-1 libxml2-dev_2.7.8.dfsg-1 libxml2-utils_2.7.8.dfsg-1 libxmlrpc-c3_1.06.27-1.1 libxmlrpc-c3-dev_1.06.27-1.1 libxmu-dev_2:1.0.5-2 libxmu-headers_2:1.0.5-2 libxmu6_2:1.0.5-2 libxmuu1_2:1.0.5-2 libxp-dev_1:1.0.0.xsf1-2 libxp6_1:1.0.0.xsf1-2 libxpm-dev_1:3.5.8-1 libxpm4_1:3.5.8-1 libxrandr-dev_2:1.3.0-3 libxrandr2_2:1.3.0-3 libxrender-dev_1:0.9.6-1 libxrender1_1:0.9.6-1 libxres-dev_2:1.0.5-1 libxres1_2:1.0.5-1 libxslt1-dev_1.1.26-6 libxslt1.1_1.1.26-6 libxss-dev_1:1.2.1-1 libxss1_1:1.2.1-1 libxt-dev_1:1.0.7-1 libxt6_1:1.0.7-1 libxtst6_2:1.1.0-3 libxv-dev_2:1.0.6-1 libxv1_2:1.0.6-1 libxxf86dga1_2:1.1.1-2 libxxf86vm-dev_1:1.1.0-2 libxxf86vm1_1:1.1.0-2 libyaml-perl_0.71-1 linux-libc-dev_2.6.35~rc6-1+armhf~experimental.2 locales_2.11.2-7 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lsb-release_3.2-26 lua50_5.0.3-4 luatex_0.60.2-1 lynx_2.8.8dev.6-1 lynx-cur_2.8.8dev.6-1 m4_1
+ .4.14-3 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mesa-common-dev_7.7.1-4 mime-support_3.48-1 mount_2.17.2-3.1+armhf mpi-default-dev_0.6 mysql-common_5.1.49-2 nano_2.2.5-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.43 netpbm_2:10.0-12.2 ocaml-base-nox_3.11.2-2 ocaml-interp_3.11.2-2 ocaml-nox_3.11.2-2 openjade_1.4devel1-19 opensp_1.5.2-8 openssl_0.9.8o-2+armhf passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 pkg-config_0.25-1.1 po-debconf_1.0.16 po4a_0.40.1-1 procps_1:3.2.8-9 psmisc_22.13-1 puredata_0.42.6-2 python_2.6.6-3+squeeze1 python-all_2.6.6-3+squeeze1 python-all-dbg_2.6.6-3+squeeze1 python-all-dev_2.6.6-3+squeeze1 python-central_0.6.16+nmu1 python-dbg_2.6.6-3+squeeze1 python-dbus_0.83.1-1 python-dbus-dbg_0.83.1-1 python-dev_2.6.6-3+squeeze1 python-libxml2_2.7.8.dfsg-1 python-minimal_2.6.6-3+squeeze1 python-ply_3.3-1 python-sip_4.10.2-1 python-sip-dbg_4.10.2-1 python-sip-dev_4.10.2-1 python-support_1.
+ 0.11 python2.5_2.5.5-10 python2.5-dbg_2.5.5-10 python2.5-dev_2.5.5-10 python2.5-minimal_2.5.5-10 python2.6_2.6.6-6 python2.6-dbg_2.6.6-6 python2.6-dev_2.6.6-6 python2.6-minimal_2.6.6-6 qt3-dev-tools_3:3.3.8b-7 qt4-qmake_4:4.6.3-3+armhf quilt_0.48-7 rarian-compat_0.8.1-5 readline-common_6.1-3 scrollkeeper_0.8.1-5 sed_4.2.1-7 sensible-utils_0.0.4 sfftw-dev_2.1.3-22 sfftw2_2.1.3-22 sgml-base_1.26+nmu1 sgml-data_2.0.4 sgmlspl_1.03ii-32 shared-mime-info_0.71-3 sharutils_1:4.9-1 sp_1.3.4-1.2.1-47 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.24-1.1 tcl8.4_8.4.19-4 tcl8.4-dev_8.4.19-4 tcl8.5_8.5.8-2 tcl8.5-dev_8.5.8-2 tclcl_1.20~RC3-1 tclcl-dev_1.20~RC3-1 tex-common_2.08 texinfo_4.13a.dfsg.1-6 texlive-base_2009-11 texlive-binaries_2009-7 texlive-common_2009-11 texlive-doc-base_2009-2 texlive-fonts-recommended_2009-11 texlive-latex-base_2009-11 texlive-latex-recommended_2009-11 tipa_2:1.3-14 tk8.4_8.4.19-4 tk8.4-dev_8.4.19-4 tk8.5_8.5.8-1 tk8.
+ 5-dev_8.5.8-1 tsconf_1.0-7 ttf-dejavu-core_2.31-1 tzdata_2010o-1 ucf_3.0025+nmu1 udev_164-1 udisks_1.0.1+git20100614-3 util-linux_2.17.2-3.1+armhf uuid-dev_2.17.2-3.1+armhf vamp-plugin-sdk_2.1-1 wget_1.12-2.1 whiptail_0.52.11-2 wx-common_2.8.10.1-3 wx2.8-headers_2.8.10.1-3 x11-common_1:7.5+8+armhf x11-utils_7.5+4 x11-xkb-utils_7.5+5 x11proto-composite-dev_1:0.4.2-1 x11proto-core-dev_7.0.19-1 x11proto-damage-dev_1:1.2.1-1 x11proto-fixes-dev_1:4.1.2-1 x11proto-input-dev_2.0-2 x11proto-kb-dev_1.0.5-1 x11proto-print-dev_1.0.3.xsf1-1 x11proto-randr-dev_1.3.2-1 x11proto-render-dev_2:0.11.1-1 x11proto-resource-dev_1.1.0-1 x11proto-scrnsaver-dev_1.2.1-1 x11proto-video-dev_2.3.1-1 x11proto-xext-dev_7.1.2-1 x11proto-xf86vidmode-dev_2.3-2 x11proto-xinerama-dev_1.2-2 xauth_1:1.0.5-1 xfonts-base_1:1.0.1 xfonts-encodings_1:1.0.3-1 xfonts-utils_1:7.5+2 xgraph_12.1-13 xkb-data_1.8-1 xml-core_0.13 xmlto_0.0.23-2 xserver-common_2:1.7.7-8 xsltproc_1.1.26-6 xtrans-dev_1.2.5-1 xvfb_2:1.7.7-7+arm
+ hf xz-utils_4.999.9beta+20100810-1 zip_3.0-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -189,12 +186,12 @@ W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
I: This option will be removed in the future; please update your configuration
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -215,25 +212,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture armhf
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/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_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/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_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -241,8 +238,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -266,9 +263,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -279,10 +277,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -295,27 +293,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -325,14 +324,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-armhf-WeJDhX/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -356,11 +355,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtool
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -394,8 +394,8 @@ dh_link -psamtools
dh_buildinfo -psamtools
Use of uninitialized value within @essentials in string ne at /usr/bin/dh_buildinfo line 164.
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -421,7 +421,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-armhf-WeJDhX/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -436,71 +436,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_armhf.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_armhf.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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_armhf.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_armhf.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1940
+Build finished at 20101117-1907
-samtools_0.1.9-1_armhf.changes:
+samtools_0.1.10-1_armhf.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: armhf
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: armhf Build Daemon (efikamx05) <buildd_armhf-efikamx05 at debian-ports...>
+Maintainer: armhf Build Daemon (efikamx01) <buildd_armhf-efikamx01 at debian-ports...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 7ee6cb576836bbdaa659191e37993817bdbb2a07 561644 samtools_0.1.9-1_armhf.deb
- f120aa00b8903ada2ee5da9b4018d873aa891e65 160424 libbam-dev_0.1.9-1_armhf.deb
+ 03ebf695f57f22bd957ba5787921d1a471f9d129 579454 samtools_0.1.10-1_armhf.deb
+ 2fe18e561bfb58a81916041adc5bd963c5d9898d 168048 libbam-dev_0.1.10-1_armhf.deb
Checksums-Sha256:
- 89df45dd8c3668b64cb861ed7b28d6603444704442323c0f888fb5d795ef99f2 561644 samtools_0.1.9-1_armhf.deb
- d9aa05e8be74bd9c896ba8e1e2207d010dd9efe0a15bd9ade6f552a5690da7e9 160424 libbam-dev_0.1.9-1_armhf.deb
+ caed4d43993d218c0136b0b20e330f039e17033d5c4acc8da8bc7d44516b67cd 579454 samtools_0.1.10-1_armhf.deb
+ 69188112d39b43a99b52108cf8273d41c96273217b1c3cd73ac1fffe02222264 168048 libbam-dev_0.1.10-1_armhf.deb
Files:
- b6647e02fcdd1928adc11008c1e7ed1c 561644 science optional samtools_0.1.9-1_armhf.deb
- 5866b8689f5d73c6d1dfef595297595f 160424 libdevel optional libbam-dev_0.1.9-1_armhf.deb
+ 62d563fddd970fa6b3d795c129276ccc 579454 science optional samtools_0.1.10-1_armhf.deb
+ 1085dd86de4b06ff411167948cd4873f 168048 libdevel optional libbam-dev_0.1.10-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_armhf.deb
-──────────────────────────
+samtools_0.1.10-1_armhf.deb
+───────────────────────────
new debian package, version 2.0.
- size 561644 bytes: control archive= 1826 bytes.
- 790 bytes, 16 lines control
+ size 579454 bytes: control archive= 1828 bytes.
+ 791 bytes, 16 lines control
2587 bytes, 39 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 868
+ Installed-Size: 888
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -513,73 +507,73 @@ samtools_0.1.9-1_armhf.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 2010-11-01 19:39 ./
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/bin/
--rwxr-xr-x root/root 239604 2010-11-01 19:39 ./usr/bin/samtools
--rwxr-xr-x root/root 20336 2010-11-01 19:39 ./usr/bin/razip
--rwxr-xr-x root/root 67784 2010-11-01 19:39 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/lib/samtools/
--rwxr-xr-x root/root 7052 2010-11-01 19:39 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 5828 2010-11-01 19:39 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 15356 2010-11-01 19:39 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 5828 2010-11-01 19:39 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10132 2010-11-01 19:39 ./usr/lib/samtools/md5fa
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2010-11-01 19:39 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-01 19:39 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-01 19:39 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1367 2010-11-01 19:39 ./usr/share/doc/samtools/buildinfo.gz
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2010-11-01 19:39 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2010-11-01 19:39 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
-lrwxrwxrwx root/root 0 2010-11-01 19:39 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_armhf.deb
-────────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/bin/
+-rwxr-xr-x root/root 20336 2010-11-17 19:07 ./usr/bin/razip
+-rwxr-xr-x root/root 259436 2010-11-17 19:07 ./usr/bin/samtools
+-rwxr-xr-x root/root 67860 2010-11-17 19:07 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/lib/samtools/
+-rwxr-xr-x root/root 15356 2010-11-17 19:07 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7052 2010-11-17 19:07 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 5828 2010-11-17 19:07 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 5828 2010-11-17 19:07 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10132 2010-11-17 19:07 ./usr/lib/samtools/md5fa
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 19:07 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 19:07 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2010-11-17 19:07 ./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 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2010-11-17 19:07 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1387 2010-11-17 19:07 ./usr/share/doc/samtools/buildinfo.gz
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./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 126609 2010-11-17 19:06 ./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 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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+lrwxrwxrwx root/root 0 2010-11-17 19:07 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_armhf.deb
+─────────────────────────────
new debian package, version 2.0.
- size 160424 bytes: control archive= 933 bytes.
- 673 bytes, 15 lines control
+ size 168048 bytes: control archive= 928 bytes.
+ 674 bytes, 15 lines control
690 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 340
+ Installed-Size: 352
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -590,24 +584,24 @@ libbam-dev_0.1.9-1_armhf.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/include/
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/lib/
--rw-r--r-- root/root 197024 2010-11-01 19:39 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 1367 2010-11-01 19:39 ./usr/share/doc/libbam-dev/buildinfo.gz
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/lib/
+-rw-r--r-- root/root 205606 2010-11-17 19:07 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1387 2010-11-17 19:07 ./usr/share/doc/libbam-dev/buildinfo.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/include/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -616,7 +610,7 @@ drwxr-xr-x root/root 0 2010-11-01 19:39 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-07ca07e8-81ea-4792-9d39-51f27d8050b5/build/buildd-samtools_0.1.9-1-armhf-WeJDhX
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-ae55037d-2fca-4bcb-92dd-9b7bd9142996/build/buildd-samtools_0.1.10-1-armhf-XV65Zs
W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
I: This option will be removed in the future; please update your configuration
W: line 7 [sid-armhf-sbuild]: Deprecated key 'run-exec-scripts' used
@@ -624,8 +618,8 @@ I: This option will be removed in the future; please update your configuration
W: line 9 [sid-armhf-sbuild]: Deprecated key 'location' used
I: This option will be removed in the future; please update your configuration
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1940
-Build needed 00:04:40, 7972k disc space
+Finished at 20101117-1907
+Build needed 00:04:45, 8232k disc space
</pre>
<p>
diff --git a/hppa.build b/hppa.build
index 6892394..50b080b 100644
--- a/hppa.build
+++ b/hppa.build
@@ -1,17 +1,17 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/hppa received Mon Nov 1 11:27:24 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=hppa">hppa</a> >> Mon Nov 1 11:27:24 2010<pre>
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/hppa received Thu Nov 18 12:29:50 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=hppa">hppa</a> >> Thu Nov 18 12:29:50 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on penalosa.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (hppa) 01 Nov 2010 11:23 ║
+║ samtools 0.1.10-1 (hppa) 18 Nov 2010 12:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: hppa
-Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-87c69730-17ce-41c0-8f2b-34db97c1d7ce/build/buildd-samtools_0.1.9-1-hppa-b9mkz4
-Start Time: 20101101-1123
+Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-87f43aa2-e412-4be4-a3af-9d9c111a30af/build/buildd-samtools_0.1.10-1-hppa-94wyup
+Start Time: 20101118-1224
Hit http://spohr.debian.org sid Release.gpg
Ign http://spohr.debian.org/debian/ sid/contrib Translation-en
Ign http://spohr.debian.org/debian/ sid/main Translation-en
@@ -31,9 +31,9 @@ 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 hppa Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib hppa Packages/DiffIndex
-Get:3 http://incoming.debian.org Sources [11.5 kB]
-Get:4 http://incoming.debian.org Packages [200 kB]
-Fetched 214 kB in 6s (34.3 kB/s)
+Hit http://incoming.debian.org Sources
+Get:3 http://incoming.debian.org Packages [261 kB]
+Fetched 263 kB in 13s (19.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,11 +54,11 @@ 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 358 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 1s (331 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://spohr.debian.org/debian/ sid/main samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://spohr.debian.org/debian/ sid/main samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://spohr.debian.org/debian/ sid/main samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 4s (83.7 kB/s)
Download complete and in download only mode
Check arch
@@ -96,9 +96,9 @@ The following NEW packages will be installed:
libcroco3 libglib2.0-0 libpcre3 libunistring0 libxml2 man-db po-debconf
zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 15 newly installed, 0 to remove and 2 not upgraded.
+0 upgraded, 15 newly installed, 0 to remove and 17 not upgraded.
Need to get 0 B/9891 kB of archives.
-After this operation, 26.0 MB of additional disk space will be used.
+After this operation, 26.1 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
(Reading database ... 11682 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_hppa.deb) ...
@@ -109,7 +109,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hppa.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_hppa.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_hppa.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_hppa.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_hppa.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -123,7 +123,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_hppa.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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -135,22 +135,22 @@ Setting up man-db (2.5.7-6) ...
Building database of manual pages ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-5-parisc64 hppa (parisc64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-2 g++-4.4_4.4.5-2 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-2 libstdc++6_4.4.5-2
-Package versions: apt_0.8.7 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7.1 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dmsetup_2:1.02.48-3 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-3 libdpkg-perl_1.15.8.5 libextutils-parsexs-perl_2.220600-1 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmodule-build-perl_0.360700-1 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline-dev_6.1-3 libreadline5_5.2-7 libreadline6_6.1-3 libreadline6-dev_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4+b1 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 libyaml-perl_0.71-1 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tcl8.4_8.4.19-4 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-2 g++-4.4_4.4.5-2 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-2 libstdc++6_4.4.5-2
+Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7.1 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.5 libextutils-parsexs-perl_2.220600-1 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmodule-build-perl_0.360700-1 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline-dev_6.1-3 libreadline5_5.2-7 libreadline6_6.1-3 libreadline6-dev_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4+b1 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 libyaml-perl_0.71-1 linux-libc-dev_2.6.32-27 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tcl8.4_8.4.19-4 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -162,12 +162,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -182,25 +182,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture hppa
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/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_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/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_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -208,8 +208,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -233,9 +233,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -246,10 +247,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -262,27 +263,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -292,14 +294,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-hppa-b9mkz4/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -323,11 +325,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -359,8 +362,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -384,7 +387,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-hppa-b9mkz4/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -399,27 +402,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_hppa.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_hppa.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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_hppa.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_hppa.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1126
+Build finished at 20101118-1229
-samtools_0.1.9-1_hppa.changes:
+samtools_0.1.10-1_hppa.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hppa
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
Maintainer: hppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd...>
@@ -428,42 +431,36 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- b18758db6d6633204bc64cb98f2ed6a4dc6bcf70 567156 samtools_0.1.9-1_hppa.deb
- 2748919838021a436240f5933b17799d8d4948a7 169618 libbam-dev_0.1.9-1_hppa.deb
+ 0546d72c9390e268b68c3957fd64008aa56c9055 582760 samtools_0.1.10-1_hppa.deb
+ febadcfa15aaeabf2bfffb52dccb3245486743e3 177016 libbam-dev_0.1.10-1_hppa.deb
Checksums-Sha256:
- 6e5fe270fafa0e60583dfdea5c6b71b108bba1c6fe31090dbb1030f81f476fb5 567156 samtools_0.1.9-1_hppa.deb
- 246dbf3f3e65373638beedd171dbaaa41c635c84996053395ad0f69ba9cd71b1 169618 libbam-dev_0.1.9-1_hppa.deb
+ bccaccda20ff9787c8bfaba5c8dfe0f8425fb7c050f90506af64fe8d0f964338 582760 samtools_0.1.10-1_hppa.deb
+ a1fd673ac2dcbd2f402f47c300409d46abe5b77373507c6a82f38775b0c8e1aa 177016 libbam-dev_0.1.10-1_hppa.deb
Files:
- b3dc2851e11c1d2b8667eccfc0bbe4e8 567156 science optional samtools_0.1.9-1_hppa.deb
- 81009b78587302b2234bc950c7741c58 169618 libdevel optional libbam-dev_0.1.9-1_hppa.deb
+ 1e5983b5cfbad6eaabfd17df7fdb73b8 582760 science optional samtools_0.1.10-1_hppa.deb
+ 3486c8c2cf602b4e9506540e978a1ce9 177016 libdevel optional libbam-dev_0.1.10-1_hppa.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_hppa.deb
-─────────────────────────
+samtools_0.1.10-1_hppa.deb
+──────────────────────────
new debian package, version 2.0.
- size 567156 bytes: control archive= 1787 bytes.
- 790 bytes, 16 lines control
+ size 582760 bytes: control archive= 1794 bytes.
+ 792 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: hppa
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 996
+ Installed-Size: 1020
Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -476,72 +473,72 @@ samtools_0.1.9-1_hppa.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 2010-11-01 11:26 ./
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/bin/
--rwxr-xr-x root/root 91480 2010-11-01 11:26 ./usr/bin/bcftools
--rwxr-xr-x root/root 319144 2010-11-01 11:26 ./usr/bin/samtools
--rwxr-xr-x root/root 26492 2010-11-01 11:26 ./usr/bin/razip
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/lib/samtools/
--rwxr-xr-x root/root 11744 2010-11-01 11:26 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7880 2010-11-01 11:26 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 18492 2010-11-01 11:26 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8744 2010-11-01 11:26 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7880 2010-11-01 11:26 ./usr/lib/samtools/maq2sam-short
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/doc/samtools/
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2010-11-01 11:26 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2010-11-01 11:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-01 11:26 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-01 11:26 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2010-11-01 11:26 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
-lrwxrwxrwx root/root 0 2010-11-01 11:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_hppa.deb
-───────────────────────────
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./usr/
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/bin/
+-rwxr-xr-x root/root 92596 2010-11-18 12:29 ./usr/bin/bcftools
+-rwxr-xr-x root/root 340948 2010-11-18 12:29 ./usr/bin/samtools
+-rwxr-xr-x root/root 26492 2010-11-18 12:29 ./usr/bin/razip
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11744 2010-11-18 12:29 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7880 2010-11-18 12:29 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 18492 2010-11-18 12:29 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8744 2010-11-18 12:29 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7880 2010-11-18 12:29 ./usr/lib/samtools/maq2sam-short
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2010-11-18 12:28 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-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 2010-11-18 12:28 ./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 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-18 12:28 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-18 12:28 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/share/samtools/
+-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 2010-11-18 12:29 ./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 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./usr/share/samtools/vcfutils.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 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+lrwxrwxrwx root/root 0 2010-11-18 12:28 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_hppa.deb
+────────────────────────────
new debian package, version 2.0.
- size 169618 bytes: control archive= 900 bytes.
- 672 bytes, 15 lines control
+ size 177016 bytes: control archive= 898 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: hppa
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 404
+ Installed-Size: 416
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -552,23 +549,23 @@ libbam-dev_0.1.9-1_hppa.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/include/
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/lib/
--rw-r--r-- root/root 263180 2010-11-01 11:26 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/include/
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/lib/
+-rw-r--r-- root/root 270710 2010-11-18 12:29 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-18 12:28 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -577,7 +574,7 @@ drwxr-xr-x root/root 0 2010-11-01 11:26 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-hppa-sbuild-87c69730-17ce-41c0-8f2b-34db97c1d7ce/build/buildd-samtools_0.1.9-1-hppa-b9mkz4
+Purging /var/lib/schroot/mount/sid-hppa-sbuild-87f43aa2-e412-4be4-a3af-9d9c111a30af/build/buildd-samtools_0.1.10-1-hppa-94wyup
(Reading database ... 12862 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
@@ -603,7 +600,7 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1126
-Build needed 00:03:40, 8728k disc space
+Finished at 20101118-1229
+Build needed 00:04:25, 9008k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/hurd-i386.build b/hurd-i386.build
index 15e560a..44af809 100644
--- a/hurd-i386.build
+++ b/hurd-i386.build
@@ -1,17 +1,17 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/hurd-i386 received Mon Nov 1 12:14:29 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=hurd-i386">hurd-i386</a> >> Mon Nov 1 12:14:29 2010<pre>
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/hurd-i386 received Wed Nov 17 12:29:04 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=hurd-i386">hurd-i386</a> >> Wed Nov 17 12:29:04 2010<pre>
sbuild (Debian sbuild) 0.59.1 (31 Jan 2010) on mozart.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (hurd-i386) 01 Nov 2010 12:10 ║
+║ samtools 0.1.10-1 (hurd-i386) 17 nov. 2010 12:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ
-Start Time: 20101101-1210
+Chroot Build Dir: /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz
+Start Time: 20101117-1220
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -23,6 +23,43 @@ Check APT
Checking available source versions...
+Update APT
+──────────
+
+Ign file: ./ Release.gpg
+Ign file:/build/local-debs/ ./ Translation-en
+Ign file: ./ Release
+Ign file: ./ Packages
+Hit http://ftp.debian-ports.org unreleased Release.gpg
+Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
+Hit http://ftp.debian-ports.org unreleased Release
+Get:1 http://incoming.debian.org Release.gpg [835B]
+Ign http://incoming.debian.org/buildd-unstable/ Translation-en
+Get:2 http://incoming.debian.org Release [1604B]
+Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Get:3 http://incoming.debian.org Sources [14.3kB]
+Get:4 http://incoming.debian.org Packages [236kB]
+Err http://ftp.uk.debian.org sid Release.gpg
+ Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+Err http://ftp.uk.debian.org/debian/ sid/contrib Translation-en
+ Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+Err http://ftp.uk.debian.org/debian/ sid/main Translation-en
+ Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+Err http://ftp.uk.debian.org/debian/ sid/non-free Translation-en
+ Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+Fetched 253kB in 4min 13s (999B/s)
+Reading package lists...
+W: Failed to fetch http://ftp.uk.debian.org/debian/dists/sid/Release.gpg Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+
+W: Failed to fetch http://ftp.uk.debian.org/debian/dists/sid/contrib/i18n/Translation-en.bz2 Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+
+W: Failed to fetch http://ftp.uk.debian.org/debian/dists/sid/main/i18n/Translation-en.bz2 Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+
+W: Failed to fetch http://ftp.uk.debian.org/debian/dists/sid/non-free/i18n/Translation-en.bz2 Could not create a socket for 2001:470:1f08:80b::2 (f=26 t=1 p=6) - socket (1073741871: Address family not supported by protocol) [IP: 2001:470:1f08:80b::2 80]
+
+W: Some index files failed to download, they have been ignored, or old ones used instead.
+Checking available source versions...
+
Download source files with APT
──────────────────────────────
@@ -31,11 +68,11 @@ 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 358kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264B]
-Fetched 358kB in 1s (185kB/s)
+Need to get 361kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332B]
+Fetched 361kB in 1s (195kB/s)
Download complete and in download only mode
Check arch
@@ -68,14 +105,14 @@ Recommended packages:
autotools-dev
The following NEW packages will be installed:
cdbs libncurses5-dev
-0 upgraded, 2 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 2 newly installed, 0 to remove and 33 not upgraded.
Need to get 0B/2809kB of archives.
After this operation, 8352kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
cdbs libncurses5-dev
Authentication warning overridden.
Selecting previously deselected package cdbs.
-(Reading database ... 14242 files and directories currently installed.)
+(Reading database ... 14206 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_hurd-i386.deb) ...
@@ -85,8 +122,8 @@ Setting up libncurses5-dev (5.7+20100313-4) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.11.2-6 dpkg-dev_1.15.8.5 hurd-dev_20100926-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-5 g++-4.4_4.4.5-5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-5 libstdc++6_4.4.5-5
-Package versions: adduser_3.112+nmu1 apt_0.8.5 apt-utils_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-5 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 deborphan_1.7.28 dialog_1.1-20100428-1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.4-2 g++-4.4_4.4.5-5 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-5 gcc-4.4-base_4.4.5-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach_2:1.3.99.dfsg.git20100732-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 hurd_20100926-1 hurd-dev_20100926-1 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libapt-pkg-dev_0.8.5 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc0.3_2.11.2-6 libc0.3-dev_2.11.2-6 libc0.3-xen_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libept-dev_1.0.3+b2 libept1_1.0.3+b2 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.2-2 libgcc1_1:4.4.5-5 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.5-2 libgomp1_4.4.5-5 libgpg-error0_1.6-1 libidn11_1.18-1 libio-stringy-perl_2.110-4 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libparted0debian1_2.3-1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-5.1 libsasl2-modules_2.1.23.dfsg1-5.1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-2 libstdc++6_4.4.5-5 libstdc++6-4.4-dev_4.4.5-5 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.11-1.1 libtasn1-3_2.7-1 libtest-pod-perl_1.42-1 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libuuid1_2.16.2-0 libwibble-dev_0.1.26-1 libwrap0_7.6.dbs-8 libxapian-dev_1.2.3-2 libxapian15_1.0.20-2 libxapian22_1.2.3-2 libxml2_2.7.7.dfsg-4 lsb-base_3.2-25 lynx-cur_2.8.8dev.5-1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 pkg-config_0.25-1 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-dejavu-core_2.31-1 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc0.3-dev_2.11.2-7 dpkg-dev_1.15.8.5 hurd-dev_20100926-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: adduser_3.112+nmu1 apt_0.8.5 apt-utils_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 deborphan_1.7.28 dialog_1.1-20100428-1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.4-2 g++-4.4_4.4.5-8 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-8 gcc-4.4-base_4.4.5-8 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach_2:1.3.99.dfsg.git20100732-1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 hurd_20100926-1 hurd-dev_20100926-1 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libapt-pkg-dev_0.8.5 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc0.3_2.11.2-7 libc0.3-dev_2.11.2-7 libc0.3-xen_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcwidget3_0.5.16-3 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libept-dev_1.0.3+b2 libept1_1.0.3+b2 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.2-2 libgcc1_1:4.4.5-8 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.5-2 libgomp1_4.4.5-8 libgpg-error0_1.6-1 libidn11_1.18-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libparted0debian1_2.3-3+hurd.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-5.1 libsasl2-modules_2.1.23.dfsg1-5.1 libsigc++-2.0-0c2a_2.2.4.2-1 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-3 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.11-1.1 libtasn1-3_2.7-1 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libuuid1_2.16.2-0 libwibble-dev_0.1.26-1 libwrap0_7.6.dbs-8 libxapian-dev_1.2.3-2 libxapian15_1.0.20-2 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-1 lsb-base_3.2-25 lynx-cur_2.8.8dev.6-3 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 pkg-config_0.25-1 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-dejavu-core_2.31-1 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -98,12 +135,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -118,34 +155,34 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/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_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/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_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
- 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
+ debian/rules build
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -169,9 +206,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -182,10 +220,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -198,27 +236,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -228,15 +267,15 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/examples'
[sam_header_read2] 2 sequences loaded.
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
@@ -255,6 +294,7 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/sam
[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
+<mpileup> Set max per-sample depth to 8000
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
@@ -263,7 +303,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -295,8 +335,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -320,7 +360,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -335,27 +375,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_hurd-i386.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_hurd-i386.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1214
+Build finished at 20101117-1228
-samtools_0.1.9-1_hurd-i386.changes:
+samtools_0.1.10-1_hurd-i386.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd...>
@@ -364,42 +404,36 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 7e3d93a739a330c2765bef725246d9103cc4ff9d 539792 samtools_0.1.9-1_hurd-i386.deb
- 2b81623f20a1901be7953383ab46dfdac474aa84 157918 libbam-dev_0.1.9-1_hurd-i386.deb
+ effd906208110c35f1d8377d3bb7e0317d9a358b 555002 samtools_0.1.10-1_hurd-i386.deb
+ e9693a3eceb7a39813280f3398d8bca06dd40e1f 164884 libbam-dev_0.1.10-1_hurd-i386.deb
Checksums-Sha256:
- f18f51e5d9045fdecee2025135d8c470bc944eedc3e9e64a017179a98d235bd2 539792 samtools_0.1.9-1_hurd-i386.deb
- 2bd99e4506d4ab1ecd737167fc2f49c14cdbaae8661d2fc29d880b3235cffb75 157918 libbam-dev_0.1.9-1_hurd-i386.deb
+ abe7170f8bd8a6cdaa58cd503271d98ee1f21c1dfb72d29432a5500cfabedba6 555002 samtools_0.1.10-1_hurd-i386.deb
+ f01bc8713b1acff855c43ba1323bc89af7d9b0ed6fc66ee795c4e58bfdc84318 164884 libbam-dev_0.1.10-1_hurd-i386.deb
Files:
- f3cd18e7f84d14ba8d97c33a2a32a0f5 539792 science optional samtools_0.1.9-1_hurd-i386.deb
- ec5a46f407acb77f70ff74f444f7bdb1 157918 libdevel optional libbam-dev_0.1.9-1_hurd-i386.deb
+ 02fa3649d60e888ad9e0ca3179553ad3 555002 science optional samtools_0.1.10-1_hurd-i386.deb
+ 73b483413c62710234dab2728a875f9d 164884 libdevel optional libbam-dev_0.1.10-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_hurd-i386.deb
-──────────────────────────────
+samtools_0.1.10-1_hurd-i386.deb
+───────────────────────────────
new debian package, version 2.0.
- size 539792 bytes: control archive= 1799 bytes.
- 797 bytes, 16 lines control
+ size 555002 bytes: control archive= 1803 bytes.
+ 798 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 948
+ Installed-Size: 972
Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -412,72 +446,72 @@ samtools_0.1.9-1_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 2010-11-01 12:13 ./
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 12:12 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-01 12:12 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-11-01 12:13 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 12:12 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-01 12:12 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-01 12:12 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/samtools/
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2010-11-01 12:13 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/bin/
--rwxr-xr-x root/root 76452 2010-11-01 12:13 ./usr/bin/bcftools
--rwxr-xr-x root/root 23740 2010-11-01 12:13 ./usr/bin/razip
--rwxr-xr-x root/root 293780 2010-11-01 12:13 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/lib/samtools/
--rwxr-xr-x root/root 17488 2010-11-01 12:13 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6336 2010-11-01 12:13 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6320 2010-11-01 12:13 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10084 2010-11-01 12:13 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6920 2010-11-01 12:13 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_hurd-i386.deb
-────────────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./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 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-17 12:27 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-17 12:27 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 12:27 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 12:27 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/samtools/
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./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
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-17 12:27 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/bin/
+-rwxr-xr-x root/root 80068 2010-11-17 12:27 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23740 2010-11-17 12:27 ./usr/bin/razip
+-rwxr-xr-x root/root 313900 2010-11-17 12:27 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17488 2010-11-17 12:27 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6336 2010-11-17 12:27 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6320 2010-11-17 12:27 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10084 2010-11-17 12:27 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6920 2010-11-17 12:27 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_hurd-i386.deb
+─────────────────────────────────
new debian package, version 2.0.
- size 157918 bytes: control archive= 904 bytes.
- 677 bytes, 15 lines control
+ size 164884 bytes: control archive= 901 bytes.
+ 678 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 376
+ Installed-Size: 388
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -488,23 +522,23 @@ libbam-dev_0.1.9-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/lib/
--rw-r--r-- root/root 236190 2010-11-01 12:13 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/include/
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 12:28 ./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 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 12:28 ./usr/lib/
+-rw-r--r-- root/root 243644 2010-11-17 12:28 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/include/
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -513,13 +547,13 @@ drwxr-xr-x root/root 0 2010-11-01 12:13 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.9-1-hurd-i386-E9c3JZ
-(Reading database ... 15351 files and directories currently installed.)
+Purging /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz
+(Reading database ... 15315 files and directories currently installed.)
Removing libncurses5-dev ...
Removing cdbs ...
Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1214
-Build needed 00:03:31, 8164k disc space
+Finished at 20101117-1228
+Build needed 00:08:37, 8412k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/i386.build b/i386.build
index f334de9..26d83cf 100644
--- a/i386.build
+++ b/i386.build
@@ -1,39 +1,41 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/i386 received Mon Nov 1 11:24:35 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=i386">i386</a> >> Mon Nov 1 11:24:35 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on murphy.debian.org
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/i386 received Wed Nov 17 11:54:05 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=i386">i386</a> >> Wed Nov 17 11:54:05 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (i386) 01 Nov 2010 11:23 ║
+║ samtools 0.1.10-1 (i386) 17 Nov 2010 11:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: i386
-Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-d4f8235a-4deb-4fa4-9a9b-1dc23ee99ffe/build/buildd-samtools_0.1.9-1-i386-tnFCBw
-Start Time: 20101101-1123
-Hit http://incoming.debian.org sid Release.gpg
-Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
-Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:1 http://incoming.debian.org Release.gpg [835 B]
+Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-a53f9891-43dc-45dc-bad2-44f8a89de5da/build/buildd-samtools_0.1.10-1-i386-QHg1ix
+Start Time: 20101117-1152
+Get:1 http://ftp.gr.debian.org unstable Release.gpg [835 B]
+Ign http://ftp.gr.debian.org/debian/ unstable/contrib Translation-en
+Ign http://ftp.gr.debian.org/debian/ unstable/main Translation-en
+Get:2 http://ftp.gr.debian.org unstable Release [104 kB]
+Get:3 http://ftp.gr.debian.org unstable/main Sources [4061 kB]
+Get:4 http://incoming.debian.org unstable Release.gpg [835 B]
+Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
+Ign http://incoming.debian.org/debian/ unstable/main Translation-en
+Get:5 http://ftp.gr.debian.org unstable/contrib Sources [39.0 kB]
+Get:6 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://incoming.debian.org sid Release
-Get:2 http://incoming.debian.org Release [1604 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/main i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
-Hit http://ftp.us.debian.org sid Release.gpg
-Ign http://ftp.us.debian.org/debian/ sid/contrib Translation-en
-Ign http://ftp.us.debian.org/debian/ sid/main Translation-en
-Hit http://ftp.us.debian.org sid Release
-Get:3 http://incoming.debian.org Sources [11.5 kB]
-Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
-Get:4 http://incoming.debian.org Packages [200 kB]
-Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.us.debian.org sid/main i386 Packages/DiffIndex
-Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
-Fetched 214 kB in 3s (54.0 kB/s)
+Get:7 http://incoming.debian.org unstable Release [104 kB]
+Get:8 http://ftp.gr.debian.org unstable/non-free Sources [83.1 kB]
+Get:9 http://ftp.gr.debian.org unstable/main i386 Packages [6923 kB]
+Get:10 http://ftp.gr.debian.org unstable/contrib i386 Packages [61.2 kB]
+Get:11 http://incoming.debian.org Release [1604 B]
+Get:12 http://incoming.debian.org unstable/main Sources [4061 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [39.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.1 kB]
+Get:15 http://incoming.debian.org unstable/main i386 Packages [6923 kB]
+Get:16 http://incoming.debian.org unstable/contrib i386 Packages [61.2 kB]
+Get:17 http://incoming.debian.org Sources [15.1 kB]
+Get:18 http://incoming.debian.org Packages [227 kB]
+Fetched 22.8 MB in 20s (1121 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,11 +56,11 @@ 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 358 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 0s (425 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 1s (253 kB/s)
Download complete and in download only mode
Check arch
@@ -96,13 +98,33 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 19 newly installed, 0 to remove and 30 not upgraded.
+Need to get 11.4 MB of archives.
+After this operation, 34.5 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.0.16 [199 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.20.1-10 [1128 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.5.7-6 [1240 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.02-1.1 [231 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-1 [827 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.24.2-1 [1029 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.7+20100313-4 [1601 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 33 not upgraded.
-Need to get 0 B/11.4 MB of archives.
-After this operation, 34.4 MB of additional disk space will be used.
+Fetched 11.4 MB in 1s (6628 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10189 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_i386.deb) ...
+(Reading database ... 10160 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_i386.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_i386.deb) ...
Selecting previously deselected package man-db.
@@ -116,7 +138,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -130,7 +152,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -139,7 +161,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_i386.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.0.16) ...
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 (1.20.1-10) ...
@@ -149,23 +171,23 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: Linux 2.6.32.25-dsa-ia32 i386 (i686)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-20 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libstdc++6_4.4.5-6
-Package versions: apt_0.8.7 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-20 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2.1 tzdata_2010m-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100713-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.26-2-amd64 i386 (x86_64)
+Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libstdc++6_4.4.5-6
+Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 dash_0.5.5.1-7.2 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -177,12 +199,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -197,25 +219,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/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_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/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_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -223,8 +245,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -248,9 +270,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -261,10 +284,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -277,27 +300,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -307,14 +331,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-i386-tnFCBw/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -338,11 +362,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -374,8 +399,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -399,7 +424,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-i386-tnFCBw/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -414,71 +439,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_i386.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_i386.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1124
+Build finished at 20101117-1154
-samtools_0.1.9-1_i386.changes:
+samtools_0.1.10-1_i386.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd...>
+Maintainer: i386 Build Daemon <buildd_i386-biber at buildd...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 450af9e52c0765166d276434320c6c6403c72136 541234 samtools_0.1.9-1_i386.deb
- cc0ebe247c496689eafa754c335502a8f95e2304 157744 libbam-dev_0.1.9-1_i386.deb
+ 7ec4ab2b401a198129224cc9ff0cf624ace52448 553262 samtools_0.1.10-1_i386.deb
+ c985e110c32555e807b6a5de6e3a3a71555a2b45 163630 libbam-dev_0.1.10-1_i386.deb
Checksums-Sha256:
- be92d2581ec4c0c7d3000764d2697c2cb3397d547086db9a3656d754a6e55f9b 541234 samtools_0.1.9-1_i386.deb
- 759bd389e6ccbec12641c5707e266552c9450588d04d2f846276913f15784f1f 157744 libbam-dev_0.1.9-1_i386.deb
+ 53eda7de0acec9a9cb60c7a1162d981fa7b0ec7c4c353a9da0d5967bdf41f279 553262 samtools_0.1.10-1_i386.deb
+ 7ecd7eacded918d932bba0ceafd1753508265cb57dc72d504fd1b4a404efd42f 163630 libbam-dev_0.1.10-1_i386.deb
Files:
- 2676551903059e2dbcc37d00f3c04bff 541234 science optional samtools_0.1.9-1_i386.deb
- e92e3c0ef3d7f10b4610b38049ba8b94 157744 libdevel optional libbam-dev_0.1.9-1_i386.deb
+ d08facd99b849089792ca3bc5f64e390 553262 science optional samtools_0.1.10-1_i386.deb
+ 8f39f35c1864f497f184a7135484b4bb 163630 libdevel optional libbam-dev_0.1.10-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_i386.deb
-─────────────────────────
+samtools_0.1.10-1_i386.deb
+──────────────────────────
new debian package, version 2.0.
- size 541234 bytes: control archive= 1788 bytes.
- 789 bytes, 16 lines control
+ size 553262 bytes: control archive= 1798 bytes.
+ 790 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 948
+ Installed-Size: 972
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -491,72 +510,72 @@ samtools_0.1.9-1_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 2010-11-01 11:24 ./
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/bin/
--rwxr-xr-x root/root 76292 2010-11-01 11:24 ./usr/bin/bcftools
--rwxr-xr-x root/root 23644 2010-11-01 11:24 ./usr/bin/razip
--rwxr-xr-x root/root 293716 2010-11-01 11:24 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/lib/samtools/
--rwxr-xr-x root/root 6680 2010-11-01 11:24 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6160 2010-11-01 11:24 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 17224 2010-11-01 11:24 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9908 2010-11-01 11:24 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6176 2010-11-01 11:24 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/man/man1/
--rw-r--r-- root/root 7265 2010-11-01 11:24 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-11-01 11:24 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/samtools/
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2010-11-01 11:24 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 126609 2010-11-01 11:24 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 1966 2010-11-01 11:24 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
-lrwxrwxrwx root/root 0 2010-11-01 11:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_i386.deb
-───────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/lib/samtools/
+-rwxr-xr-x root/root 6680 2010-11-17 11:53 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6176 2010-11-17 11:53 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6160 2010-11-17 11:53 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9908 2010-11-17 11:53 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17224 2010-11-17 11:53 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/bin/
+-rwxr-xr-x root/root 80068 2010-11-17 11:53 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23644 2010-11-17 11:53 ./usr/bin/razip
+-rwxr-xr-x root/root 313868 2010-11-17 11:53 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./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 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./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 2010-11-17 11:53 ./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 764 2010-11-17 04:16 ./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 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2010-11-17 11:53 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/man/man1/
+-rw-r--r-- root/root 7544 2010-11-17 11:53 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-11-17 11:53 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/samtools/
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./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
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-17 11:53 ./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 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 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+lrwxrwxrwx root/root 0 2010-11-17 11:53 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_i386.deb
+────────────────────────────
new debian package, version 2.0.
- size 157744 bytes: control archive= 898 bytes.
- 672 bytes, 15 lines control
+ size 163630 bytes: control archive= 898 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 376
+ Installed-Size: 388
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -567,23 +586,23 @@ libbam-dev_0.1.9-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/include/
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/lib/
--rw-r--r-- root/root 236102 2010-11-01 11:24 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/lib/
+-rw-r--r-- root/root 243660 2010-11-17 11:53 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./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 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/include/
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -592,39 +611,10 @@ drwxr-xr-x root/root 0 2010-11-01 11:24 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-i386-sbuild-d4f8235a-4deb-4fa4-9a9b-1dc23ee99ffe/build/buildd-samtools_0.1.9-1-i386-tnFCBw
-(Reading database ... 12559 files and directories currently installed.)
-Removing zlib1g-dev ...
-Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
-Removing libncurses5-dev ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing intltool-debian ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing gettext ...
-Removing file ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
+Purging /var/lib/schroot/mount/sid-i386-sbuild-a53f9891-43dc-45dc-bad2-44f8a89de5da/build/buildd-samtools_0.1.10-1-i386-QHg1ix
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1124
-Build needed 00:00:55, 8172k disc space
+Finished at 20101117-1154
+Build needed 00:01:54, 8412k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/ia64.build b/ia64.build
index aef6d79..621c772 100644
--- a/ia64.build
+++ b/ia64.build
@@ -1,41 +1,39 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/ia64 received Mon Nov 1 11:23:56 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=ia64">ia64</a> >> Mon Nov 1 11:23:56 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on mundy.debian.org
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/ia64 received Wed Nov 17 11:56:51 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=ia64">ia64</a> >> Wed Nov 17 11:56:51 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on caballero.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (ia64) 01 Nov 2010 11:20 ║
+║ samtools 0.1.10-1 (ia64) 17 Nov 2010 11:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: ia64
-Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-05f89c18-7b53-4c5d-8067-f9cf40c1dc35/build/buildd-samtools_0.1.9-1-ia64-EZGcte
-Start Time: 20101101-1120
-Get:1 http://spohr.debian.org unstable Release.gpg [835 B]
-Ign http://spohr.debian.org/debian/ unstable/contrib Translation-en
-Ign http://spohr.debian.org/debian/ unstable/main Translation-en
-Get:2 http://spohr.debian.org unstable Release [104 kB]
-Get:3 http://spohr.debian.org unstable/main Sources [4011 kB]
-Get:4 http://incoming.debian.org unstable Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:5 http://incoming.debian.org Release.gpg [835 B]
+Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-d9e2caf8-1341-4fa7-a06e-552450c63fb2/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu
+Start Time: 20101117-1154
+Hit http://mirror.positive-internet.com sid Release.gpg
+Ign http://mirror.positive-internet.com/debian/ sid/contrib Translation-en
+Ign http://mirror.positive-internet.com/debian/ sid/main Translation-en
+Hit http://mirror.positive-internet.com sid Release
+Hit http://mirror.positive-internet.com sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid Release.gpg
+Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
+Ign http://incoming.debian.org/debian/ sid/main Translation-en
+Get:1 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:6 http://incoming.debian.org unstable Release [104 kB]
-Get:7 http://spohr.debian.org unstable/contrib Sources [38.7 kB]
-Get:8 http://spohr.debian.org unstable/non-free Sources [81.3 kB]
-Get:9 http://spohr.debian.org unstable/main ia64 Packages [6671 kB]
-Get:10 http://incoming.debian.org Release [1604 B]
-Get:11 http://incoming.debian.org unstable/main Sources [4011 kB]
-Get:12 http://spohr.debian.org unstable/contrib ia64 Packages [51.4 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [81.3 kB]
-Get:15 http://incoming.debian.org unstable/main ia64 Packages [6671 kB]
-Get:16 http://incoming.debian.org unstable/contrib ia64 Packages [51.4 kB]
-Get:17 http://incoming.debian.org Sources [11.5 kB]
-Get:18 http://incoming.debian.org Packages [200 kB]
-Fetched 22.1 MB in 19s (1153 kB/s)
+Hit http://mirror.positive-internet.com sid/contrib Sources/DiffIndex
+Hit http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex
+Hit http://mirror.positive-internet.com sid/contrib ia64 Packages/DiffIndex
+Hit http://incoming.debian.org sid Release
+Get:2 http://incoming.debian.org Release [1604 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/main ia64 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
+Get:3 http://incoming.debian.org Sources [15.1 kB]
+Get:4 http://incoming.debian.org Packages [227 kB]
+Fetched 244 kB in 5s (48.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -56,11 +54,11 @@ 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 358 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 1s (206 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 0s (426 kB/s)
Download complete and in download only mode
Check arch
@@ -85,60 +83,33 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
- po-debconf
+ gettext gettext-base groff-base html2text intltool-debian libcroco3
+ libglib2.0-0 libpcre3 libunistring0 libxml2 man-db po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ devscripts doc-base dh-make gettext-doc groff less www-browser
+ libmail-box-perl
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 file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 19 newly installed, 0 to remove and 20 not upgraded.
-Need to get 14.0 MB of archives.
-After this operation, 52.2 MB of additional disk space will be used.
-Get:1 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.0.13 [236 kB]
-Get:2 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.20.1-10 [1387 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.5.7-6 [1952 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.04-5 [263 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5 [51.9 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-3 [174 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.02-1.1 [286 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.7.dfsg-4 [1180 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:10 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.24.2-1 [1395 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
-Get:12 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-3 [469 kB]
-Get:13 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 intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16 [224 kB]
-Get:16 http://spohr.debian.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.7+20100313-4 [1707 kB]
-Get:19 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
+ cdbs debhelper gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libncurses5-dev libpcre3 libunistring0 libxml2 man-db
+ po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 14.0 MB in 1s (13.9 MB/s)
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10083 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_ia64.deb) ...
+0 upgraded, 16 newly installed, 0 to remove and 30 not upgraded.
+Need to get 0 B/13.5 MB of archives.
+After this operation, 49.0 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
+(Reading database ... 10382 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_ia64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.7-6_ia64.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_ia64.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_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_8.02-1.1_ia64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -152,7 +123,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -161,24 +132,19 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_ia64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
-Setting up bsdmainutils (8.0.13) ...
-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 (1.20.1-10) ...
Setting up man-db (2.5.7-6) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
@@ -186,8 +152,8 @@ Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: libc6.1-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-24 gcc-4.4_4.4.5-2 g++-4.4_4.4.5-2 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-2 libstdc++6_4.4.5-2
-Package versions: apt_0.8.6 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-2 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-2 gcc_4:4.4.5-1 gcc-4.4_4.4.5-2 gcc-4.4-base_4.4.5-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6.1_2.11.2-6 libc6.1-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-2 libstdc++6-4.4-dev_4.4.5-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-24 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-25 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6.1-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-8 libstdc++6_4.4.5-8
+Package versions: apt_0.8.8 autoconf_2.67-2 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 gcc-4.4_4.4.5-8 gcc-4.4-base_4.4.5-8 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6.1_2.11.2-7 libc6.1-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-8 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 lzma_4.43-14 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010o-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -199,12 +165,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -219,25 +185,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture ia64
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/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_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/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_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -245,8 +211,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -264,9 +230,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -277,10 +244,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -293,27 +260,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -323,14 +291,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-ia64-EZGcte/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -354,11 +322,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -390,8 +359,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -415,7 +384,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-ia64-EZGcte/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -430,71 +399,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_ia64.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_ia64.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1123
+Build finished at 20101117-1156
-samtools_0.1.9-1_ia64.changes:
+samtools_0.1.10-1_ia64.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd...>
+Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 9c272a486f8f2cf2ae14683a7c497294b3df7c97 686444 samtools_0.1.9-1_ia64.deb
- f77711f87a1eafa6041affe93998da54c94c4d55 218876 libbam-dev_0.1.9-1_ia64.deb
+ 78b7c1852767f71d9874d899f520318e4ae0f0a3 709634 samtools_0.1.10-1_ia64.deb
+ 6c4403d37577f8b7c299c44ecb1b09cec3b5da4b 228678 libbam-dev_0.1.10-1_ia64.deb
Checksums-Sha256:
- b096dd4d2df53ca6fdee0517ee319054ad49948ccc17f6fabc04c22df63c8461 686444 samtools_0.1.9-1_ia64.deb
- d903edebf285f7c2ca3a62a06d5e45f1cf4a186b675e9bf5f39496a8f90297b7 218876 libbam-dev_0.1.9-1_ia64.deb
+ cafae5c3f5e09ec061533831e3871c1253bebcf7d5f58189dacafe4f625f8793 709634 samtools_0.1.10-1_ia64.deb
+ 34845a981de99feb539e5b0477de26aaf1fa6f202b627e55951de34db513437d 228678 libbam-dev_0.1.10-1_ia64.deb
Files:
- aa2d3a0531bc045722e937a755ac8f32 686444 science optional samtools_0.1.9-1_ia64.deb
- 23204b1c451fb2995305da6909a69764 218876 libdevel optional libbam-dev_0.1.9-1_ia64.deb
+ cfe3ca029cce695f6512f81a33c1d1de 709634 science optional samtools_0.1.10-1_ia64.deb
+ 63b504f33daffefe126f731236f23a8d 228678 libdevel optional libbam-dev_0.1.10-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_ia64.deb
-─────────────────────────
+samtools_0.1.10-1_ia64.deb
+──────────────────────────
new debian package, version 2.0.
- size 686444 bytes: control archive= 1795 bytes.
- 792 bytes, 16 lines control
+ size 709634 bytes: control archive= 1792 bytes.
+ 793 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1512
+ Installed-Size: 1560
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -507,72 +470,72 @@ samtools_0.1.9-1_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 2010-11-01 11:23 ./
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2010-11-01 11:23 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-01 11:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2010-11-01 11:23 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/man/man1/
--rw-r--r-- root/root 7265 2010-11-01 11:23 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-11-01 11:23 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/bin/
--rwxr-xr-x root/root 660008 2010-11-01 11:23 ./usr/bin/samtools
--rwxr-xr-x root/root 52456 2010-11-01 11:23 ./usr/bin/razip
--rwxr-xr-x root/root 202480 2010-11-01 11:23 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/lib/samtools/
--rwxr-xr-x root/root 13296 2010-11-01 11:23 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13360 2010-11-01 11:23 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 14944 2010-11-01 11:23 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 30712 2010-11-01 11:23 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 22384 2010-11-01 11:23 ./usr/lib/samtools/md5fa
-lrwxrwxrwx root/root 0 2010-11-01 11:23 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_ia64.deb
-───────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./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 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-17 11:56 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-17 11:56 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 11:56 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 11:56 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/samtools/
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./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
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-17 11:56 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/bin/
+-rwxr-xr-x root/root 205344 2010-11-17 11:56 ./usr/bin/bcftools
+-rwxr-xr-x root/root 52456 2010-11-17 11:56 ./usr/bin/razip
+-rwxr-xr-x root/root 707608 2010-11-17 11:56 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30712 2010-11-17 11:56 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13360 2010-11-17 11:56 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13296 2010-11-17 11:56 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 22384 2010-11-17 11:56 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2010-11-17 11:56 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2010-11-17 11:56 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_ia64.deb
+────────────────────────────
new debian package, version 2.0.
- size 218876 bytes: control archive= 894 bytes.
- 672 bytes, 15 lines control
+ size 228678 bytes: control archive= 894 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 640
+ Installed-Size: 660
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -583,23 +546,23 @@ libbam-dev_0.1.9-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/include/
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
-drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/lib/
--rw-r--r-- root/root 505764 2010-11-01 11:23 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./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 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/lib/
+-rw-r--r-- root/root 521174 2010-11-17 11:56 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/include/
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -608,10 +571,34 @@ drwxr-xr-x root/root 0 2010-11-01 11:23 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-05f89c18-7b53-4c5d-8067-f9cf40c1dc35/build/buildd-samtools_0.1.9-1-ia64-EZGcte
-Not removing build depends: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-d9e2caf8-1341-4fa7-a06e-552450c63fb2/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu
+(Reading database ... 12620 files and directories currently installed.)
+Removing libncurses5-dev ...
+Removing zlib1g-dev ...
+Removing cdbs ...
+Removing debhelper ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1123
-Build needed 00:03:17, 12248k disc space
+Finished at 20101117-1156
+Build needed 00:02:06, 12692k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/kfreebsd-amd64.build b/kfreebsd-amd64.build
index 4c0eaa9..0ea1f96 100644
--- a/kfreebsd-amd64.build
+++ b/kfreebsd-amd64.build
@@ -1,36 +1,39 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/kfreebsd-amd64 received Mon Nov 1 22:26:33 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=kfreebsd-amd64">kfreebsd-amd64</a> >> Mon Nov 1 22:26:33 2010<pre>
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/kfreebsd-amd64 received Wed Nov 17 21:08:01 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=kfreebsd-amd64">kfreebsd-amd64</a> >> Wed Nov 17 21:08:01 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (kfreebsd-amd64) 01 Nov 2010 22:24 ║
+║ samtools 0.1.10-1 (kfreebsd-amd64) 17 Nov 2010 21:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: kfreebsd-amd64
-Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ
-Start Time: 20101101-2224
+Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN
+Start Time: 20101117-2106
Hit http://ftp.ca.debian.org sid Release.gpg
-Hit http://incoming.debian.org sid Release.gpg
+Get:1 http://incoming.debian.org sid Release.gpg [835 B]
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
Ign http://ftp.ca.debian.org/debian/ sid/main Translation-en
Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Get:1 http://incoming.debian.org Release.gpg [835 B]
+Get:2 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://incoming.debian.org sid Release
-Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org sid Release [104 kB]
Hit http://ftp.ca.debian.org sid Release
-Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
Hit http://ftp.ca.debian.org sid/main Sources/DiffIndex
+Get:4 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.ca.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Get:5 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Get:3 http://incoming.debian.org Packages [225 kB]
-Hit http://ftp.ca.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Get:6 http://incoming.debian.org Packages [314 kB]
+Get:7 http://incoming.debian.org sid/main kfreebsd-amd64 2010-11-17-2012.17.pdiff [1668 B]
+Get:8 http://incoming.debian.org sid/main kfreebsd-amd64 2010-11-17-2012.17.pdiff [1668 B]
+Get:9 http://incoming.debian.org sid/main kfreebsd-amd64 2010-11-17-2012.17.pdiff [1668 B]
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Fetched 227 kB in 2s (98.6 kB/s)
+Fetched 424 kB in 5s (82.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -51,11 +54,11 @@ 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 358 kB of source archives.
-Get:1 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 1s (311 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 0s (461 kB/s)
Download complete and in download only mode
Check arch
@@ -93,9 +96,9 @@ The following NEW packages will be installed:
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libunistring0 libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 18 not upgraded.
Need to get 0 B/11.8 MB of archives.
-After this operation, 33.3 MB of additional disk space will be used.
+After this operation, 33.4 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
(Reading database ... 11774 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-amd64.deb) ...
@@ -110,7 +113,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_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.
@@ -124,7 +127,7 @@ 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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -140,14 +143,14 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
@@ -155,8 +158,8 @@ Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-6 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libc0.1-dev_2.11.2-6 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.7 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc0.1_2.11.2-6 libc0.1-dev_2.11.2-6 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-6 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 type-handling_0.2.23 tzdata_2010m-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-8 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-8 libc0.1-dev_2.11.2-7 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-8 gcc-4.4-base_4.4.5-8 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc0.1_2.11.2-7 libc0.1-dev_2.11.2-7 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-8 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 type-handling_0.2.23 tzdata_2010m-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -168,12 +171,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -188,25 +191,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture kfreebsd-amd64
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/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_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/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_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -214,8 +217,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -233,9 +236,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -246,10 +250,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -262,27 +266,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -292,14 +297,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -323,11 +328,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6Hovr
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -359,8 +365,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -384,7 +390,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -399,27 +405,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_kfreebsd-amd64.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-2226
+Build finished at 20101117-2107
-samtools_0.1.9-1_kfreebsd-amd64.changes:
+samtools_0.1.10-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd...>
@@ -428,42 +434,36 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 280232479f09eb11980a995ee7e090e76a22bf86 539902 samtools_0.1.9-1_kfreebsd-amd64.deb
- 775e6feac0c1bf9e655053b0e086a9b1d041a9a8 156660 libbam-dev_0.1.9-1_kfreebsd-amd64.deb
+ ca5e0c3e1f7735d05ec237ba58ed833513a38b2c 556548 samtools_0.1.10-1_kfreebsd-amd64.deb
+ 334801d9cb0d75cf144e5107ba852f5f6b06dd65 164026 libbam-dev_0.1.10-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 89c234de415310b216b956a7c95b62603e21b05f8b6474a58936a38767d054fe 539902 samtools_0.1.9-1_kfreebsd-amd64.deb
- d799113f668f7613026b3dab6d7a8134205eb3f63825ddc33f0ce793fad7a00c 156660 libbam-dev_0.1.9-1_kfreebsd-amd64.deb
+ f770b722aec7a55776eaeb314fdefb74fdaa80c5595598cfdcdd977b313dbb7b 556548 samtools_0.1.10-1_kfreebsd-amd64.deb
+ d697257fba7f6e5f910a107ed18028eeed8d8566b55d87ec60edab3804da7630 164026 libbam-dev_0.1.10-1_kfreebsd-amd64.deb
Files:
- 9b0a409ad574bee92d55c6483c3816d2 539902 science optional samtools_0.1.9-1_kfreebsd-amd64.deb
- 4e5209d3fc547b8d9a90566a6574d25a 156660 libdevel optional libbam-dev_0.1.9-1_kfreebsd-amd64.deb
+ 96b8860cd897a0addcb08b7491747b15 556548 science optional samtools_0.1.10-1_kfreebsd-amd64.deb
+ ea9188348bd1efa5e645ba13c9405cec 164026 libdevel optional libbam-dev_0.1.10-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_kfreebsd-amd64.deb
-───────────────────────────────────
+samtools_0.1.10-1_kfreebsd-amd64.deb
+────────────────────────────────────
new debian package, version 2.0.
- size 539902 bytes: control archive= 1800 bytes.
- 801 bytes, 16 lines control
+ size 556548 bytes: control archive= 1803 bytes.
+ 802 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 916
+ Installed-Size: 936
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -476,72 +476,72 @@ samtools_0.1.9-1_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 2010-11-01 22:26 ./
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-01 22:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-11-01 22:26 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-01 22:26 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-01 22:26 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/samtools/
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2010-11-01 22:26 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/bin/
--rwxr-xr-x root/root 81864 2010-11-01 22:26 ./usr/bin/bcftools
--rwxr-xr-x root/root 24824 2010-11-01 22:26 ./usr/bin/razip
--rwxr-xr-x root/root 298008 2010-11-01 22:26 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/lib/samtools/
--rwxr-xr-x root/root 19248 2010-11-01 22:26 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8248 2010-11-01 22:26 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8200 2010-11-01 22:26 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11712 2010-11-01 22:26 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8520 2010-11-01 22:26 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_kfreebsd-amd64.deb
-─────────────────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./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 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-17 21:07 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-17 21:07 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 21:07 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 21:07 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/samtools/
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./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
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-17 21:07 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/bin/
+-rwxr-xr-x root/root 85384 2010-11-17 21:07 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24824 2010-11-17 21:07 ./usr/bin/razip
+-rwxr-xr-x root/root 318672 2010-11-17 21:07 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19248 2010-11-17 21:07 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8248 2010-11-17 21:07 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8200 2010-11-17 21:07 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11712 2010-11-17 21:07 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8520 2010-11-17 21:07 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_kfreebsd-amd64.deb
+──────────────────────────────────────
new debian package, version 2.0.
- size 156660 bytes: control archive= 900 bytes.
- 682 bytes, 15 lines control
+ size 164026 bytes: control archive= 900 bytes.
+ 683 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 416
+ Installed-Size: 434
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -552,23 +552,23 @@ libbam-dev_0.1.9-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/lib/
--rw-r--r-- root/root 284580 2010-11-01 22:26 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/include/
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./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 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/lib/
+-rw-r--r-- root/root 295158 2010-11-17 21:07 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/include/
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -577,7 +577,7 @@ drwxr-xr-x root/root 0 2010-11-01 22:26 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.9-1-kfreebsd-amd64-6HovrQ
+Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN
(Reading database ... 14036 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
@@ -607,7 +607,7 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-2226
-Build needed 00:01:17, 9344k disc space
+Finished at 20101117-2107
+Build needed 00:01:17, 9682k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/kfreebsd-i386.build b/kfreebsd-i386.build
index 4b36a3a..7f31a8c 100644
--- a/kfreebsd-i386.build
+++ b/kfreebsd-i386.build
@@ -1,17 +1,17 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/kfreebsd-i386 received Mon Nov 1 11:49:31 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=kfreebsd-i386">kfreebsd-i386</a> >> Mon Nov 1 11:49:31 2010<pre>
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/kfreebsd-i386 received Wed Nov 17 11:54:53 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=kfreebsd-i386">kfreebsd-i386</a> >> Wed Nov 17 11:54:53 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (kfreebsd-i386) 01 Nov 2010 11:47 ║
+║ samtools 0.1.10-1 (kfreebsd-i386) 17 Nov 2010 11:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: kfreebsd-i386
-Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm
-Start Time: 20101101-1147
+Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5
+Start Time: 20101117-1153
Hit http://ftp.ca.debian.org sid Release.gpg
Hit http://incoming.debian.org sid Release.gpg
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
@@ -31,15 +31,15 @@ Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Get:3 http://incoming.debian.org Sources [11.5 kB]
+Get:3 http://incoming.debian.org Sources [15.1 kB]
Hit http://ftp.ca.debian.org sid/main Sources/DiffIndex
-Get:4 http://incoming.debian.org Packages [194 kB]
+Get:4 http://incoming.debian.org Packages [227 kB]
Hit http://ftp.ca.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.ca.debian.org sid/non-free Sources/DiffIndex
Hit http://ftp.ca.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
Hit http://ftp.ca.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://ftp.ca.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Fetched 208 kB in 3s (59.8 kB/s)
+Fetched 244 kB in 3s (70.9 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -60,11 +60,11 @@ 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 358 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 1s (267 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 1s (292 kB/s)
Download complete and in download only mode
Check arch
@@ -102,9 +102,9 @@ The following NEW packages will be installed:
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libunistring0 libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 18 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 22 not upgraded.
Need to get 0 B/11.1 MB of archives.
-After this operation, 31.2 MB of additional disk space will be used.
+After this operation, 31.3 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
(Reading database ... 13368 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-i386.deb) ...
@@ -119,7 +119,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_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.
@@ -133,7 +133,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -149,14 +149,14 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
@@ -164,8 +164,8 @@ Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686 kfreebsd-i386 (i686)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-6 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libc0.1-dev_2.11.2-6 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.7 autotools-dev_20100122.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc0.1_2.11.2-6 libc0.1-dev_2.11.2-6 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-6 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 type-handling_0.2.23 tzdata_2010m-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 vim_2:7.3.000+hg~ee53a39d5896-1 vim-common_2:7.3.000+hg~ee53a39d5896-1 vim-runtime_2:7.3.000+hg~ee53a39d5896-1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-8 gcc-4.4_4.4.5-8 g++-4.4_4.4.5-8 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-8 libc0.1-dev_2.11.2-7 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.8 autotools-dev_20100122.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-8 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-2+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-8 gcc-4.4-base_4.4.5-8 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc0.1_2.11.2-7 libc0.1-dev_2.11.2-7 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-8 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-8 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-8 libstdc++6-4.4-dev_4.4.5-8 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 type-handling_0.2.23 tzdata_2010m-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 vim_2:7.3.000+hg~ee53a39d5896-1 vim-common_2:7.3.000+hg~ee53a39d5896-1 vim-runtime_2:7.3.000+hg~ee53a39d5896-1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -177,12 +177,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -197,25 +197,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture kfreebsd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/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_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/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_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -223,8 +223,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -248,9 +248,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -261,10 +262,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -277,27 +278,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -307,14 +309,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -338,11 +340,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -374,8 +377,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -399,7 +402,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -414,27 +417,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_kfreebsd-i386.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1149
+Build finished at 20101117-1154
-samtools_0.1.9-1_kfreebsd-i386.changes:
+samtools_0.1.10-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd...>
@@ -443,42 +446,36 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 97f76d60f55dd4e7c8b937ae2fe31d282f72a663 539118 samtools_0.1.9-1_kfreebsd-i386.deb
- 265951e78ac03392a1f07ee413edb87e9794d1e7 157878 libbam-dev_0.1.9-1_kfreebsd-i386.deb
+ c437a7e820a1d824230e54b896170dafac365761 554156 samtools_0.1.10-1_kfreebsd-i386.deb
+ 56dc83cc9c08a228a5752fb934451b6bcc618acd 164816 libbam-dev_0.1.10-1_kfreebsd-i386.deb
Checksums-Sha256:
- 85a61852962192bb507a1f21fd0a01d5bfc9fd1fb278fe94fbaf18ff7ca605d8 539118 samtools_0.1.9-1_kfreebsd-i386.deb
- 2a9e0e05045427c7afc4e0b420bc3a1d60e2b9aab6000d534fc8be99ad77347d 157878 libbam-dev_0.1.9-1_kfreebsd-i386.deb
+ 30d7d78e6a4127808baeb2de38f9525348a0ff3f4e7ae66ef2f9b40a30417d5d 554156 samtools_0.1.10-1_kfreebsd-i386.deb
+ eb3adc973590bc229b4ef3b71b4af42b7fa1e85d4a1832cd126df6a8a3bec0ea 164816 libbam-dev_0.1.10-1_kfreebsd-i386.deb
Files:
- 71a2408befd0a604c3f09ef4f87835a0 539118 science optional samtools_0.1.9-1_kfreebsd-i386.deb
- 0a037129c4ad8a29332a61b31d1cae07 157878 libdevel optional libbam-dev_0.1.9-1_kfreebsd-i386.deb
+ e562e2d400f454659411eacd45cfcf7d 554156 science optional samtools_0.1.10-1_kfreebsd-i386.deb
+ 1f3cb1b93a5a3d8798f4307d76df9fb8 164816 libdevel optional libbam-dev_0.1.10-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_kfreebsd-i386.deb
-──────────────────────────────────
+samtools_0.1.10-1_kfreebsd-i386.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 539118 bytes: control archive= 1797 bytes.
- 800 bytes, 16 lines control
+ size 554156 bytes: control archive= 1797 bytes.
+ 801 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 882
+ Installed-Size: 914
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -491,72 +488,72 @@ samtools_0.1.9-1_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 2010-11-01 11:49 ./
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-01 11:48 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-11-01 11:49 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-01 11:49 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-01 11:49 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/samtools/
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2010-11-01 11:49 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/bin/
--rwxr-xr-x root/root 76228 2010-11-01 11:49 ./usr/bin/bcftools
--rwxr-xr-x root/root 23564 2010-11-01 11:49 ./usr/bin/razip
--rwxr-xr-x root/root 293652 2010-11-01 11:49 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/lib/samtools/
--rwxr-xr-x root/root 17296 2010-11-01 11:49 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6160 2010-11-01 11:49 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6144 2010-11-01 11:49 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9876 2010-11-01 11:49 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6632 2010-11-01 11:49 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_kfreebsd-i386.deb
-────────────────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./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 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-17 11:54 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-17 11:54 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 11:54 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 11:54 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/samtools/
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./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
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-17 11:54 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/bin/
+-rwxr-xr-x root/root 77092 2010-11-17 11:54 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23564 2010-11-17 11:54 ./usr/bin/razip
+-rwxr-xr-x root/root 313804 2010-11-17 11:54 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17296 2010-11-17 11:54 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6160 2010-11-17 11:54 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6144 2010-11-17 11:54 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9876 2010-11-17 11:54 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6632 2010-11-17 11:54 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_kfreebsd-i386.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 157878 bytes: control archive= 902 bytes.
- 681 bytes, 15 lines control
+ size 164816 bytes: control archive= 899 bytes.
+ 682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 368
+ Installed-Size: 370
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -567,23 +564,23 @@ libbam-dev_0.1.9-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/lib/
--rw-r--r-- root/root 236150 2010-11-01 11:49 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/include/
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./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 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/lib/
+-rw-r--r-- root/root 243604 2010-11-17 11:54 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/include/
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -592,7 +589,7 @@ drwxr-xr-x root/root 0 2010-11-01 11:49 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.9-1-kfreebsd-i386-m8gRhm
+Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5
(Reading database ... 15628 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
@@ -622,7 +619,7 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1149
-Build needed 00:01:15, 7850k disc space
+Finished at 20101117-1154
+Build needed 00:01:18, 8096k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/mips.build b/mips.build
index 0504845..59b73d0 100644
--- a/mips.build
+++ b/mips.build
@@ -1,41 +1,41 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/mips received Tue Nov 2 02:17:00 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=mips">mips</a> >> Tue Nov 2 02:17:00 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on corelli.debian.org
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/mips received Thu Nov 18 08:46:05 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=mips">mips</a> >> Thu Nov 18 08:46:05 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on ball.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (mips) 02 Nov 2010 01:34 ║
+║ samtools 0.1.10-1 (mips) 18 Nov 2010 08:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: mips
-Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-d008a992-98d3-4ffd-a976-7671d1c59eb3/build/buildd-samtools_0.1.9-1-mips-dNWPFV
-Start Time: 20101102-0134
-Get:1 http://mirrors.ece.ubc.ca unstable Release.gpg [835B]
-Ign http://mirrors.ece.ubc.ca/debian/ unstable/contrib Translation-en
-Ign http://mirrors.ece.ubc.ca/debian/ unstable/main Translation-en
-Get:2 http://mirrors.ece.ubc.ca unstable Release [104kB]
+Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-b522fcbb-8ede-4893-98db-96e883e922ef/build/buildd-samtools_0.1.10-1-mips-Tg8JD2
+Start Time: 20101118-0838
+Get:1 http://debian.netcologne.de unstable Release.gpg [835B]
+Ign http://debian.netcologne.de/debian/ unstable/contrib Translation-en
+Ign http://debian.netcologne.de/debian/ unstable/main Translation-en
+Get:2 http://debian.netcologne.de unstable Release [104kB]
Get:3 http://incoming.debian.org unstable Release.gpg [835B]
Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
Ign http://incoming.debian.org/debian/ unstable/main Translation-en
Get:4 http://incoming.debian.org Release.gpg [835B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://mirrors.ece.ubc.ca unstable/main Sources [4008kB]
+Get:6 http://debian.netcologne.de unstable/main Sources [4056kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4008kB]
-Get:9 http://mirrors.ece.ubc.ca unstable/contrib Sources [38.7kB]
-Get:10 http://mirrors.ece.ubc.ca unstable/non-free Sources [81.3kB]
-Get:11 http://mirrors.ece.ubc.ca unstable/main mips Packages [6660kB]
-Get:12 http://mirrors.ece.ubc.ca unstable/contrib mips Packages [51.5kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [81.3kB]
-Get:15 http://incoming.debian.org unstable/main mips Packages [6660kB]
+Get:8 http://incoming.debian.org unstable/main Sources [4057kB]
+Get:9 http://debian.netcologne.de unstable/contrib Sources [39.0kB]
+Get:10 http://debian.netcologne.de unstable/non-free Sources [83.1kB]
+Get:11 http://debian.netcologne.de unstable/main mips Packages [6725kB]
+Get:12 http://debian.netcologne.de unstable/contrib mips Packages [51.5kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [38.9kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.2kB]
+Get:15 http://incoming.debian.org unstable/main mips Packages [6724kB]
Get:16 http://incoming.debian.org unstable/contrib mips Packages [51.5kB]
-Get:17 http://incoming.debian.org Sources [17.0kB]
-Get:18 http://incoming.debian.org Packages [266kB]
-Fetched 22.2MB in 47s (464kB/s)
+Get:17 http://incoming.debian.org Sources [14.4kB]
+Get:18 http://incoming.debian.org Packages [249kB]
+Fetched 22.4MB in 49s (453kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -53,14 +53,13 @@ Download source files with APT
Reading package lists...
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 358kB of source archives.
-Get:1 http://mirrors.ece.ubc.ca/debian/ unstable/main samtools 0.1.9-1 (dsc) [1932B]
-Get:2 http://mirrors.ece.ubc.ca/debian/ unstable/main samtools 0.1.9-1 (tar) [350kB]
-Get:3 http://mirrors.ece.ubc.ca/debian/ unstable/main samtools 0.1.9-1 (diff) [6264B]
-Fetched 358kB in 0s (3066kB/s)
+Need to get 361kB of source archives.
+Get:1 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.10-1 (dsc) [1939B]
+Get:2 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.10-1 (tar) [353kB]
+Get:3 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.10-1 (diff) [6332B]
+Fetched 361kB in 0s (1826kB/s)
Download complete and in download only mode
Check arch
@@ -83,7 +82,6 @@ Checking for source dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
-Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libunistring0 libxml2
@@ -100,43 +98,43 @@ The following NEW packages will be installed:
libunistring0 libxml2 man-db po-debconf zlib1g-dev
The following packages will be upgraded:
libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 41 not upgraded.
+2 upgraded, 19 newly installed, 0 to remove and 50 not upgraded.
Need to get 12.3MB of archives.
-After this operation, 37.0MB of additional disk space will be used.
-Get:1 http://mirrors.ece.ubc.ca/debian/ unstable/main ncurses-bin mips 5.7+20100313-4 [317kB]
-Get:2 http://mirrors.ece.ubc.ca/debian/ unstable/main libncurses5 mips 5.7+20100313-4 [349kB]
-Get:3 http://mirrors.ece.ubc.ca/debian/ unstable/main bsdmainutils mips 8.0.13 [207kB]
-Get:4 http://mirrors.ece.ubc.ca/debian/ unstable/main groff-base mips 1.20.1-10 [1190kB]
-Get:5 http://mirrors.ece.ubc.ca/debian/ unstable/main man-db mips 2.5.7-6 [1251kB]
-Get:6 http://mirrors.ece.ubc.ca/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
-Get:7 http://mirrors.ece.ubc.ca/debian/ unstable/main file mips 5.04-5 [49.7kB]
-Get:8 http://mirrors.ece.ubc.ca/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
-Get:9 http://mirrors.ece.ubc.ca/debian/ unstable/main libpcre3 mips 8.02-1.1 [232kB]
-Get:10 http://mirrors.ece.ubc.ca/debian/ unstable/main libxml2 mips 2.7.7.dfsg-4 [835kB]
-Get:11 http://mirrors.ece.ubc.ca/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
-Get:12 http://mirrors.ece.ubc.ca/debian/ unstable/main libglib2.0-0 mips 2.24.2-1 [1043kB]
-Get:13 http://mirrors.ece.ubc.ca/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
-Get:14 http://mirrors.ece.ubc.ca/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
-Get:15 http://mirrors.ece.ubc.ca/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
-Get:16 http://mirrors.ece.ubc.ca/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:17 http://mirrors.ece.ubc.ca/debian/ unstable/main po-debconf all 1.0.16 [224kB]
-Get:18 http://mirrors.ece.ubc.ca/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:19 http://mirrors.ece.ubc.ca/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:20 http://mirrors.ece.ubc.ca/debian/ unstable/main libncurses5-dev mips 5.7+20100313-4 [1643kB]
-Get:21 http://mirrors.ece.ubc.ca/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
+After this operation, 37.2MB of additional disk space will be used.
+Get:1 http://debian.netcologne.de/debian/ unstable/main ncurses-bin mips 5.7+20100313-4 [317kB]
+Get:2 http://debian.netcologne.de/debian/ unstable/main libncurses5 mips 5.7+20100313-4 [349kB]
+Get:3 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mips 8.0.16 [208kB]
+Get:4 http://debian.netcologne.de/debian/ unstable/main groff-base mips 1.20.1-10 [1190kB]
+Get:5 http://debian.netcologne.de/debian/ unstable/main man-db mips 2.5.7-6 [1251kB]
+Get:6 http://debian.netcologne.de/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
+Get:7 http://debian.netcologne.de/debian/ unstable/main file mips 5.04-5 [49.7kB]
+Get:8 http://debian.netcologne.de/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
+Get:9 http://debian.netcologne.de/debian/ unstable/main libpcre3 mips 8.02-1.1 [232kB]
+Get:10 http://debian.netcologne.de/debian/ unstable/main libxml2 mips 2.7.8.dfsg-1 [836kB]
+Get:11 http://debian.netcologne.de/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
+Get:12 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 mips 2.24.2-1 [1043kB]
+Get:13 http://debian.netcologne.de/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
+Get:14 http://debian.netcologne.de/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
+Get:15 http://debian.netcologne.de/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
+Get:16 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
+Get:17 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
+Get:18 http://debian.netcologne.de/debian/ unstable/main debhelper all 8.0.0 [454kB]
+Get:19 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.89 [1240kB]
+Get:20 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev mips 5.7+20100313-4 [1643kB]
+Get:21 http://debian.netcologne.de/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.3MB in 2s (4873kB/s)
-(Reading database ... 10143 files and directories currently installed.)
+Fetched 12.3MB in 2s (4993kB/s)
+(Reading database ... 10123 files and directories currently installed.)
Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-4_mips.deb) ...
Unpacking replacement ncurses-bin ...
Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 10143 files and directories currently installed.)
+(Reading database ... 10123 files and directories currently installed.)
Preparing to replace libncurses5 5.7+20100313-3 (using .../libncurses5_5.7+20100313-4_mips.deb) ...
Unpacking replacement libncurses5 ...
Setting up libncurses5 (5.7+20100313-4) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10143 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mips.deb) ...
+(Reading database ... 10123 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_mips.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_mips.deb) ...
Selecting previously deselected package man-db.
@@ -150,7 +148,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mips.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -164,7 +162,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -173,7 +171,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_mips.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.0.16) ...
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 (1.20.1-10) ...
@@ -183,23 +181,23 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-22 gcc-4.4_4.4.4-14 g++-4.4_4.4.4-14 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-14 libstdc++6_4.4.4-14
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-5 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-14 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-14 gcc_4:4.4.4-2 gcc-4.4_4.4.4-14 gcc-4.4-base_4.4.4-14 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-5 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-14 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-14 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-14 libstdc++6-4.4-dev_4.4.4-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-22 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32.2-dsa-mips-swarm mips (mips64)
+Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.4-15 g++-4.4_4.4.4-15 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-15 libstdc++6_4.4.4-15
+Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-15 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-15 gcc_4:4.4.4-2 gcc-4.4_4.4.4-15 gcc-4.4-base_4.4.4-15 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-15 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-15 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-15 libstdc++6-4.4-dev_4.4.4-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -211,12 +209,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -231,25 +229,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture mips
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/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_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/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_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -257,8 +255,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -282,9 +280,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -295,10 +294,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -311,27 +310,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -341,14 +341,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-mips-dNWPFV/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -372,11 +372,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -408,8 +409,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -433,7 +434,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-mips-dNWPFV/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -448,71 +449,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_mips.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_mips.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101102-0216
+Build finished at 20101118-0845
-samtools_0.1.9-1_mips.changes:
+samtools_0.1.10-1_mips.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli at buildd...>
+Maintainer: Debian Build Daemon <buildd_mips-ball at buildd...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- fb9a8ae8127f45af6a328b7c16353f31b36d41ff 566378 samtools_0.1.9-1_mips.deb
- 3a7036e5101c84fc704add883fb47cbe0c2e651a 174246 libbam-dev_0.1.9-1_mips.deb
+ 91b18f69b3472ed9cb8ca63ac969207792a96111 585154 samtools_0.1.10-1_mips.deb
+ 01a953be595d2aa1a7818282a22645f566e54298 182112 libbam-dev_0.1.10-1_mips.deb
Checksums-Sha256:
- 565bdab5a3bbb70558272218bb670eda6c03ef7fa2fed8574e3efc16fc51c6f6 566378 samtools_0.1.9-1_mips.deb
- 686ce5a3435fabff4309d8621119b4419dacba3cf451fd992fd996bbe396b9be 174246 libbam-dev_0.1.9-1_mips.deb
+ 393625a5e362ebccf51ca7712b2d7495d88efd29ca42ad427bf82383dda10b83 585154 samtools_0.1.10-1_mips.deb
+ 18d45b59e94cea5cd6033613025ff87da541b3e277c0bea6d0f5b248ef50e314 182112 libbam-dev_0.1.10-1_mips.deb
Files:
- 7faad07b09ac925f3e644b6dbfe47545 566378 science optional samtools_0.1.9-1_mips.deb
- af0d13f8c8db652a534456f2e8c1ff8d 174246 libdevel optional libbam-dev_0.1.9-1_mips.deb
+ c932c08bfb17e566c3d717c11b6cbc22 585154 science optional samtools_0.1.10-1_mips.deb
+ e2662d646ba35be2603b795afbb34ff0 182112 libdevel optional libbam-dev_0.1.10-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_mips.deb
-─────────────────────────
+samtools_0.1.10-1_mips.deb
+──────────────────────────
new debian package, version 2.0.
- size 566378 bytes: control archive= 1797 bytes.
- 790 bytes, 16 lines control
+ size 585154 bytes: control archive= 1795 bytes.
+ 791 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1080
+ Installed-Size: 1112
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -525,72 +520,72 @@ samtools_0.1.9-1_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 2010-11-02 02:15 ./
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./usr/
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/share/samtools/
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5778 2010-11-02 02:16 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-02 02:15 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-02 02:15 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2010-11-02 01:42 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2010-11-02 02:15 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/lib/samtools/
--rwxr-xr-x root/root 13268 2010-11-02 02:16 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2010-11-02 02:16 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7764 2010-11-02 02:16 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9768 2010-11-02 02:16 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 19928 2010-11-02 02:16 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/bin/
--rwxr-xr-x root/root 104996 2010-11-02 02:16 ./usr/bin/bcftools
--rwxr-xr-x root/root 382712 2010-11-02 02:16 ./usr/bin/samtools
--rwxr-xr-x root/root 30616 2010-11-02 02:16 ./usr/bin/razip
-lrwxrwxrwx root/root 0 2010-11-02 02:15 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_mips.deb
-───────────────────────────
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-18 08:45 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./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 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./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 2010-11-18 08:44 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-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 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/man/man1/
+-rw-r--r-- root/root 7544 2010-11-18 08:45 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-11-18 08:45 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/samtools/
+-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 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 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 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 5778 2010-11-18 08:45 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/bin/
+-rwxr-xr-x root/root 30616 2010-11-18 08:45 ./usr/bin/razip
+-rwxr-xr-x root/root 410760 2010-11-18 08:45 ./usr/bin/samtools
+-rwxr-xr-x root/root 108636 2010-11-18 08:45 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19928 2010-11-18 08:45 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9768 2010-11-18 08:45 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2010-11-18 08:45 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13268 2010-11-18 08:45 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2010-11-18 08:45 ./usr/lib/samtools/maq2sam-short
+lrwxrwxrwx root/root 0 2010-11-18 08:45 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_mips.deb
+────────────────────────────
new debian package, version 2.0.
- size 174246 bytes: control archive= 901 bytes.
- 672 bytes, 15 lines control
+ size 182112 bytes: control archive= 893 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 432
+ Installed-Size: 448
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -601,23 +596,23 @@ libbam-dev_0.1.9-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/include/
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-02 02:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/lib/
--rw-r--r-- root/root 293636 2010-11-02 02:16 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/include/
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/lib/
+-rw-r--r-- root/root 303282 2010-11-18 08:45 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -626,10 +621,10 @@ drwxr-xr-x root/root 0 2010-11-02 02:16 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mips-sbuild-d008a992-98d3-4ffd-a976-7671d1c59eb3/build/buildd-samtools_0.1.9-1-mips-dNWPFV
+Purging /var/lib/schroot/mount/sid-mips-sbuild-b522fcbb-8ede-4893-98db-96e883e922ef/build/buildd-samtools_0.1.10-1-mips-Tg8JD2
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101102-0216
-Build needed 00:42:18, 8988k disc space
+Finished at 20101118-0845
+Build needed 00:07:09, 9300k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/mipsel.build b/mipsel.build
index 6e7cd77..ef0a316 100644
--- a/mipsel.build
+++ b/mipsel.build
@@ -1,41 +1,39 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/mipsel received Mon Nov 1 13:47:12 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=mipsel">mipsel</a> >> Mon Nov 1 13:47:12 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rem.debian.org
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/mipsel received Wed Nov 17 11:59:57 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=mipsel">mipsel</a> >> Wed Nov 17 11:59:57 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (mipsel) 01 Nov 2010 13:40 ║
+║ samtools 0.1.10-1 (mipsel) 17 Nov 2010 11:55 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-a883700a-d75c-4df2-846f-1762fa3f02e1/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ
-Start Time: 20101101-1340
-Get:1 http://source.rfc822.org unstable Release.gpg [835B]
-Ign http://source.rfc822.org/debian/ unstable/contrib Translation-en
-Ign http://source.rfc822.org/debian/ unstable/main Translation-en
-Get:2 http://source.rfc822.org unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://incoming.debian.org Release.gpg [835B]
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-d2e83b5b-a7e9-465d-b67c-107d04df1392/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY
+Start Time: 20101117-1155
+Hit http://debian.oregonstate.edu sid Release.gpg
+Ign http://debian.oregonstate.edu/debian/ sid/contrib Translation-en
+Ign http://debian.oregonstate.edu/debian/ sid/main Translation-en
+Hit http://debian.oregonstate.edu sid Release
+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
+Hit http://incoming.debian.org sid Release.gpg
+Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
+Ign http://incoming.debian.org/debian/ sid/main Translation-en
+Get:1 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://source.rfc822.org unstable/main Sources [4011kB]
-Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4011kB]
-Get:9 http://source.rfc822.org unstable/contrib Sources [38.7kB]
-Get:10 http://source.rfc822.org unstable/non-free Sources [81.3kB]
-Get:11 http://source.rfc822.org unstable/main mipsel Packages [6677kB]
-Get:12 http://source.rfc822.org unstable/contrib mipsel Packages [51.7kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [81.3kB]
-Get:15 http://incoming.debian.org unstable/main mipsel Packages [6677kB]
-Get:16 http://incoming.debian.org unstable/contrib mipsel Packages [51.7kB]
-Get:17 http://incoming.debian.org Sources [11.7kB]
-Get:18 http://incoming.debian.org Packages [137kB]
-Fetched 22.1MB in 43s (506kB/s)
+Hit http://incoming.debian.org sid Release
+Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Get:3 http://incoming.debian.org Sources [15.1 kB]
+Get:4 http://incoming.debian.org Packages [227 kB]
+Fetched 244 kB in 1s (131 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -56,11 +54,11 @@ 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 358kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264B]
-Fetched 358kB in 1s (338kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 0s (435 kB/s)
Download complete and in download only mode
Check arch
@@ -74,135 +72,44 @@ Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.0.0
+debhelper: already installed (8.0.0 >= 7 is satisfied)
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
- libslang2
+ udev
Use 'apt-get autoremove' to remove them.
-The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ devscripts doc-base
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 40 not upgraded.
-Need to get 12.3MB of archives.
-After this operation, 37.1MB of additional disk space will be used.
-Get:1 http://source.rfc822.org/debian/ unstable/main ncurses-bin mipsel 5.7+20100313-4 [319kB]
-Get:2 http://source.rfc822.org/debian/ unstable/main libncurses5 mipsel 5.7+20100313-4 [346kB]
-Get:3 http://source.rfc822.org/debian/ unstable/main bsdmainutils mipsel 8.0.13 [205kB]
-Get:4 http://source.rfc822.org/debian/ unstable/main groff-base mipsel 1.20.1-10 [1188kB]
-Get:5 http://source.rfc822.org/debian/ unstable/main man-db mipsel 2.5.7-6 [1247kB]
-Get:6 http://source.rfc822.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238kB]
-Get:7 http://source.rfc822.org/debian/ unstable/main file mipsel 5.04-5 [49.5kB]
-Get:8 http://source.rfc822.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152kB]
-Get:9 http://source.rfc822.org/debian/ unstable/main libpcre3 mipsel 8.02-1.1 [233kB]
-Get:10 http://source.rfc822.org/debian/ unstable/main libxml2 mipsel 2.7.7.dfsg-4 [832kB]
-Get:11 http://source.rfc822.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103kB]
-Get:12 http://source.rfc822.org/debian/ unstable/main libglib2.0-0 mipsel 2.24.2-1 [1039kB]
-Get:13 http://source.rfc822.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110kB]
-Get:14 http://source.rfc822.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411kB]
-Get:15 http://source.rfc822.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023kB]
-Get:16 http://source.rfc822.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:17 http://source.rfc822.org/debian/ unstable/main po-debconf all 1.0.16 [224kB]
-Get:18 http://source.rfc822.org/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:19 http://source.rfc822.org/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:20 http://source.rfc822.org/debian/ unstable/main libncurses5-dev mipsel 5.7+20100313-4 [1639kB]
-Get:21 http://source.rfc822.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192kB]
+ cdbs libncurses5-dev zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.3MB in 3s (3788kB/s)
-(Reading database ... 10145 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-4_mipsel.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 10145 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-3 (using .../libncurses5_5.7+20100313-4_mipsel.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10145 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_mipsel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_mipsel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_mipsel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5_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_8.02-1.1_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.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.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_mipsel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mipsel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+0 upgraded, 3 newly installed, 0 to remove and 31 not upgraded.
+Need to get 0 B/3072 kB of archives.
+After this operation, 9052 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
+(Reading database ... 11650 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_mipsel.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up bsdmainutils (8.0.13) ...
-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 (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
+Processing triggers for man-db ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: Linux 2.6.32-mipsel-swarm mipsel (mips64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-22 gcc-4.4_4.4.4-14 g++-4.4_4.4.4-14 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-14 libstdc++6_4.4.4-14
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-5 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-14 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-14 gcc_4:4.4.4-2 gcc-4.4_4.4.4-14 gcc-4.4-base_4.4.4-14 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-5 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-14 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-14 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-14 libstdc++6-4.4-dev_4.4.4-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-22 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-23.1 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010l-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-7 g++-4.4_4.4.5-7 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-7 libstdc++6_4.4.5-7
+Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-7 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-7 gcc_4:4.4.5-1 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-7 gcc-4.4-base_4.4.5-7 gettext_0.18.1.1-2 gettext-base_0.18.1.1-2 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.5 libgcc1_1:4.4.5-7 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-7 liblocale-gettext-perl_1.05-6 liblzma1_4.999.9beta+20091116-1 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-7 libstdc++6-4.4-dev_4.4.5-7 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-27 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-23.1 lzma_4.43-14 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-2 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010o-1 udev_164-2 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -214,12 +121,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -234,25 +141,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture mipsel
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/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_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/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_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -260,8 +167,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -285,9 +192,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -298,10 +206,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -314,27 +222,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -344,14 +253,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -375,11 +284,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtoo
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -411,8 +321,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -436,7 +346,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -451,71 +361,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_mipsel.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_mipsel.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1347
+Build finished at 20101117-1159
-samtools_0.1.9-1_mipsel.changes:
+samtools_0.1.10-1_mipsel.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: mipsel Build Daemon (rem) <buildd_mips-rem at buildd...>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 92f33dbfe3e1bdc0ae3050ef67a12ddf135f8c78 570576 samtools_0.1.9-1_mipsel.deb
- 20d7205c523680d116e4026568497414a94b97a1 174784 libbam-dev_0.1.9-1_mipsel.deb
+ eaab4b8f1f63bec010b44d386d19f4360ba51158 586618 samtools_0.1.10-1_mipsel.deb
+ 41b74aaf5f325847427b23d59315dfb3a770a26d 182386 libbam-dev_0.1.10-1_mipsel.deb
Checksums-Sha256:
- 808d828a334d513686c932b5cd3f72dd5ca5575654916b5f549601bb796ea824 570576 samtools_0.1.9-1_mipsel.deb
- 7814a721a84e5d8b66be7c9fd560a1965c09bd61aee7605a536747a4a79ea5ac 174784 libbam-dev_0.1.9-1_mipsel.deb
+ 3a76a0552d7e7a6695889464f41ed8421ba8b18c7479a4c992b6dd31fb618604 586618 samtools_0.1.10-1_mipsel.deb
+ a7f066c7f76e015518e0116a6572cf8feda3d5f146ff0ee80b1eee42443a0e0f 182386 libbam-dev_0.1.10-1_mipsel.deb
Files:
- 555141fe620301b2913b802b571c2290 570576 science optional samtools_0.1.9-1_mipsel.deb
- fd2ed721b4fecc99c03f486b5f4c1004 174784 libdevel optional libbam-dev_0.1.9-1_mipsel.deb
+ 2f161c4ec5673172c159b692884b3ea6 586618 science optional samtools_0.1.10-1_mipsel.deb
+ ca2e77036f0009b7cdccd794edbd1e83 182386 libdevel optional libbam-dev_0.1.10-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_mipsel.deb
-───────────────────────────
+samtools_0.1.10-1_mipsel.deb
+────────────────────────────
new debian package, version 2.0.
- size 570576 bytes: control archive= 1792 bytes.
- 792 bytes, 16 lines control
+ size 586618 bytes: control archive= 1793 bytes.
+ 793 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1080
+ Installed-Size: 1112
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -528,72 +432,72 @@ samtools_0.1.9-1_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 2010-11-01 13:46 ./
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/bin/
--rwxr-xr-x root/root 382808 2010-11-01 13:46 ./usr/bin/samtools
--rwxr-xr-x root/root 105060 2010-11-01 13:46 ./usr/bin/bcftools
--rwxr-xr-x root/root 30488 2010-11-01 13:46 ./usr/bin/razip
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/samtools/
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5778 2010-11-01 13:46 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-01 13:46 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-01 13:46 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/doc/samtools/
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2010-11-01 13:46 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-01 13:46 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/lib/samtools/
--rwxr-xr-x root/root 19944 2010-11-01 13:46 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9768 2010-11-01 13:46 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2010-11-01 13:46 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13268 2010-11-01 13:46 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2010-11-01 13:46 ./usr/lib/samtools/maq2sam-short
-lrwxrwxrwx root/root 0 2010-11-01 13:46 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_mipsel.deb
-─────────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:58 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./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 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-17 11:58 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-17 11:59 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 11:59 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 11:59 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/share/samtools/
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./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
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-17 11:59 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/bin/
+-rwxr-xr-x root/root 108636 2010-11-17 11:59 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30488 2010-11-17 11:59 ./usr/bin/razip
+-rwxr-xr-x root/root 410760 2010-11-17 11:59 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19944 2010-11-17 11:59 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7764 2010-11-17 11:59 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7764 2010-11-17 11:59 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13268 2010-11-17 11:59 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9768 2010-11-17 11:59 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2010-11-17 11:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_mipsel.deb
+──────────────────────────────
new debian package, version 2.0.
- size 174784 bytes: control archive= 894 bytes.
- 674 bytes, 15 lines control
+ size 182386 bytes: control archive= 897 bytes.
+ 675 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 432
+ Installed-Size: 444
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -604,23 +508,23 @@ libbam-dev_0.1.9-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/include/
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/lib/
--rw-r--r-- root/root 293740 2010-11-01 13:46 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./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 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/lib/
+-rw-r--r-- root/root 302994 2010-11-17 11:59 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/include/
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -629,10 +533,14 @@ drwxr-xr-x root/root 0 2010-11-01 13:46 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-a883700a-d75c-4df2-846f-1762fa3f02e1/build/buildd-samtools_0.1.9-1-mipsel-uzFbzZ
-Not removing build depends: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-d2e83b5b-a7e9-465d-b67c-107d04df1392/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY
+(Reading database ... 12788 files and directories currently installed.)
+Removing libncurses5-dev ...
+Removing cdbs ...
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1347
-Build needed 00:06:20, 8996k disc space
+Finished at 20101117-1159
+Build needed 00:04:30, 9292k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/powerpc.build b/powerpc.build
index 688cdb7..79b9da6 100644
--- a/powerpc.build
+++ b/powerpc.build
@@ -1,36 +1,41 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/powerpc received Mon Nov 1 11:37:48 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=powerpc">powerpc</a> >> Mon Nov 1 11:37:48 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on praetorius.debian.org
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/powerpc received Wed Nov 17 11:54:58 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=powerpc">powerpc</a> >> Wed Nov 17 11:54:58 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (powerpc) 01 Nov 2010 11:34 ║
+║ samtools 0.1.10-1 (powerpc) 17 Nov 2010 11:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: powerpc
-Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-219e00c9-ea31-4ed9-9fa0-fd51755ff3f4/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ
-Start Time: 20101101-1134
-Get:1 http://ftp.se.debian.org unstable Release.gpg [835B]
-Get:2 http://ftp.se.debian.org unstable Release [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Get:4 http://incoming.debian.org Release.gpg [835B]
-Get:5 http://ftp.se.debian.org unstable/main Packages [6778kB]
-Get:6 http://incoming.debian.org unstable Release [104kB]
-Get:7 http://ftp.se.debian.org unstable/contrib Packages [50.1kB]
-Get:8 http://ftp.se.debian.org unstable/main Sources [4011kB]
-Get:9 http://ftp.se.debian.org unstable/contrib Sources [38.7kB]
-Get:10 http://incoming.debian.org Release [1604B]
-Get:11 http://ftp.se.debian.org unstable/non-free Sources [81.3kB]
-Get:12 http://incoming.debian.org unstable/main Packages [6778kB]
-Get:13 http://incoming.debian.org unstable/contrib Packages [50.1kB]
-Get:14 http://incoming.debian.org unstable/main Sources [4011kB]
-Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:16 http://incoming.debian.org unstable/non-free Sources [81.3kB]
-Get:17 http://incoming.debian.org Packages [194kB]
-Get:18 http://incoming.debian.org Sources [11.5kB]
-Fetched 22.3MB in 27s (821kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-05b829a1-dae0-44c0-a5bc-eab137be8825/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp
+Start Time: 20101117-1152
+Get:1 http://ftp.uk.debian.org unstable Release.gpg [835 B]
+Ign http://ftp.uk.debian.org/debian/ unstable/contrib Translation-en
+Ign http://ftp.uk.debian.org/debian/ unstable/main Translation-en
+Get:2 http://ftp.uk.debian.org unstable Release [104 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [4061 kB]
+Get:4 http://incoming.debian.org unstable Release.gpg [835 B]
+Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
+Ign http://incoming.debian.org/debian/ unstable/main Translation-en
+Get:5 http://incoming.debian.org Release.gpg [835 B]
+Ign http://incoming.debian.org/buildd-unstable/ Translation-en
+Get:6 http://incoming.debian.org unstable Release [104 kB]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://incoming.debian.org unstable/main Sources [4061 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib Sources [39.0 kB]
+Get:10 http://ftp.uk.debian.org unstable/non-free Sources [83.1 kB]
+Get:11 http://ftp.uk.debian.org unstable/main powerpc Packages [6834 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [50.1 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [39.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.1 kB]
+Get:15 http://incoming.debian.org unstable/main powerpc Packages [6834 kB]
+Get:16 http://incoming.debian.org unstable/contrib powerpc Packages [50.1 kB]
+Get:17 http://incoming.debian.org Sources [15.1 kB]
+Get:18 http://incoming.debian.org Packages [227 kB]
+Fetched 22.6 MB in 26s (841 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -49,11 +54,13 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-Need to get 358kB of source archives.
-Get:1 http://incoming.debian.org samtools 0.1.9-1 (dsc) [1932B]
-Get:2 http://incoming.debian.org samtools 0.1.9-1 (tar) [350kB]
-Get:3 http://incoming.debian.org samtools 0.1.9-1 (diff) [6264B]
-Fetched 358kB in 1s (280kB/s)
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 361 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 1s (296 kB/s)
Download complete and in download only mode
Check arch
@@ -79,57 +86,45 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 59 not upgraded.
-Need to get 12.5MB of archives.
-After this operation, 36.1MB of additional disk space will be used.
-Get:1 http://ftp.se.debian.org unstable/main ncurses-bin 5.7+20100313-4 [319kB]
-Get:2 http://ftp.se.debian.org unstable/main libncurses5 5.7+20100313-4 [360kB]
-Get:3 http://ftp.se.debian.org unstable/main bsdmainutils 8.0.13 [205kB]
-Get:4 http://ftp.se.debian.org unstable/main groff-base 1.20.1-10 [1196kB]
-Get:5 http://ftp.se.debian.org unstable/main man-db 2.5.7-6 [1285kB]
-Get:6 http://ftp.se.debian.org unstable/main libmagic1 5.04-5 [241kB]
-Get:7 http://ftp.se.debian.org unstable/main file 5.04-5 [49.9kB]
-Get:8 http://ftp.se.debian.org unstable/main gettext-base 0.18.1.1-3 [141kB]
-Get:9 http://ftp.se.debian.org unstable/main libpcre3 8.02-1.1 [231kB]
-Get:10 http://ftp.se.debian.org unstable/main libxml2 2.7.7.dfsg-4 [848kB]
-Get:11 http://ftp.se.debian.org unstable/main html2text 1.3.2a-15 [105kB]
-Get:12 http://ftp.se.debian.org unstable/main libglib2.0-0 2.24.2-1 [1111kB]
-Get:13 http://ftp.se.debian.org unstable/main libcroco3 0.6.2-1 [128kB]
-Get:14 http://ftp.se.debian.org unstable/main libunistring0 0.9.3-3 [422kB]
-Get:15 http://ftp.se.debian.org unstable/main gettext 0.18.1.1-3 [2046kB]
-Get:16 http://ftp.se.debian.org unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
-Get:17 http://ftp.se.debian.org unstable/main po-debconf 1.0.16 [224kB]
-Get:18 http://ftp.se.debian.org unstable/main debhelper 8.0.0 [454kB]
-Get:19 http://ftp.se.debian.org unstable/main cdbs 0.4.89 [1240kB]
-Get:20 http://ftp.se.debian.org unstable/main libncurses5-dev 5.7+20100313-4 [1633kB]
-Get:21 http://ftp.se.debian.org unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [190kB]
+0 upgraded, 19 newly installed, 0 to remove and 21 not upgraded.
+Need to get 11.8 MB of archives.
+After this operation, 36.2 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.0.16 [207 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.20.1-10 [1196 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.5.7-6 [1285 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5 [241 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5 [49.9 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.02-1.1 [231 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-1 [849 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.24.2-1 [1111 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-3 [422 kB]
+Get:13 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 intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.7+20100313-4 [1633 kB]
+Get:19 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 12.5MB in 1s (10.0MB/s)
-(Reading database ... 9867 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-2 (using .../ncurses-bin_5.7+20100313-4_powerpc.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 9867 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-2 (using .../libncurses5_5.7+20100313-4_powerpc.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
+Fetched 11.8 MB in 2s (4685 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 9867 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_powerpc.deb) ...
+(Reading database ... 10126 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_powerpc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_powerpc.deb) ...
Selecting previously deselected package man-db.
@@ -143,7 +138,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_powerpc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_powerpc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -157,7 +152,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -166,7 +161,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_powerpc.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.0.16) ...
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 (1.20.1-10) ...
@@ -176,14 +171,14 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
@@ -191,8 +186,8 @@ Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: libc6-dev_2.11.1-3 dpkg-dev_1.15.7.2 linux-libc-dev_2.6.32-15 gcc-4.4_4.4.4-4 g++-4.4_4.4.4-4 binutils_2.20.1-10 libstdc++6-4.4-dev_4.4.4-4 libstdc++6_4.4.4-4
-Package versions: apt_0.7.25.3 base-files_5.7 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-10 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-4 dash_0.5.5.1-6 debconf_1.5.32 debconf-i18n_1.5.32 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.2.3 diffutils_1:3.0-1 dpkg_1.15.7.2 dpkg-dev_1.15.7.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-4 gcc_4:4.4.4-2 gcc-4.4_4.4.4-4 gcc-4.4-base_4.4.4-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-7 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3 libbz2-1.0_1.0.5-4 libc-bin_2.11.1-3 libc-dev-bin_2.11.1-3 libc6_2.11.1-3 libc6-dev_2.11.1-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-1 libdpkg-perl_1.15.7.2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-4 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-4 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100527-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.94-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-4 libstdc++6-4.4-dev_4.4.4-4 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-15 libuuid1_2.17.2-3 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-15 login_1:4.1.4.2-1 lsb-base_3.2-23.1 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-13 perl-base_5.10.1-13 perl-modules_5.10.1-13 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p6-1 sysv-rc_2.88dsf-7 sysvinit_2.88dsf-7 sysvinit-utils_2.88dsf-7 tar_1.23-1 tzdata_2010j-1 util-linux_2.17.2-3 xz-utils_4.999.9beta+20100527-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libstdc++6_4.4.5-6
+Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 dash_0.5.5.1-7.2 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-6 gcc_4:4.4.5-1 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-27 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.25-1 tzdata_2010o-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -204,12 +199,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -218,30 +213,31 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
+dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.9-1
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture powerpc
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/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_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/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_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -249,8 +245,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -274,9 +270,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -287,10 +284,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -303,27 +300,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -333,14 +331,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -364,11 +362,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samto
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -400,8 +399,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -425,7 +424,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-powerpc-dMvknZ/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -440,70 +439,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_powerpc.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_powerpc.deb'.
dpkg-genchanges -B
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-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1137
+Build finished at 20101117-1154
-samtools_0.1.9-1_powerpc.changes:
+samtools_0.1.10-1_powerpc.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd...>
+Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- c47a8e9e41083467c3744de1acaba681dfa93983 560756 samtools_0.1.9-1_powerpc.deb
- 4e68b09c9d94ba505032a2285a98935b437cb3c3 161220 libbam-dev_0.1.9-1_powerpc.deb
+ 556f78d19102f12234c63222841fcaf9d08417ac 574438 samtools_0.1.10-1_powerpc.deb
+ 54e1cd80b2fae6dddbb3f28ea831598f4724cb5f 169458 libbam-dev_0.1.10-1_powerpc.deb
Checksums-Sha256:
- f0382fa0c5f5ea005b049af48e8c707cf0c92c43a59bc91083131f33dfce1160 560756 samtools_0.1.9-1_powerpc.deb
- 57c8f3d7443fcdaf0cd47604fdc4c3407ecb8544fcb362010320aa10014dfe55 161220 libbam-dev_0.1.9-1_powerpc.deb
+ fe7cd01804d159d3b77895f8381170f2a5e5dd80280f819965aa59ac0369d212 574438 samtools_0.1.10-1_powerpc.deb
+ 018ca127bdec9afe0eaaa81c57710710ee63497d8f70f68b2ce4572955483f72 169458 libbam-dev_0.1.10-1_powerpc.deb
Files:
- 62c0e819fd4908ab645bd17e4de653f9 560756 science optional samtools_0.1.9-1_powerpc.deb
- 7b7cde250912fe30414f9c7e94fa654d 161220 libdevel optional libbam-dev_0.1.9-1_powerpc.deb
+ 98e2158975397738fc69e15422f4c400 574438 science optional samtools_0.1.10-1_powerpc.deb
+ a9ab9475739c025590eff674f377c2fa 169458 libdevel optional libbam-dev_0.1.10-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_powerpc.deb
-────────────────────────────
+samtools_0.1.10-1_powerpc.deb
+─────────────────────────────
new debian package, version 2.0.
- size 560756 bytes: control archive= 1787 bytes.
- 792 bytes, 16 lines control
+ size 574438 bytes: control archive= 1792 bytes.
+ 794 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 992
+ Installed-Size: 1016
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -516,72 +510,72 @@ samtools_0.1.9-1_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 2010-11-01 11:37 ./
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/bin/
--rwxr-xr-x root/root 89396 2010-11-01 11:37 ./usr/bin/bcftools
--rwxr-xr-x root/root 26828 2010-11-01 11:37 ./usr/bin/razip
--rwxr-xr-x root/root 320548 2010-11-01 11:37 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/lib/samtools/
--rwxr-xr-x root/root 7352 2010-11-01 11:37 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11116 2010-11-01 11:37 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 19388 2010-11-01 11:37 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7352 2010-11-01 11:37 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8008 2010-11-01 11:37 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/man/man1/
--rw-r--r-- root/root 7265 2010-11-01 11:37 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-11-01 11:37 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1031 2010-07-15 01:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2010-11-01 11:37 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 114565 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-07-12 02:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-07-12 02:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 764 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-10-28 02:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 1966 2010-11-01 11:37 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2010-07-13 12:02 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2010-07-12 02:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5778 2010-11-01 11:37 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2397 2010-07-12 02:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 02:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2696 2010-07-12 02:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 02:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 02:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 13410 2010-10-28 02:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2010-07-12 02:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 02:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2415 2010-07-12 02:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 02:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13005 2010-10-28 02:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 3224 2010-10-28 02:48 ./usr/share/samtools/bcf-fix.pl
-lrwxrwxrwx root/root 0 2010-11-01 11:37 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_powerpc.deb
-──────────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/bin/
+-rwxr-xr-x root/root 93512 2010-11-17 11:54 ./usr/bin/bcftools
+-rwxr-xr-x root/root 343524 2010-11-17 11:54 ./usr/bin/samtools
+-rwxr-xr-x root/root 26828 2010-11-17 11:54 ./usr/bin/razip
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/samtools/
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.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
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./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 5778 2010-11-17 11:54 ./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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./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 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/man/man1/
+-rw-r--r-- root/root 7544 2010-11-17 11:54 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-11-17 11:54 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-17 11:54 ./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 2010-11-17 11:54 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19388 2010-11-17 11:54 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8008 2010-11-17 11:54 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7352 2010-11-17 11:54 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7352 2010-11-17 11:54 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11116 2010-11-17 11:54 ./usr/lib/samtools/md5fa
+lrwxrwxrwx root/root 0 2010-11-17 11:54 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_powerpc.deb
+───────────────────────────────
new debian package, version 2.0.
- size 161220 bytes: control archive= 898 bytes.
- 675 bytes, 15 lines control
+ size 169458 bytes: control archive= 896 bytes.
+ 676 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 392
+ Installed-Size: 404
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -592,23 +586,23 @@ libbam-dev_0.1.9-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/lib/
--rw-r--r-- root/root 253152 2010-11-01 11:37 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/include/
--rw-r--r-- root/root 16522 2010-07-12 02:41 ./usr/include/khash.h
--rw-r--r-- root/root 4599 2010-07-12 02:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 24002 2010-10-28 02:48 ./usr/include/bam.h
--rw-r--r-- root/root 3188 2010-07-12 02:41 ./usr/include/faidx.h
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 994 2010-11-01 11:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-07-12 02:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 11:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 5646 2010-10-28 02:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 27497 2010-10-28 02:48 ./usr/share/doc/libbam-dev/changelog.gz
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./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 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/include/
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/lib/
+-rw-r--r-- root/root 260786 2010-11-17 11:54 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -617,10 +611,10 @@ drwxr-xr-x root/root 0 2010-11-01 11:37 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-219e00c9-ea31-4ed9-9fa0-fd51755ff3f4/build/buildd-samtools_0.1.9-1-powerpc-dMvknZ
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-05b829a1-dae0-44c0-a5bc-eab137be8825/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1137
-Build needed 00:02:53, 8632k disc space
+Finished at 20101117-1154
+Build needed 00:02:22, 8908k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/powerpcspe.build b/powerpcspe.build
index eb846be..14ccf89 100644
--- a/powerpcspe.build
+++ b/powerpcspe.build
@@ -1,17 +1,17 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>File `log' in samtools_0.1.9-1_powerpcspe (Nov 1 16:16)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
-<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.9-1_powerpcspe (Nov 1 16:16)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=powerpcspe">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=powerpcspe">0.1.9-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=powerpcspe&stamp=1288628204">Nov 1 16:16</a> >> log</td></tr></table><p><pre>
+<html><head><title>File `log' in samtools_0.1.10-1_powerpcspe (Nov 17 15:41)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
+<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.10-1_powerpcspe (Nov 17 15:41)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=powerpcspe">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.10-1&arch=powerpcspe">0.1.10-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.10-1&arch=powerpcspe&stamp=1290008507">Nov 17 15:41</a> >> log</td></tr></table><p><pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on baako.tec.linutronix.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (powerpcspe) 01 Nov 2010 17:10 ║
+║ samtools 0.1.10-1 (powerpcspe) 18 Nov 2010 16:35 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: powerpcspe
-Chroot Build Dir: /var/lib/schroot/mount/spestage-66d46ce3-ace3-4b09-a4f1-2c96c3a0f48a/spestage/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x
-Start Time: 20101101-1710
+Chroot Build Dir: /var/lib/schroot/mount/spestage-cf4674fc-a146-42b9-b7a0-74ac784f424b/spestage/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX
+Start Time: 20101118-1635
Hit http://merkur sid Release.gpg
Hit http://merkur sid Release.gpg
Ign http://merkur/debian/debian-ports/ sid/main Translation-en
@@ -21,16 +21,20 @@ Hit http://merkur sid Release
Hit http://merkur sid Release
Hit http://merkur unreleased Release
Hit http://merkur sid/main Sources/DiffIndex
-Hit http://ftp.de.debian.org sid Release.gpg
-Hit http://incoming.debian-ports.org unstable Release.gpg
+Get:1 http://ftp.de.debian.org sid Release.gpg [835 B]
+Get:2 http://incoming.debian-ports.org unstable Release.gpg [835 B]
Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
Hit http://merkur sid/main powerpcspe Packages
Hit http://merkur unreleased/main powerpcspe Packages
-Hit http://ftp.de.debian.org sid Release
-Hit http://incoming.debian-ports.org unstable Release
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
+Get:3 http://ftp.de.debian.org sid Release [104 kB]
+Get:4 http://incoming.debian-ports.org unstable Release [8817 B]
Hit http://incoming.debian-ports.org unstable/main Sources
-Hit http://incoming.debian-ports.org unstable/main powerpcspe Packages
+Get:5 http://incoming.debian-ports.org unstable/main powerpcspe Packages [14 B]
+Get:6 http://ftp.de.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:7 http://ftp.de.debian.org sid/main 2010-11-17-1411.17.pdiff [3704 B]
+Get:8 http://ftp.de.debian.org sid/main 2010-11-17-1411.17.pdiff [3704 B]
+Get:9 http://ftp.de.debian.org sid/main 2010-11-17-1411.17.pdiff [3704 B]
+Fetched 120 kB in 4s (29.7 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -51,11 +55,11 @@ 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 358 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 2s (167 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 1s (203 kB/s)
Download complete and in download only mode
Check arch
@@ -93,33 +97,33 @@ The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 19 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 19 newly installed, 0 to remove and 21 not upgraded.
Need to get 11.7 MB of archives.
-After this operation, 35.5 MB of additional disk space will be used.
-Get:1 http://merkur/debian/debian-ports/ sid/main bsdmainutils powerpcspe 8.0.13 [203 kB]
+After this operation, 35.6 MB of additional disk space will be used.
+Get:1 http://merkur/debian/debian-ports/ sid/main bsdmainutils powerpcspe 8.0.16 [203 kB]
Get:2 http://merkur/debian/debian-ports/ sid/main groff-base powerpcspe 1.20.1-10+b100 [1195 kB]
Get:3 http://merkur/debian/debian-ports/ sid/main man-db powerpcspe 2.5.7-6 [1256 kB]
Get:4 http://merkur/debian/debian-ports/ sid/main libmagic1 powerpcspe 5.04-5 [240 kB]
Get:5 http://merkur/debian/debian-ports/ sid/main file powerpcspe 5.04-5 [49.4 kB]
Get:6 http://merkur/debian/debian-ports/ sid/main gettext-base powerpcspe 0.18.1.1-3 [131 kB]
Get:7 http://merkur/debian/debian-ports/ sid/main libpcre3 powerpcspe 8.02-1.1 [232 kB]
-Get:8 http://merkur/debian/debian-ports/ sid/main libxml2 powerpcspe 2.7.7.dfsg-4+b1 [837 kB]
+Get:8 http://merkur/debian/debian-ports/ sid/main libxml2 powerpcspe 2.7.8.dfsg-1 [838 kB]
Get:9 http://merkur/debian/debian-ports/ sid/main html2text powerpcspe 1.3.2a-15+b100 [104 kB]
Get:10 http://merkur/debian/debian-ports/ sid/main libglib2.0-0 powerpcspe 2.24.2-1 [1101 kB]
Get:11 http://merkur/debian/debian-ports/ sid/main libcroco3 powerpcspe 0.6.2-1+b100 [117 kB]
Get:12 http://merkur/debian/debian-ports/ sid/main libunistring0 powerpcspe 0.9.3-3 [428 kB]
Get:13 http://merkur/debian/debian-ports/ sid/main gettext powerpcspe 0.18.1.1-3 [2017 kB]
Get:14 http://merkur/debian/debian-ports/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://merkur/debian/debian-ports/ sid/main po-debconf all 1.0.16 [224 kB]
+Get:15 http://merkur/debian/debian-ports/ sid/main po-debconf all 1.0.16+nmu1 [223 kB]
Get:16 http://merkur/debian/debian-ports/ sid/main debhelper all 8.0.0 [454 kB]
Get:17 http://merkur/debian/debian-ports/ sid/main cdbs all 0.4.89 [1240 kB]
Get:18 http://merkur/debian/debian-ports/ sid/main libncurses5-dev powerpcspe 5.7+20100313-4 [1631 kB]
Get:19 http://merkur/debian/debian-ports/ sid/main zlib1g-dev powerpcspe 1:1.2.3.4.dfsg-3+b110 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.7 MB in 0s (12.4 MB/s)
+Fetched 11.7 MB in 0s (15.7 MB/s)
Selecting previously deselected package bsdmainutils.
(Reading database ... 10179 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_powerpcspe.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_powerpcspe.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10+b100_powerpcspe.deb) ...
Selecting previously deselected package man-db.
@@ -133,7 +137,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpcspe.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_powerpcspe.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4+b1_powerpcspe.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_powerpcspe.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b100_powerpcspe.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -147,7 +151,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_powerpcspe.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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -156,7 +160,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_powerpcspe.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3+b110_powerpcspe.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.0.16) ...
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 (1.20.1-10+b100) ...
@@ -166,26 +170,26 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4+b1) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15+b100) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1+b100) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b110) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-Kernel: Linux 2.6.35 powerpcspe (ppc)
+Kernel: Linux 2.6.36 powerpcspe (ppc)
Toolchain package versions: libc6-dev_2.11.1-2+powerpcspe1 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-13+powerpcspe1 gcc-4.4_4.4.4-4+powerpcspe4.5 g++-4.4_4.4.4-4+powerpcspe4.5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-4+powerpcspe4.5 libstdc++6_4.4.4-4+powerpcspe4.5
-Package versions: apt_0.8.7 base-files_5.9 base-passwd_3.5.22+b110 bash_4.1-3+b111 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5+b100 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1+b1 cpio_2.11-4+b100 cpp_4:4.4.4-2+powerpcspe1 cpp-4.4_4.4.4-4+powerpcspe4.5 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-powerpcspe-archive-keyring_2009.10.13-2 debianutils_3.4.1 diff_1:3.0-1 diffutils_1:3.0-1+b110 dmsetup_2:1.02.48-3 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2+b100 e2fsprogs_1.41.12-2+b100 fakeroot_1.14.4-1+b100 file_5.04-5 findutils_4.4.2-1+b110 g++_4:4.4.4-2+powerpcspe1 g++-4.4_4.4.4-4+powerpcspe4.5 gcc_4:4.4.4-2+powerpcspe1 gcc-4.4_4.4.4-4+powerpcspe4.5 gcc-4.4-base_4.4.4-4+powerpcspe4.5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4+b100 gpgv_1.4.10-4+b100 grep_2.6.3-3+b110 groff-base_1.20.1-10+b100 gzip_1.3.12-9+b110 hostname_3.04+b110 html2text_1.3.2a-15+b100 inits!
+Package versions: apt_0.8.7 base-files_5.9 base-passwd_3.5.22+b110 bash_4.1-3+b111 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.3 build-essential_11.5+b100 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1+b1 cpio_2.11-4+b100 cpp_4:4.4.4-2+powerpcspe1 cpp-4.4_4.4.4-4+powerpcspe4.5 dash_0.5.5.1-7 debconf_1.5.36 debconf-i18n_1.5.36 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-powerpcspe-archive-keyring_2009.10.13-2 debianutils_3.4.1 diff_1:3.0-1 diffutils_1:3.0-1+b110 dmsetup_2:1.02.48-3 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2+b100 e2fsprogs_1.41.12-2+b100 fakeroot_1.14.4-1+b100 file_5.04-5 findutils_4.4.2-1+b110 g++_4:4.4.4-2+powerpcspe1 g++-4.4_4.4.4-4+powerpcspe4.5 gcc_4:4.4.4-2+powerpcspe1 gcc-4.4_4.4.4-4+powerpcspe4.5 gcc-4.4-base_4.4.4-4+powerpcspe4.5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4+b100 gpgv_1.4.10-4+b100 grep_2.6.3-3+b110 groff-base_1.20.1-10+b100 gzip_1.3.12-9+b110 hostname_3.04+b110 html2text_1.3.2a-15+b100 inits!
cripts_2.88dsf-12 insserv_1.14.0-2+b100 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2+b110 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.1-2+powerpcspe1 libc-dev-bin_2.11.1-2+powerpcspe1 libc6_2.11.1-2+powerpcspe1 libc6-dev_2.11.1-2+powerpcspe1 libcomerr2_1.41.12-2+b100 libcroco3_0.6.2-1+b100 libdb4.7_4.7.25-9+powerpcspe1 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-3 libdpkg-perl_1.15.8.5 libgcc1_1:4.4.4-4+powerpcspe4.5 libgdbm3_1.8.3-9+b110 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1+b3 libgomp1_4.4.4-4+powerpcspe4.5 liblocale-gettext-perl_1.05-6+b110 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3+b2 libmudflap0_4.4.4-4+powerpcspe4.5 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline5_5.2-7+b100 libreadline6_6.1-3+b100 libselinux1_2.0.96-1 libsepol1_2.0.41-1+b110 libslang2_2.2.2-4!
+b100 libss2_1.41.12-2+b100 libstdc++6_4.4.4-4+powerpcspe4.5 libstdc++
-6-4.4-dev_4.4.4-4+powerpcspe4.5 libtext-charwidth-perl_0.04-6+b110 libtext-iconv-perl_1.7-2+b110 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_163-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4+b1 linux-libc-dev_2.6.32-13+powerpcspe1 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14+b100 make_3.81-8+b1 makedev_2.3.1-89 man-db_2.5.7-6 mawk_1.3.3-15+b111 mktemp_8.5-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 procps_1:3.2.8-9+b100 readline-common_6.1-3 sed_4.2.1-7+b111 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3+b110 zlib1g-dev_1:1.2.3.4.dfsg-3+b110
+6-4.4-dev_4.4.4-4+powerpcspe4.5 libtext-charwidth-perl_0.04-6+b110 libtext-iconv-perl_1.7-2+b110 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_163-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-13+powerpcspe1 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14+b100 make_3.81-8+b1 makedev_2.3.1-89 man-db_2.5.7-6 mawk_1.3.3-15+b111 mktemp_8.5-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9+b100 readline-common_6.1-3 sed_4.2.1-7+b111 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3+b110 zlib1g-dev_1:1.2.3.4.dfsg-3+b110
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -197,12 +201,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/var/lib/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -217,25 +221,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture powerpcspe
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/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_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/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_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -243,8 +247,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -268,9 +272,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -281,10 +286,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -297,27 +302,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -327,14 +333,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -358,11 +364,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/sa
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -394,8 +401,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -419,7 +426,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -434,27 +441,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_powerpcspe.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_powerpcspe.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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_powerpcspe.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_powerpcspe.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1716
+Build finished at 20101118-1641
-samtools_0.1.9-1_powerpcspe.changes:
+samtools_0.1.10-1_powerpcspe.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpcspe
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
Maintainer: powerpcspe Build Daemon (baako) <baako at breakpoint...>
@@ -463,42 +470,36 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 7db686c6dd92cd738b3c537a0a401b6300b7bf2a 585514 samtools_0.1.9-1_powerpcspe.deb
- 2bc7a213a504cf45b91aa6f307e62c1b6754aa29 158602 libbam-dev_0.1.9-1_powerpcspe.deb
+ c4f1431d843d098b4fd19e1c7397ccb572edc516 600110 samtools_0.1.10-1_powerpcspe.deb
+ cbb42a446f3c7595f902a9aaac0fd520c56898a4 166310 libbam-dev_0.1.10-1_powerpcspe.deb
Checksums-Sha256:
- 94fb1def1fc6632e6f16903e29f8d643119381181fb06d3545f94dcfeadf01ed 585514 samtools_0.1.9-1_powerpcspe.deb
- e79a6eead202f012692e263401df70f0f8ccd2011b88e9c2be1c72fad73b0894 158602 libbam-dev_0.1.9-1_powerpcspe.deb
+ ea16d571f3fe7af2465987d5f350e2496b34270b322dbac0d884aeeab72dcd86 600110 samtools_0.1.10-1_powerpcspe.deb
+ c6b176f35b08b282f677af2c95c6f2b73deb512f5e9aee445b463c37a8674acb 166310 libbam-dev_0.1.10-1_powerpcspe.deb
Files:
- dcc6528995fcf65a3027d4d663b6e24e 585514 science optional samtools_0.1.9-1_powerpcspe.deb
- a2a2c2a60c51c90d2b5e2ffa5228bf89 158602 libdevel optional libbam-dev_0.1.9-1_powerpcspe.deb
+ a635ecd3626ac563933ab62caf55989f 600110 science optional samtools_0.1.10-1_powerpcspe.deb
+ 6d392128f0107d0946a0ea87538b519c 166310 libdevel optional libbam-dev_0.1.10-1_powerpcspe.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_powerpcspe.deb
-───────────────────────────────
+samtools_0.1.10-1_powerpcspe.deb
+────────────────────────────────
new debian package, version 2.0.
- size 585514 bytes: control archive= 1799 bytes.
- 797 bytes, 16 lines control
+ size 600110 bytes: control archive= 1800 bytes.
+ 798 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: powerpcspe
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1016
+ Installed-Size: 1040
Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -511,72 +512,72 @@ samtools_0.1.9-1_powerpcspe.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 2010-11-01 17:16 ./
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/bin/
--rwxr-xr-x root/root 319204 2010-11-01 17:16 ./usr/bin/samtools
--rwxr-xr-x root/root 104992 2010-11-01 17:16 ./usr/bin/bcftools
--rwxr-xr-x root/root 23988 2010-11-01 17:16 ./usr/bin/razip
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/lib/samtools/
--rwxr-xr-x root/root 36448 2010-11-01 17:16 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7536 2010-11-01 17:16 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 10384 2010-11-01 17:16 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6736 2010-11-01 17:16 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 6736 2010-11-01 17:16 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/samtools/
--rwxr-xr-x root/root 2696 2010-07-12 04:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 04:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 04:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 3224 2010-10-28 04:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 5989 2010-07-12 04:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 04:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2397 2010-07-12 04:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 04:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2415 2010-07-12 04:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 04:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2010-11-01 17:16 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2729 2010-07-12 04:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 13005 2010-10-28 04:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 13410 2010-10-28 04:48 ./usr/share/samtools/samtools.pl
-drwxr-xr-x root/root 0 2010-11-01 17:15 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/man/man1/
--rw-r--r-- root/root 7265 2010-11-01 17:15 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-11-01 17:15 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-11-01 17:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/doc/samtools/
--rw-r--r-- root/root 5646 2010-10-28 04:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 4814 2010-11-01 12:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2010-07-13 14:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 27497 2010-10-28 04:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2010-07-12 04:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2010-07-15 03:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 994 2010-11-01 12:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 764 2010-10-28 04:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-01 17:12 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-07-12 04:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-10-28 04:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-07-12 04:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 04:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 1966 2010-11-01 17:16 ./usr/share/doc/samtools/README.bcftools
-lrwxrwxrwx root/root 0 2010-11-01 17:16 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_powerpcspe.deb
-─────────────────────────────────
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/bin/
+-rwxr-xr-x root/root 340180 2010-11-18 16:41 ./usr/bin/samtools
+-rwxr-xr-x root/root 105972 2010-11-18 16:41 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23988 2010-11-18 16:41 ./usr/bin/razip
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/lib/samtools/
+-rwxr-xr-x root/root 36448 2010-11-18 16:41 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7536 2010-11-18 16:41 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 10384 2010-11-18 16:41 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6736 2010-11-18 16:41 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 6736 2010-11-18 16:41 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/samtools/
+-rwxr-xr-x root/root 2696 2010-11-17 05:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 05:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 05:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 3224 2010-11-17 05:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 5989 2010-11-17 05:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 05:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2397 2010-11-17 05:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 05:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 05:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 15255 2010-11-17 05:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-18 16:41 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2729 2010-11-17 05:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 11934 2010-11-17 05:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 14299 2010-11-17 05:16 ./usr/share/samtools/samtools.pl
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/man/man1/
+-rw-r--r-- root/root 7544 2010-11-18 16:41 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-11-18 16:41 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-11-18 16:40 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 6101 2010-11-17 05:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 4925 2010-11-17 12:27 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2010-11-17 12:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 29821 2010-11-17 05:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2010-11-17 12:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1008 2010-11-17 12:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 764 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-18 16:37 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 886 2010-11-17 05:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 1966 2010-11-18 16:41 ./usr/share/doc/samtools/README.bcftools
+lrwxrwxrwx root/root 0 2010-11-18 16:41 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_powerpcspe.deb
+──────────────────────────────────
new debian package, version 2.0.
- size 158602 bytes: control archive= 904 bytes.
- 678 bytes, 15 lines control
+ size 166310 bytes: control archive= 908 bytes.
+ 679 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: powerpcspe
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 376
+ Installed-Size: 388
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -587,23 +588,23 @@ libbam-dev_0.1.9-1_powerpcspe.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/include/
--rw-r--r-- root/root 3188 2010-07-12 04:41 ./usr/include/faidx.h
--rw-r--r-- root/root 16522 2010-07-12 04:41 ./usr/include/khash.h
--rw-r--r-- root/root 24002 2010-10-28 04:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 04:41 ./usr/include/bgzf.h
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/lib/
--rw-r--r-- root/root 237348 2010-11-01 17:16 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 5646 2010-10-28 04:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 4814 2010-11-01 12:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 04:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-07-12 04:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 994 2010-11-01 12:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/include/
+-rw-r--r-- root/root 3188 2010-11-17 05:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 16522 2010-11-17 05:16 ./usr/include/khash.h
+-rw-r--r-- root/root 24124 2010-11-17 05:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 05:16 ./usr/include/bgzf.h
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/lib/
+-rw-r--r-- root/root 245266 2010-11-18 16:41 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 6101 2010-11-17 05:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 4925 2010-11-17 12:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 05:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 1008 2010-11-17 12:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -612,7 +613,7 @@ drwxr-xr-x root/root 0 2010-11-01 17:16 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/spestage-66d46ce3-ace3-4b09-a4f1-2c96c3a0f48a/spestage/build/buildd-samtools_0.1.9-1-powerpcspe-OGYW7x
+Purging /var/lib/schroot/mount/spestage-cf4674fc-a146-42b9-b7a0-74ac784f424b/spestage/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX
(Reading database ... 12556 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
@@ -644,8 +645,8 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1716
-Build needed 00:05:47, 8688k disc space
+Finished at 20101118-1641
+Build needed 00:05:59, 8952k disc space
</pre>
<p>
diff --git a/s390.build b/s390.build
index a956a71..6e1ebe2 100644
--- a/s390.build
+++ b/s390.build
@@ -1,49 +1,42 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/s390 received Mon Nov 1 11:22:46 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=s390">s390</a> >> Mon Nov 1 11:22:46 2010<pre>
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/s390 received Wed Nov 17 11:54:41 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=s390">s390</a> >> Wed Nov 17 11:54:41 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on lxdebian.bfinv.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (s390) 01 Nov 2010 12:21 ║
+║ samtools 0.1.10-1 (s390) 17 Nov 2010 12:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: s390
-Chroot Build Dir: /var/lib/schroot/mount/sid-s390-buildd-c212120c-8742-4636-8c13-7745dc25c1fc/build/buildd-samtools_0.1.9-1-s390-DHkzkU
-Start Time: 20101101-1221
-Get:1 http://ftp.de.debian.org sid Release.gpg [835 B]
+Chroot Build Dir: /var/lib/schroot/mount/sid-s390-buildd-777088bb-9547-42ca-a22d-302a22e300ea/build/buildd-samtools_0.1.10-1-s390-EQyK8C
+Start Time: 20101117-1253
+Hit http://ftp.de.debian.org sid Release.gpg
Ign http://ftp.de.debian.org/debian/ sid/contrib Translation-en
Ign http://ftp.de.debian.org/debian/ sid/main Translation-en
Ign http://ftp.de.debian.org/debian/ sid/non-free Translation-en
-Get:2 http://ftp.de.debian.org sid Release [104 kB]
+Hit http://ftp.de.debian.org sid Release
+Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid Release.gpg
Ign http://incoming.debian.org/debian/ sid/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/main Translation-en
-Get:3 http://ftp.de.debian.org sid/main Sources/DiffIndex [2038 B]
Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Get:4 http://incoming.debian.org Release.gpg [835 B]
+Hit http://incoming.debian.org Release.gpg
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Hit http://incoming.debian.org sid Release
Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Get:5 http://ftp.de.debian.org sid/main s390 Packages/DiffIndex [2038 B]
+Hit http://ftp.de.debian.org sid/main s390 Packages/DiffIndex
Hit http://ftp.de.debian.org sid/contrib s390 Packages/DiffIndex
Hit http://ftp.de.debian.org sid/non-free s390 Packages/DiffIndex
-Get:6 http://incoming.debian.org Release [1604 B]
-Get:7 http://ftp.de.debian.org sid/main 2010-11-01-0808.15.pdiff [1358 B]
-Get:8 http://ftp.de.debian.org sid/main s390 2010-11-01-0808.15.pdiff [630 B]
-Get:9 http://ftp.de.debian.org sid/main 2010-11-01-0808.15.pdiff [1358 B]
-Get:10 http://ftp.de.debian.org sid/main s390 2010-11-01-0808.15.pdiff [630 B]
-Get:11 http://ftp.de.debian.org sid/main 2010-11-01-0808.15.pdiff [1358 B]
+Hit http://incoming.debian.org sid Release
+Hit http://incoming.debian.org Release
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 s390 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib s390 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free s390 Packages/DiffIndex
-Get:12 http://ftp.de.debian.org sid/main s390 2010-11-01-0808.15.pdiff [630 B]
-Get:13 http://incoming.debian.org Sources [11.5 kB]
-Get:14 http://incoming.debian.org Packages [200 kB]
-Fetched 325 kB in 5s (55.6 kB/s)
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -64,11 +57,11 @@ 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 358 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 1s (324 kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 1s (347 kB/s)
Download complete and in download only mode
Check arch
@@ -82,38 +75,100 @@ Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: already installed (8.0.0 >= 7 is satisfied)
+debhelper: missing
+Using default version 8.0.0
cdbs: missing
libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev
+Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following extra packages will be installed:
+ bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
- devscripts doc-base
+ wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
+ groff less www-browser libmail-box-perl
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev
+ bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 2 newly installed, 0 to remove and 21 not upgraded.
-Need to get 0 B/2874 kB of archives.
-After this operation, 8507 kB of additional disk space will be used.
+0 upgraded, 19 newly installed, 0 to remove and 23 not upgraded.
+Need to get 0 B/11.8 MB of archives.
+After this operation, 35.7 MB of additional disk space will be used.
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10966 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_s390.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.20.1-10_s390.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-6_s390.deb) ...
+Selecting previously deselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.04-5_s390.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../archives/file_5.04-5_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_8.02-1.1_s390.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_s390.deb) ...
+Selecting previously deselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
+Selecting previously deselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_s390.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_s390.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_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_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 25914 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_s390.deb) ...
-Processing triggers for man-db ...
+Selecting previously deselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
+Setting up bsdmainutils (8.0.16) ...
+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 (1.20.1-10) ...
+Setting up man-db (2.5.7-6) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libpcre3 (8.02-1.1) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libunistring0 (0.9.3-3) ...
+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 (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-5 g++-4.4_4.4.5-5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-5 libstdc++6_4.4.5-5
-Package versions: apt_0.8.7 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 cdebootstrap-helper-rc.d_1 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.3_4.3.5-4 cpp-4.4_4.4.5-5 dash_0.5.5.1-7 debconf_1.5.36 debconf-english_1.5.36 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diff_1:3.0-1 diffutils_1:3.0-1 dmsetup_2:1.02.48-3 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.5-1 g++-4.3_4.3.5-4 g++-4.4_4.4.5-5 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.3_4.3.5-4 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-5 gcc-4.4-base_4.4.5-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libasound2_1.0.23-2.1 libasyncns0_0.3-1 libattr1_1:2.4.44-2 libaudio2_1.9.2-3 libblkid1_2.17.2-3.3 libboost-date-time-dev_1.42.0.1 libboost-date-time1.42-dev_1.42.0-4 libboost-date-time1.42.0_1.42.0-4 libboost-dev_1.42.0.1 libboost-filesystem-dev_1.42.0.1 libboost-filesystem1.42-dev_1.42.0-4 libboost-filesystem1.42.0_1.42.0-4 libboost-serialization1.42-dev_1.42.0-4 libboost-serialization1.42.0_1.42.0-4 libboost-system-dev_1.42.0.1 libboost-system1.42-dev_1.42.0-4 libboost-system1.42.0_1.42.0-4 libboost-thread-dev_1.42.0.1 libboost-thread1.42-dev_1.42.0-4 libboost-thread1.42.0_1.42.0-4 libboost1.42-dev_1.42.0-4 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcap2_1:2.19-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.6_4.6.21-16 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdbus-1-3_1.2.24-3 libdevmapper1.02.1_2:1.02.48-3 libdpkg-perl_1.15.8.5 libexpat1_2.0.1-7 libflac8_1.2.1-3 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.2-2 libgcc1_1:4.4.5-5 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libgeoip-dev_1.4.7~beta6+dfsg-1 libgeoip1_1.4.7~beta6+dfsg-1 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-5 libgpg-error0_1.6-1 libice6_2:1.0.6-2 libicu44_4.4.2-1 libjpeg62_6b1-1 liblcms1_1.18.dfsg-1.2+b3 libldap-2.4-2_2.4.23-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmng1_1.0.10-1+b1 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libogg0_1.2.0~dfsg-1 libopencdk10_0.6.6-1 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libphonon4_4:4.6.0really4.4.2-1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpulse-mainloop-glib0_0.9.21-3 libpulse0_0.9.21-3 libqt4-assistant_4:4.6.3-4 libqt4-dbus_4:4.6.3-4 libqt4-designer_4:4.6.3-4 libqt4-dev_4:4.6.3-4 libqt4-help_4:4.6.3-4 libqt4-multimedia_4:4.6.3-4 libqt4-network_4:4.6.3-4 libqt4-qt3support_4:4.6.3-4 libqt4-script_4:4.6.3-4 libqt4-scripttools_4:4.6.3-4 libqt4-sql_4:4.6.3-4 libqt4-svg_4:4.6.3-4 libqt4-test_4:4.6.3-4 libqt4-webkit_4:4.6.3-4 libqt4-xml_4:4.6.3-4 libqt4-xmlpatterns_4:4.6.3-4 libqtcore4_4:4.6.3-4 libqtgui4_4:4.6.3-4 libreadline5_5.2-7 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libsm6_2:1.1.1-1 libsndfile1_1.0.23-1 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libssl-dev_0.9.8o-2 libssl0.9.8_0.9.8o-2 libstdc++6_4.4.5-5 libstdc++6-4.3-dev_4.3.5-4 libstdc++6-4.4-dev_4.4.5-5 libtasn1-3_2.7-1 libtiff4_3.9.4-5 libtimedate-perl_1.2000-1 libtorrent-rasterbar-dev_0.14.10-2+b1 libtorrent-rasterbar5_0.14.10-2+b1 libudev0_164-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libvorbis0a_1.3.1-1 libvorbisenc2_1.3.1-1 libwrap0_7.6.q-19 libx11-6_2:1.3.3-3 libx11-data_2:1.3.3-3 libxau6_1:1.0.6-1 libxcb1_1.6-1 libxdmcp6_1:1.0.3-2 libxext6_2:1.1.2-1 libxi6_2:1.3-4 libxml2_2.7.7.dfsg-4 libxrender1_1:0.9.6-1 libxt6_1:1.0.7-1 libxtst6_2:1.1.0-3 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-25 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mktemp_8.5-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 pkg-config_0.25-1.1 po-debconf_1.0.16 qt4-qmake_4:4.6.3-4 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-dejavu-core_2.31-1 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.17.2-3.3 x11-common_1:7.5+8 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-7 g++-4.4_4.4.5-7 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-7 libstdc++6_4.4.5-7
+Package versions: apt_0.8.8 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 cdebootstrap-helper-rc.d_1 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.3_4.3.5-4 cpp-4.4_4.4.5-7 dash_0.5.5.1-7.2 debconf_1.5.36 debconf-english_1.5.36 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diff_1:3.0-1 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.3_4.3.5-4 g++-4.4_4.4.5-7 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.3_4.3.5-4 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-7 gcc-4.4-base_4.4.5-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.6_4.6.21-16 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.5 libgcc1_1:4.4.5-7 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-7 libgpg-error0_1.6-1 libldap-2.4-2_2.4.23-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libopencdk10_0.6.6-1 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libreadline5_5.2-7 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-7 libstdc++6-4.3-dev_4.3.5-4 libstdc++6-4.4-dev_4.4.5-7 libtasn1-3_2.7-1 libtimedate-perl_1.2000-1 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-27 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mktemp_8.5-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.24-1 tzdata_2010o-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -125,12 +180,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/srv/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -145,25 +200,25 @@ 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 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture s390
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/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_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/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_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -171,8 +226,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -190,9 +245,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -203,10 +259,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -219,27 +275,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -249,14 +306,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-s390-DHkzkU/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -280,11 +337,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -316,8 +374,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -341,7 +399,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-s390-DHkzkU/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -356,27 +414,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_s390.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_s390.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1222
+Build finished at 20101117-1254
-samtools_0.1.9-1_s390.changes:
+samtools_0.1.10-1_s390.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
Maintainer: s390 Build Daemon <buildd_s390-lxdebian at buildd...>
@@ -385,42 +443,36 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- a80ce6e7cbbe339cb69ee4b5706cd787fd178063 560952 samtools_0.1.9-1_s390.deb
- 5ad14751d409b07d11c3b8875b01f7649513ab00 163204 libbam-dev_0.1.9-1_s390.deb
+ 3545d36c6f22e6aa8d8c020440d5c0142bf97483 576734 samtools_0.1.10-1_s390.deb
+ 45cae76a9077521cf580b945cfb6777cc75bd522 170246 libbam-dev_0.1.10-1_s390.deb
Checksums-Sha256:
- 3e1d8b2ef433bf007b529a2259d25bcf9ba23d6d2dfd665f5317f4ad11281a7f 560952 samtools_0.1.9-1_s390.deb
- 752a65858aa6123502a2f2d1d8257fed8684d28c44d5c8a01f0c0dac695f9273 163204 libbam-dev_0.1.9-1_s390.deb
+ dec401782b35283d8d15d305eaee85b4aa499cbb09debbed2caf5f498398f99c 576734 samtools_0.1.10-1_s390.deb
+ fe780b1ce5e070dc1924672ce72fc3479ac3d3b4572cc465c2a38912f23415f7 170246 libbam-dev_0.1.10-1_s390.deb
Files:
- 34ff6bcd0606886189d3ce877a349495 560952 science optional samtools_0.1.9-1_s390.deb
- b82769bf2dc551911fc9e5f84789d7e6 163204 libdevel optional libbam-dev_0.1.9-1_s390.deb
+ 0ea7c7f733c9ab9063f1bebcda25a28a 576734 science optional samtools_0.1.10-1_s390.deb
+ b66bdbe36bd5b0016dade99af3e165b9 170246 libdevel optional libbam-dev_0.1.10-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_s390.deb
-─────────────────────────
+samtools_0.1.10-1_s390.deb
+──────────────────────────
new debian package, version 2.0.
- size 560952 bytes: control archive= 1785 bytes.
- 790 bytes, 16 lines control
+ size 576734 bytes: control archive= 1790 bytes.
+ 791 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1004
+ Installed-Size: 1028
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -433,72 +485,72 @@ samtools_0.1.9-1_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 2010-11-01 12:22 ./
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-07-12 04:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2010-07-13 14:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-07-15 03:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 4814 2010-11-01 12:00 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-07-12 04:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 04:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-07-12 04:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-10-28 04:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-10-28 04:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-01 12:22 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 27497 2010-10-28 04:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-11-01 12:22 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5646 2010-10-28 04:48 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 12:06 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-01 12:22 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-01 12:22 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/samtools/
--rwxr-xr-x root/root 3224 2010-10-28 04:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 13005 2010-10-28 04:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-07-12 04:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 04:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-07-12 04:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-07-12 04:41 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-07-12 04:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 04:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 04:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13410 2010-10-28 04:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-07-12 04:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-07-12 04:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-07-12 04:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2010-11-01 12:22 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/bin/
--rwxr-xr-x root/root 92244 2010-11-01 12:22 ./usr/bin/bcftools
--rwxr-xr-x root/root 27252 2010-11-01 12:22 ./usr/bin/razip
--rwxr-xr-x root/root 331132 2010-11-01 12:22 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/lib/samtools/
--rwxr-xr-x root/root 18572 2010-11-01 12:22 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7188 2010-11-01 12:22 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7188 2010-11-01 12:22 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11324 2010-11-01 12:22 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7932 2010-11-01 12:22 ./usr/lib/samtools/md5sum-lite
-lrwxrwxrwx root/root 0 2010-11-01 12:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_s390.deb
-───────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2010-11-17 12:21 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-11-17 12:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4925 2010-11-17 12:27 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2010-11-17 05:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 764 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2010-11-17 12:54 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 29821 2010-11-17 05:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-11-17 12:54 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6101 2010-11-17 05:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 12:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-11-17 12:54 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7544 2010-11-17 12:54 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/samtools/
+-rwxr-xr-x root/root 3224 2010-11-17 05:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 11934 2010-11-17 05:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 05:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 05:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 15255 2010-11-17 05:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 05:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 05:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 05:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 05:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 05:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 05:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 05:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 05:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2010-11-17 12:54 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/bin/
+-rwxr-xr-x root/root 92244 2010-11-17 12:54 ./usr/bin/bcftools
+-rwxr-xr-x root/root 27252 2010-11-17 12:54 ./usr/bin/razip
+-rwxr-xr-x root/root 354320 2010-11-17 12:54 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18572 2010-11-17 12:54 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7188 2010-11-17 12:54 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7188 2010-11-17 12:54 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11324 2010-11-17 12:54 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7932 2010-11-17 12:54 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2010-11-17 12:54 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_s390.deb
+────────────────────────────
new debian package, version 2.0.
- size 163204 bytes: control archive= 895 bytes.
- 672 bytes, 15 lines control
+ size 170246 bytes: control archive= 891 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 388
+ Installed-Size: 400
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -509,23 +561,23 @@ libbam-dev_0.1.9-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-07-12 04:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 4814 2010-11-01 12:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 27497 2010-10-28 04:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5646 2010-10-28 04:48 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 994 2010-11-01 12:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/lib/
--rw-r--r-- root/root 249628 2010-11-01 12:22 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/include/
--rw-r--r-- root/root 24002 2010-10-28 04:48 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-07-12 04:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 04:41 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-07-12 04:41 ./usr/include/faidx.h
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 4925 2010-11-17 12:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 29821 2010-11-17 05:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6101 2010-11-17 05:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1008 2010-11-17 12:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/lib/
+-rw-r--r-- root/root 256626 2010-11-17 12:54 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/include/
+-rw-r--r-- root/root 24124 2010-11-17 05:16 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 05:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 16522 2010-11-17 05:16 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 05:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -534,13 +586,39 @@ drwxr-xr-x root/root 0 2010-11-01 12:22 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390-buildd-c212120c-8742-4636-8c13-7745dc25c1fc/build/buildd-samtools_0.1.9-1-s390-DHkzkU
-(Reading database ... 27023 files and directories currently installed.)
-Removing libncurses5-dev ...
+Purging /var/lib/schroot/mount/sid-s390-buildd-777088bb-9547-42ca-a22d-302a22e300ea/build/buildd-samtools_0.1.10-1-s390-EQyK8C
+(Reading database ... 13343 files and directories currently installed.)
+Removing zlib1g-dev ...
Removing cdbs ...
-Processing triggers for man-db ...
+Removing debhelper ...
+Removing po-debconf ...
+Removing libncurses5-dev ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing intltool-debian ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing gettext ...
+Removing file ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing gettext-base ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1222
-Build needed 00:00:51, 8912k disc space
+Finished at 20101117-1254
+Build needed 00:00:57, 9196k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/sh4.build b/sh4.build
index ef4bfe6..855bc6f 100644
--- a/sh4.build
+++ b/sh4.build
@@ -1,37 +1,42 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>File `log' in samtools_0.1.9-1_sh4 (Nov 1 16:48)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
-<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.9-1_sh4 (Nov 1 16:48)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=sh4">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=sh4">0.1.9-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=sh4&stamp=1288630080">Nov 1 16:48</a> >> log</td></tr></table><p><pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on localhost
+<html><head><title>File `log' in samtools_0.1.10-1_sh4 (Nov 17 16:57)</title><meta http-equiv="content-type" content="text/html;charset=utf-8"></head><body bgcolor="#ffffff">
+<table width="100%"><tr valign=top><td align=left><h2>File `log' in samtools_0.1.10-1_sh4 (Nov 17 16:57)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=sh4">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.10-1&arch=sh4">0.1.10-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.10-1&arch=sh4&stamp=1290013077">Nov 17 16:57</a> >> log</td></tr></table><p><pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on nagato
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (sh4) 02 Nov 2010 00:28 ║
+║ samtools 0.1.10-1 (sh4) 17 Nov 2010 15:32 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: sh4
-Chroot Build Dir: /srv/chroot/sid/build/buildd-samtools_0.1.9-1-sh4-ymPrBP
-Start Time: 20101102-0028
-Get:1 http://incoming.debian-ports.org unstable Release.gpg [835B]
-Get:2 http://ftp.debian-ports.org unstable Release.gpg [835B]
+Chroot Build Dir: /srv/chroot/sid/build/buildd-samtools_0.1.10-1-sh4-we5E9N
+Start Time: 20101117-1532
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+Get:1 http://incoming.debian-ports.org unstable Release.gpg [835 B]
+Hit http://ftp.debian-ports.org unstable Release.gpg
Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
-Get:3 http://ftp.debian.org unstable Release.gpg [835B]
Ign http://ftp.debian-ports.org/debian/ unstable/main Translation-en
-Get:4 http://ftp.debian-ports.org unreleased Release.gpg [835B]
+Hit http://ftp.debian.org unstable Release.gpg
+Hit http://ftp.debian-ports.org unreleased Release.gpg
Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-Get:5 http://incoming.debian-ports.org unstable Release [8817B]
-Get:6 http://ftp.debian-ports.org unstable Release [15.4kB]
-Get:7 http://ftp.debian.org unstable Release [104kB]
-Get:8 http://ftp.debian-ports.org unreleased Release [17.4kB]
+Get:2 http://incoming.debian-ports.org unstable Release [8817 B]
+Hit http://ftp.debian-ports.org unstable Release
+Hit http://ftp.debian.org unstable Release
+Hit http://ftp.debian-ports.org unreleased Release
+Hit http://ftp.debian.org unstable/main Sources/DiffIndex
+Hit http://ftp.debian-ports.org unstable/main sh4 Packages
Hit http://incoming.debian-ports.org unstable/main Sources
-Get:9 http://ftp.debian-ports.org unstable/main sh4 Packages [6663kB]
-Hit http://incoming.debian-ports.org unstable/main sh4 Packages
-Get:10 http://ftp.debian.org unstable/main Sources/DiffIndex [2038B]
-Get:11 http://ftp.debian.org unstable/main 2010-11-01-1409.21.pdiff [3126B]
-Get:12 http://ftp.debian.org unstable/main 2010-11-01-1409.21.pdiff [3126B]
-Get:13 http://ftp.debian.org unstable/main 2010-11-01-1409.21.pdiff [3126B]
Hit http://ftp.debian-ports.org unreleased/main sh4 Packages
-Fetched 6818kB in 1min 48s (62.7kB/s)
+Get:3 http://incoming.debian-ports.org unstable/main sh4 Packages [7227 B]
+Fetched 16.9 kB in 5s (2968 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -43,20 +48,28 @@ Check APT
─────────
Checking available source versions...
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Download source files with APT
──────────────────────────────
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 358kB of source archives.
-Get:1 http://ftp.debian.org/debian/ unstable/main samtools 0.1.9-1 (dsc) [1932B]
-Get:2 http://ftp.debian.org/debian/ unstable/main samtools 0.1.9-1 (tar) [350kB]
-Get:3 http://ftp.debian.org/debian/ unstable/main samtools 0.1.9-1 (diff) [6264B]
-Fetched 358kB in 2s (121kB/s)
+Need to get 361 kB of source archives.
+Get:1 http://ftp.debian.org/debian/ unstable/main samtools 0.1.10-1 (dsc) [1939 B]
+Get:2 http://ftp.debian.org/debian/ unstable/main samtools 0.1.10-1 (tar) [353 kB]
+Get:3 http://ftp.debian.org/debian/ unstable/main samtools 0.1.10-1 (diff) [6332 B]
+Fetched 361 kB in 2s (124 kB/s)
Download complete and in download only mode
Check arch
@@ -64,92 +77,80 @@ Check arch
** Using build dependencies supplied by package:
Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
-N: Can't select versions from package 'libc-dev' as it purely virtual
-N: Can't select versions from package 'awk' as it purely virtual
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.0.0
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+debhelper: already installed (8.0.0 >= 7 is satisfied)
cdbs: missing
libncurses5-dev: missing
-zlib1g-dev: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for source dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+Installing positive dependencies: cdbs libncurses5-dev
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Reading package lists...
Building dependency tree...
Reading state information...
-The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
- libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc libmail-box-perl
+ devscripts doc-base
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 file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2 po-debconf
- zlib1g-dev
+ cdbs libncurses5-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 15 newly installed, 0 to remove and 43 not upgraded.
-Need to get 0B/8925kB of archives.
-After this operation, 27.2MB of additional disk space will be used.
-Selecting previously deselected package libmagic1.
-(Reading database ... 13953 files and directories currently installed.)
-Unpacking libmagic1 (from .../libmagic1_5.04-5_sh4.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_sh4.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sh4.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_sh4.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_sh4.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_sh4.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sh4.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_sh4.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_sh4.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_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
+0 upgraded, 2 newly installed, 0 to remove and 18 not upgraded.
+Need to get 0 B/2851 kB of archives.
+After this operation, 8425 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
+(Reading database ... 15524 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_sh4.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sh4.deb) ...
Processing triggers for man-db ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
-Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
Kernel: Linux 2.6.33.5-00003-g0ef7fb0-dirty sh4 (sh4a)
-Toolchain package versions: libc6-dev_2.11.2-2 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-21 gcc-4.4_4.4.5-5 g++-4.4_4.4.5-5 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-5 libstdc++6_4.4.5-5
-Package versions: apt_0.8.0 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.89 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.4-2 cpp-4.4_4.4.5-5 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4 diffutils_1:3.0-1 dmsetup_2:1.02.48-3 dpkg_1.15.8.4 dpkg-dev_1.15.8.4 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.5-5 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.4-2 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-5 gcc-4.4-base_4.4.5-5 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-2 libc-dev-bin_2.11.2-2 libc6_2.11.2-2 libc6-dev_2.11.2-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.1-1 libdb4.6_4.6.21-16 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-3 libdpkg-perl_1.15.8.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-5 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-5 libgpg-error0_1.6-1 libgssapi-krb5-2_1.8.3+dfsg-2 libidn11_1.18-1 libk5crypto3_1.8.3+dfsg-2 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-2 libkrb5support0_1.8.3+dfsg-2 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libnewt0.52_0.52.11-1 libpam-modules_1.1.1-4 libpam-runtime_1.1.1-4 libpam0g_1.1.1-6 libpci3_1:3.1.7-5 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsasl2-modules_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libssl0.9.8_0.9.8o-2 libstdc++6_4.4.5-5 libstdc++6-4.4-dev_4.4.5-5 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_161-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libvolume-id1_0.141-1 libwrap0_7.6.q-19 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-21 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-4 manpages_3.25-1 manpages-dev_3.25-1 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 openssl_0.9.8o-2 passwd_1:4.1.4.2-1 patch_2.6-2 pciutils_1:3.1.7-5 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16 procps_1:3.2.8-9 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-2.1 tzdata_2010m-1 udev_161-1 usbutils_0.87-5 util-linux_2.17.2-3.1 wget_1.12-2 whiptail_0.52.11-1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-6 g++-4.4_4.4.5-6 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-6 libstdc++6_4.4.5-6
+Package versions: apt_0.8.8 autoconf_2.67-2 autoconf2.59_2.59-1 autogen_1:5.10-1.1 automake1.9_1.9.6+nogfdl-3.1 autotools-dev_20100122.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bison_1:2.4.1.dfsg-3 bsdmainutils_8.0.15 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.89 chrpath_0.13-2 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-6 dash_0.5.5.1-7.2 debconf_1.5.36 debconf-i18n_1.5.36 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 dejagnu_1.4.4.git20080407-1.1 diff_1:3.0-1 diffstat_1.53-1 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 expect_5.44.1.15-4 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 flex_2.5.35-10 g++_4:4.4.5-1 g++-4.4_4.4.5-6 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-6 gcc-4.4-base_4.4.5-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gperf_3.0.3-1 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 guile-1.8-libs_1.8.7+1-3 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libalgorithm-diff-perl_1.19.02-2 libalgorithm-merge-perl_0.08-2 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcloog-ppl-dev_0.15.9-2 libcloog-ppl0_0.15.9-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.2-1 libdb4.6_4.6.21-16 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.5 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-6 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3-dev_2:4.3.2+dfsg-1 libgmp3c2_2:4.3.2+dfsg-1 libgmpxx4ldbl_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-6 libgpg-error0_1.6-1 libgpm2_1.20.4-3.3 libgssapi-krb5-2_1.8.3+dfsg-2 libidn11_1.18-1 libk5crypto3_1.8.3+dfsg-2 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-2 libkrb5support0_1.8.3+dfsg-2 libldap-2.4-2_2.4.23-6 liblocale-gettext-perl_1.05-6 libltdl7_2.2.6b-2 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr-dev_3.0.0-2 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libopts25_1:5.10-1.1 libopts25-dev_1:5.10-1.1 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 libppl-c2_0.10.2-9 libppl0.10-dev_0.10.2-9 libppl7_0.10.2-9 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-6 libsasl2-modules_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libssl0.9.8_0.9.8o-2 libstdc++6_4.4.5-6 libstdc++6-4.4-dev_4.4.5-6 libtasn1-3_2.7-1 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtool_2.2.6b-2 libudev0_164-2 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-27 locales_2.11.2-7 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lsb-release_3.2-26 lzma_4.43-14 m4_1.4.14-3 make_3.81-8 makedev_2.3.1-89 man-db_2.5.7-6 mawk_1.3.3-15 mime-support_3.48-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 netbase_4.43 openssl_0.9.8o-2 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 patchutils_0.3.1-2 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16 procps_1:3.2.8-9 python_2.6.6-3+squeeze1 python-minimal_2.6.6-3+squeeze1 python-support_1.0.11 python2.6_2.6.6-6 python2.6-minimal_2.6.6-6 quilt_0.48-7 readline-common_6.1-3 realpath_1.15 sed_4.2.1-7 sensible-utils_0.0.4 sharutils_1:4.9-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.24-1.1 tcl8.5_8.5.8-2 texinfo_4.13a.dfsg.1-6 tzdata_2010o-1 util-linux_2.17.2-3.3 wget_1.12-2.1 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -159,14 +160,18 @@ Package versions: apt_0.8.0 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutil
Unpack source
─────────────
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -175,31 +180,35 @@ Check disc space
dpkg-buildpackage
─────────────────
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.9-1
- dpkg-source --before-build samtools-0.1.9
+dpkg-buildpackage: source version 0.1.10-1
+ dpkg-source --before-build samtools-0.1.10
dpkg-buildpackage: host architecture sh4
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/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_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/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_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -207,8 +216,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -232,9 +241,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -245,10 +255,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -261,27 +271,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -291,14 +302,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-sh4-ymPrBP/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -322,11 +333,12 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -358,8 +370,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -383,7 +395,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.9-1-sh4-ymPrBP/samtools-0.1.9/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -398,71 +410,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.9-1_sh4.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_sh4.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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.9-1_sh4.deb'.
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_sh4.deb'.
dpkg-genchanges -B
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-0.1.9
+ dpkg-source --after-build samtools-0.1.10
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101102-0139
+Build finished at 20101117-1646
-samtools_0.1.9-1_sh4.changes:
+samtools_0.1.10-1_sh4.changes:
Format: 1.8
-Date: Mon, 01 Nov 2010 20:06:32 +0900
+Date: Wed, 17 Nov 2010 20:32:40 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: sh4
-Version: 0.1.9-1
+Version: 0.1.10-1
Distribution: unstable
Urgency: low
-Maintainer: Debian SH4 buildd <buildd-sh4-hiei at superh...>
+Maintainer: Debian SH4 buildd <buildd-sh4-nagato at superh...>
Changed-By: Charles Plessy <plessy at debian...>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.9-1) unstable; urgency=low
+ samtools (0.1.10-1) unstable; urgency=low
.
- * New upstream release, and new program: bcftools.
- * debian/rules, debian/samtools.install: install bcftools, its manpage,
- and bcf-fix.pl and vcfutils.pl.
- * debian/samtools.examples, debian/rules: install and clean new examples.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Updated and reformatted debian/copyright according to latest DEP-5 draft.
+ * New upstream release.
Checksums-Sha1:
- 038d9d06b54ee9685ceb88f1dd43be83dd708974 572296 samtools_0.1.9-1_sh4.deb
- a6c5e1c7b8305605b2a9c0cb9e06eedd1c260fc3 168672 libbam-dev_0.1.9-1_sh4.deb
+ 1579dfa8869ef1dd1c41f0df52a14d40f282edab 589112 samtools_0.1.10-1_sh4.deb
+ b28db8e9fa96a3c0fd9ec4eaa13319734ec110ee 176392 libbam-dev_0.1.10-1_sh4.deb
Checksums-Sha256:
- b3a4ca749f90b0e412e9dcb24c2cf0cbba5831eb3506cf7054c54d733fba9bf0 572296 samtools_0.1.9-1_sh4.deb
- 93cbf487fa84a285e020ef60922ac7a399c0c77f28a5d53261d05b59714afee5 168672 libbam-dev_0.1.9-1_sh4.deb
+ 334bb25e4fb77f69ea5d061e822618d2f733e0c9f170e071e0eabc3b643f2fa2 589112 samtools_0.1.10-1_sh4.deb
+ 985fa5597a619aa5bdf6c32933c506a31b1ac0d1313db8536d8302024439ac43 176392 libbam-dev_0.1.10-1_sh4.deb
Files:
- 6f8e6b679508e1c427f8abd16bf0414d 572296 science optional samtools_0.1.9-1_sh4.deb
- 296cc364236547582f13c2eb1b032f41 168672 libdevel optional libbam-dev_0.1.9-1_sh4.deb
+ 1e07d7aca17d754ec118507b2c078a36 589112 science optional samtools_0.1.10-1_sh4.deb
+ fba1e26450f9ffc2e50a50e8d9cb05e4 176392 libdevel optional libbam-dev_0.1.10-1_sh4.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.9-1_sh4.deb
-────────────────────────
+samtools_0.1.10-1_sh4.deb
+─────────────────────────
new debian package, version 2.0.
- size 572296 bytes: control archive= 1789 bytes.
- 789 bytes, 16 lines control
+ size 589112 bytes: control archive= 1801 bytes.
+ 790 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: sh4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 960
+ Installed-Size: 984
Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -475,72 +481,72 @@ samtools_0.1.9-1_sh4.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 2010-11-02 01:36 ./
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-02 01:36 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/share/doc/samtools/
--rw-r--r-- root/root 994 2010-11-01 20:06 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-07-12 11:41 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2010-11-02 01:37 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-07-12 11:41 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-07-12 11:41 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2010-11-02 00:49 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 764 2010-10-28 11:48 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2010-10-28 11:48 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2010-07-12 11:41 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 27497 2010-10-28 11:48 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 4814 2010-11-01 20:00 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2010-07-15 10:42 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2010-07-13 21:02 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 5646 2010-10-28 11:48 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/share/samtools/
--rwxr-xr-x root/root 15255 2010-07-12 11:41 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2010-11-02 01:37 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2397 2010-07-12 11:41 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2415 2010-07-12 11:41 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 3224 2010-10-28 11:48 ./usr/share/samtools/bcf-fix.pl
--rwxr-xr-x root/root 13005 2010-10-28 11:48 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2696 2010-07-12 11:41 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 7881 2010-07-12 11:41 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 13410 2010-10-28 11:48 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5989 2010-07-12 11:41 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-07-12 11:41 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2112 2010-07-12 11:41 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2729 2010-07-12 11:41 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 4996 2010-07-12 11:41 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2010-11-02 01:36 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-02 01:36 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7265 2010-11-02 01:36 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/bin/
--rwxr-xr-x root/root 80400 2010-11-02 01:37 ./usr/bin/bcftools
--rwxr-xr-x root/root 24892 2010-11-02 01:37 ./usr/bin/razip
--rwxr-xr-x root/root 297280 2010-11-02 01:37 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/lib/samtools/
--rwxr-xr-x root/root 6864 2010-11-02 01:37 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 16724 2010-11-02 01:37 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6688 2010-11-02 01:37 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9760 2010-11-02 01:37 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6624 2010-11-02 01:37 ./usr/lib/samtools/maq2sam-short
-lrwxrwxrwx root/root 0 2010-11-02 01:37 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.9-1_sh4.deb
-──────────────────────────
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2010-11-17 16:45 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 11934 2010-11-17 04:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.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 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 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+drwxr-xr-x root/root 0 2010-11-17 16:43 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1966 2010-11-17 16:44 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./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 126609 2010-11-17 15:52 ./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 764 2010-11-17 04:16 ./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 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/share/man/man1/
+-rw-r--r-- root/root 7544 2010-11-17 16:44 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-11-17 16:44 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/bin/
+-rwxr-xr-x root/root 318572 2010-11-17 16:45 ./usr/bin/samtools
+-rwxr-xr-x root/root 84068 2010-11-17 16:45 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24892 2010-11-17 16:45 ./usr/bin/razip
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/lib/
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/lib/samtools/
+-rwxr-xr-x root/root 16724 2010-11-17 16:45 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6864 2010-11-17 16:45 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 9760 2010-11-17 16:45 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6624 2010-11-17 16:45 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 6688 2010-11-17 16:45 ./usr/lib/samtools/maq2sam-long
+lrwxrwxrwx root/root 0 2010-11-17 16:44 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.10-1_sh4.deb
+───────────────────────────
new debian package, version 2.0.
- size 168672 bytes: control archive= 900 bytes.
- 671 bytes, 15 lines control
+ size 176392 bytes: control archive= 902 bytes.
+ 672 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.9-1
+ Version: 0.1.10-1
Architecture: sh4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 372
+ Installed-Size: 384
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -551,23 +557,23 @@ libbam-dev_0.1.9-1_sh4.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-02 01:38 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 994 2010-11-01 20:06 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-07-12 11:41 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 27497 2010-10-28 11:48 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 4814 2010-11-01 20:00 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 5646 2010-10-28 11:48 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2010-11-02 01:37 ./usr/include/
--rw-r--r-- root/root 4599 2010-07-12 11:41 ./usr/include/bgzf.h
--rw-r--r-- root/root 16522 2010-07-12 11:41 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-07-12 11:41 ./usr/include/faidx.h
--rw-r--r-- root/root 24002 2010-10-28 11:48 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2010-11-02 01:38 ./usr/lib/
--rw-r--r-- root/root 230860 2010-11-02 01:38 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/share/
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2010-11-17 16:44 ./usr/include/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/lib/
+-rw-r--r-- root/root 238286 2010-11-17 16:45 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -576,33 +582,22 @@ drwxr-xr-x root/root 0 2010-11-02 01:38 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/chroot/sid/build/buildd-samtools_0.1.9-1-sh4-ymPrBP
-(Reading database ... 15834 files and directories currently installed.)
+Purging /srv/chroot/sid/build/buildd-samtools_0.1.10-1-sh4-we5E9N
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+W: line 16 [sid]: Deprecated key 'priority' used
+I: This option will be removed in the future; please update your configuration
+W: line 15 [sid]: Deprecated key 'location' used
+I: This option will be removed in the future; please update your configuration
+(Reading database ... 16624 files and directories currently installed.)
Removing libncurses5-dev ...
-Removing zlib1g-dev ...
Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing file ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101102-0139
-Build needed 01:10:52, 8596k disc space
+Finished at 20101117-1646
+Build needed 01:14:27, 8888k disc space
</pre>
<p>
diff --git a/sparc.build b/sparc.build
index dfa65f0..ee0ba82 100644
--- a/sparc.build
+++ b/sparc.build
@@ -1,36 +1,36 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.9-1/sparc received Mon Nov 1 11:57:35 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1">0.1.9-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.9-1;arch=sparc">sparc</a> >> Mon Nov 1 11:57:35 2010<pre>
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on lebrun.debian.org
+<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/sparc received Wed Nov 17 12:00:33 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=sparc">sparc</a> >> Wed Nov 17 12:00:33 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on spontini.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (sparc) 01 Nov 2010 11:54 ║
+║ samtools 0.1.10-1 (sparc) 17 Nov 2010 11:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.10-1
Architecture: sparc
-Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-7d7863af-7540-42de-bbe5-3676bd980e1d/build/buildd-samtools_0.1.9-1-sparc-VXbPsv
-Start Time: 20101101-1154
-Get:1 http://debian.carnet.hr unstable Release.gpg [835B]
-Get:2 http://incoming.debian.org unstable Release.gpg [835B]
-Get:3 http://incoming.debian.org Release.gpg [835B]
-Get:4 http://debian.carnet.hr unstable Release [104kB]
+Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-ee0cabb2-61cd-481d-a707-e4a6682674d0/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z
+Start Time: 20101117-1153
+Get:1 http://mirrors.ece.ubc.ca unstable Release.gpg [835B]
+Get:2 http://mirrors.ece.ubc.ca unstable Release [104kB]
+Get:3 http://incoming.debian.org unstable Release.gpg [835B]
+Get:4 http://incoming.debian.org Release.gpg [835B]
Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://debian.carnet.hr unstable/main Packages [6707kB]
+Get:6 http://mirrors.ece.ubc.ca unstable/main Packages [6781kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Packages [6707kB]
-Get:9 http://debian.carnet.hr unstable/contrib Packages [51.2kB]
-Get:10 http://debian.carnet.hr unstable/main Sources [4011kB]
-Get:11 http://debian.carnet.hr unstable/contrib Sources [38.7kB]
-Get:12 http://debian.carnet.hr unstable/non-free Sources [81.3kB]
+Get:8 http://incoming.debian.org unstable/main Packages [6781kB]
+Get:9 http://mirrors.ece.ubc.ca unstable/contrib Packages [51.2kB]
+Get:10 http://mirrors.ece.ubc.ca unstable/main Sources [4061kB]
+Get:11 http://mirrors.ece.ubc.ca unstable/contrib Sources [39.0kB]
+Get:12 http://mirrors.ece.ubc.ca unstable/non-free Sources [83.1kB]
Get:13 http://incoming.debian.org unstable/contrib Packages [51.2kB]
-Get:14 http://incoming.debian.org unstable/main Sources [4011kB]
-Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:16 http://incoming.debian.org unstable/non-free Sources [81.3kB]
-Get:17 http://incoming.debian.org Packages [199kB]
-Get:18 http://incoming.debian.org Sources [12.0kB]
-Fetched 22.2MB in 23s (927kB/s)
+Get:14 http://incoming.debian.org unstable/main Sources [4061kB]
+Get:15 http://incoming.debian.org unstable/contrib Sources [39.0kB]
+Get:16 http://incoming.debian.org unstable/non-free Sources [83.1kB]
+Get:17 http://incoming.debian.org Packages [227kB]
+Get:18 http://incoming.debian.org Sources [15.1kB]
+Fetched 22.5MB in 52s (430kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -49,11 +49,11 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-Need to get 358kB of source archives.
-Get:1 http://incoming.debian.org samtools 0.1.9-1 (dsc) [1932B]
-Get:2 http://incoming.debian.org samtools 0.1.9-1 (tar) [350kB]
-Get:3 http://incoming.debian.org samtools 0.1.9-1 (diff) [6264B]
-Fetched 358kB in 1s (262kB/s)
+Need to get 361kB of source archives.
+Get:1 http://incoming.debian.org samtools 0.1.10-1 (dsc) [1939B]
+Get:2 http://incoming.debian.org samtools 0.1.10-1 (tar) [353kB]
+Get:3 http://incoming.debian.org samtools 0.1.10-1 (diff) [6332B]
+Fetched 361kB in 1s (340kB/s)
Download complete and in download only mode
Check arch
@@ -93,43 +93,43 @@ The following NEW packages will be installed:
libunistring0 libxml2 man-db po-debconf zlib1g-dev
The following packages will be upgraded:
libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 69 not upgraded.
+2 upgraded, 19 newly installed, 0 to remove and 72 not upgraded.
Need to get 12.3MB of archives.
-After this operation, 35.4MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr unstable/main ncurses-bin 5.7+20100313-4 [322kB]
-Get:2 http://debian.carnet.hr unstable/main libncurses5 5.7+20100313-4 [349kB]
-Get:3 http://debian.carnet.hr unstable/main bsdmainutils 8.0.13 [203kB]
-Get:4 http://debian.carnet.hr unstable/main groff-base 1.20.1-10 [1146kB]
-Get:5 http://debian.carnet.hr unstable/main man-db 2.5.7-6 [1283kB]
-Get:6 http://debian.carnet.hr unstable/main libmagic1 5.04-5 [239kB]
-Get:7 http://debian.carnet.hr unstable/main file 5.04-5 [49.5kB]
-Get:8 http://debian.carnet.hr unstable/main gettext-base 0.18.1.1-3 [140kB]
-Get:9 http://debian.carnet.hr unstable/main libpcre3 8.02-1.1 [237kB]
-Get:10 http://debian.carnet.hr unstable/main libxml2 2.7.7.dfsg-4 [840kB]
-Get:11 http://debian.carnet.hr unstable/main html2text 1.3.2a-15 [100kB]
-Get:12 http://debian.carnet.hr unstable/main libglib2.0-0 2.24.2-1 [1074kB]
-Get:13 http://debian.carnet.hr unstable/main libcroco3 0.6.2-1 [119kB]
-Get:14 http://debian.carnet.hr unstable/main libunistring0 0.9.3-3 [424kB]
-Get:15 http://debian.carnet.hr unstable/main gettext 0.18.1.1-3 [2006kB]
-Get:16 http://debian.carnet.hr unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
-Get:17 http://debian.carnet.hr unstable/main po-debconf 1.0.16 [224kB]
-Get:18 http://debian.carnet.hr unstable/main debhelper 8.0.0 [454kB]
-Get:19 http://debian.carnet.hr unstable/main cdbs 0.4.89 [1240kB]
-Get:20 http://debian.carnet.hr unstable/main libncurses5-dev 5.7+20100313-4 [1610kB]
-Get:21 http://debian.carnet.hr unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [189kB]
+After this operation, 35.6MB of additional disk space will be used.
+Get:1 http://mirrors.ece.ubc.ca unstable/main ncurses-bin 5.7+20100313-4 [322kB]
+Get:2 http://mirrors.ece.ubc.ca unstable/main libncurses5 5.7+20100313-4 [349kB]
+Get:3 http://mirrors.ece.ubc.ca unstable/main bsdmainutils 8.0.16 [201kB]
+Get:4 http://mirrors.ece.ubc.ca unstable/main groff-base 1.20.1-10 [1146kB]
+Get:5 http://mirrors.ece.ubc.ca unstable/main man-db 2.5.7-6 [1283kB]
+Get:6 http://mirrors.ece.ubc.ca unstable/main libmagic1 5.04-5 [239kB]
+Get:7 http://mirrors.ece.ubc.ca unstable/main file 5.04-5 [49.5kB]
+Get:8 http://mirrors.ece.ubc.ca unstable/main gettext-base 0.18.1.1-3 [140kB]
+Get:9 http://mirrors.ece.ubc.ca unstable/main libpcre3 8.02-1.1 [237kB]
+Get:10 http://mirrors.ece.ubc.ca unstable/main libxml2 2.7.8.dfsg-1 [840kB]
+Get:11 http://mirrors.ece.ubc.ca unstable/main html2text 1.3.2a-15 [100kB]
+Get:12 http://mirrors.ece.ubc.ca unstable/main libglib2.0-0 2.24.2-1 [1074kB]
+Get:13 http://mirrors.ece.ubc.ca unstable/main libcroco3 0.6.2-1 [119kB]
+Get:14 http://mirrors.ece.ubc.ca unstable/main libunistring0 0.9.3-3 [424kB]
+Get:15 http://mirrors.ece.ubc.ca unstable/main gettext 0.18.1.1-3 [2006kB]
+Get:16 http://mirrors.ece.ubc.ca unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
+Get:17 http://mirrors.ece.ubc.ca unstable/main po-debconf 1.0.16+nmu1 [223kB]
+Get:18 http://mirrors.ece.ubc.ca unstable/main debhelper 8.0.0 [454kB]
+Get:19 http://mirrors.ece.ubc.ca unstable/main cdbs 0.4.89 [1240kB]
+Get:20 http://mirrors.ece.ubc.ca unstable/main libncurses5-dev 5.7+20100313-4 [1610kB]
+Get:21 http://mirrors.ece.ubc.ca unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [189kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.3MB in 8s (1483kB/s)
-(Reading database ... 10174 files and directories currently installed.)
+Fetched 12.3MB in 2s (4531kB/s)
+(Reading database ... 10166 files and directories currently installed.)
Preparing to replace ncurses-bin 5.7+20100313-2 (using .../ncurses-bin_5.7+20100313-4_sparc.deb) ...
Unpacking replacement ncurses-bin ...
Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 10174 files and directories currently installed.)
+(Reading database ... 10166 files and directories currently installed.)
Preparing to replace libncurses5 5.7+20100313-2 (using .../libncurses5_5.7+20100313-4_sparc.deb) ...
Unpacking replacement libncurses5 ...
Setting up libncurses5 (5.7+20100313-4) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10174 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_sparc.deb) ...
+(Reading database ... 10166 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_sparc.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_sparc.deb) ...
Selecting previously deselected package man-db.
@@ -143,7 +143,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_sparc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -157,7 +157,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_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_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -166,7 +166,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_sparc.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+Setting up bsdmainutils (8.0.16) ...
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 (1.20.1-10) ...
@@ -176,14 +176,14 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
@@ -192,7 +192,7 @@ Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc (sparc64)
Toolchain package versions: libc6-dev_2.11.2-2 dpkg-dev_1.15.7.2 linux-libc-dev_2.6.32-17 gcc-4.4_4.4.4-6 g++-4.4_4.4.4-6 binutils_2.20.1-12 libstdc++6-4.4-dev_4.4.4-6 libstdc++6_4.4.4-6
-Package versions: apt_0.7.25.3 base-files_5.8 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-12 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-6 dash_0.5.5.1-7 debconf_1.5.33 debconf-i18n_1.5.33 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.3 diffutils_1:3.0-1 dpkg_1.15.7.2 dpkg-dev_1.15.7.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-6 gcc_4:4.4.4-2 gcc-4.4_4.4.4-6 gcc-4.4-base_4.4.4-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-4 libc-bin_2.11.2-2 libc-dev-bin_2.11.2-2 libc6_2.11.2-2 libc6-dev_2.11.2-2 libc6-dev-sparc64_2.11.2-2 libc6-sparc64_2.11.2-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.26-3 libdpkg-perl_1.15.7.2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100527-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.94-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-6 libstdc++6-4.4-dev_4.4.4-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-15 libuuid1_2.17.2-3.1 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-17 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 netbase_4.42 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-13 perl-base_5.10.1-13 perl-modules_5.10.1-13 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2 tzdata_2010j-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100527-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.7.25.3 base-files_5.8 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-12 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.1 build-essential_11.5 bzip2_1.0.5-4 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-6 dash_0.5.5.1-7 debconf_1.5.33 debconf-i18n_1.5.33 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2009.01.31 debianutils_3.3 diffutils_1:3.0-1 dpkg_1.15.7.2 dpkg-dev_1.15.7.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-6 gcc_4:4.4.4-2 gcc-4.4_4.4.4-6 gcc-4.4-base_4.4.4-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-11 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-3 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1 libbz2-1.0_1.0.5-4 libc-bin_2.11.2-2 libc-dev-bin_2.11.2-2 libc6_2.11.2-2 libc6-dev_2.11.2-2 libc6-dev-sparc64_2.11.2-2 libc6-sparc64_2.11.2-2 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.26-3 libdpkg-perl_1.15.7.2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-6 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-6 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100527-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-3 libpam-runtime_1.1.1-3 libpam0g_1.1.1-3 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.94-1 libsepol1_2.0.41-1 libss2_1.41.12-2 libstdc++6_4.4.4-6 libstdc++6-4.4-dev_4.4.4-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-15 libuuid1_2.17.2-3.1 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-17 login_1:4.1.4.2-1 lsb-base_3.2-23.1 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.1 ncurses-base_5.7+20100313-2 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2-1 patch_2.6-2 perl_5.10.1-13 perl-base_5.10.1-13 perl-modules_5.10.1-13 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.2p7-1 sysv-rc_2.88dsf-11 sysvinit_2.88dsf-11 sysvinit-utils_2.88dsf-11 tar_1.23-2 tzdata_2010j-1 util-linux_2.17.2-3.1 xz-utils_4.999.9beta+20100527-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -204,12 +204,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 1 11:10:35 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.9-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.9
-dpkg-source: info: unpacking samtools_0.1.9.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.9-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.10
+dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
Check disc space
────────────────
@@ -224,24 +224,24 @@ 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 0.1.9-1
+dpkg-buildpackage: source version 0.1.10-1
dpkg-buildpackage: host architecture sparc
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/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_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/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_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
rm -f debian/stamp-makefile-check
dh_clean
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
@@ -249,8 +249,8 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -274,9 +274,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+ar -cru 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 glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -287,10 +288,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -303,27 +304,28 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
-gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
+gcc -g -O2 -g -Wall -O2 -fPIC -o samtools bam_tview.o bam_maqcns.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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -333,30 +335,30 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -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_0.1.9-1-sparc-VXbPsv/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/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_0.1.9-1-sparc-VXbPsv/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101101-1157
+Build finished at 20101117-1200
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-7d7863af-7540-42de-bbe5-3676bd980e1d/build/buildd-samtools_0.1.9-1-sparc-VXbPsv
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-ee0cabb2-61cd-481d-a707-e4a6682674d0/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101101-1157
-Build needed 00:03:18, 4972k disc space
+Finished at 20101117-1200
+Build needed 00:06:35, 5188k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
--
Processing of sequence alignments in SAM and BAM formats.
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