[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. 22d8b30aee59b08f51600e57d50334f324b4da4f
Charles Plessy
plessy at debian.org
Sat Dec 4 03:37:36 UTC 2010
The following commit has been merged in the meta branch:
commit 22d8b30aee59b08f51600e57d50334f324b4da4f
Author: Charles Plessy <plessy at debian.org>
Date: Sat Dec 4 12:36:47 2010 +0900
# Collected all build logs except mips (late).
diff --git a/alpha.build b/alpha.build
index 6ca0787..d5b8196 100644
--- a/alpha.build
+++ b/alpha.build
@@ -1,91 +1,73 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/alpha received Fri Dec 3 09:30:16 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=alpha">alpha</a> >> Fri Dec 3 09:30:16 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goedel.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (alpha) 17 Nov 2010 11:53 ║
+║ samtools 0.1.12a-1 (alpha) 03 Dec 2010 09:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: alpha
-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]
+Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-8c0a09a0-0453-4a03-9ecf-2d62cbdb7eda/build/buildd-samtools_0.1.12a-1-alpha-NKtcft
+Start Time: 20101203-0921
+Get:1 http://ftp.de.debian.org sid Release.gpg [835 B]
+Ign http://ftp.de.debian.org/debian/ sid/contrib Translation-en
+Ign http://ftp.de.debian.org/debian/ sid/main Translation-en
+Get:2 http://ftp.de.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
-Get:4 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:4 http://ftp.de.debian.org sid/main alpha Packages/DiffIndex [2038 B]
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 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)
+Hit http://ftp.de.debian.org sid/contrib alpha Packages/DiffIndex
+Get:7 http://ftp.de.debian.org sid/main alpha 2010-12-01-1412.04.pdiff [499 B]
+Get:8 http://incoming.debian.org Release [1604 B]
+Get:9 http://ftp.de.debian.org sid/main alpha 2010-12-01-1412.04.pdiff [499 B]
+Get:10 http://ftp.de.debian.org sid/main alpha 2010-12-01-1412.04.pdiff [499 B]
+Get:11 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:12 http://incoming.debian.org sid/main alpha Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib alpha Packages/DiffIndex
+Get:13 http://incoming.debian.org Sources [8014 B]
+Get:14 http://incoming.debian.org Packages [169 kB]
+Get:15 http://incoming.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:16 http://incoming.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
+Get:17 http://incoming.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:18 http://incoming.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
+Get:19 http://incoming.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:20 http://ftp.de.debian.org sid/main alpha 2010-12-01-2014.11.pdiff [1392 B]
+Get:21 http://ftp.de.debian.org sid/main alpha 2010-12-01-2014.11.pdiff [1392 B]
+Get:22 http://incoming.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
+Get:23 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:24 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:25 http://ftp.de.debian.org sid/main alpha 2010-12-01-2014.11.pdiff [1392 B]
+Get:26 http://incoming.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
+Get:27 http://incoming.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
+Get:28 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:29 http://ftp.de.debian.org sid/main alpha 2010-12-02-0209.58.pdiff [1681 B]
+Get:30 http://ftp.de.debian.org sid/main alpha 2010-12-02-0209.58.pdiff [1681 B]
+Get:31 http://incoming.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
+Get:32 http://ftp.de.debian.org sid/main alpha 2010-12-02-0209.58.pdiff [1681 B]
+Get:33 http://ftp.de.debian.org sid/main alpha 2010-12-02-0815.49.pdiff [225 B]
+Get:34 http://ftp.de.debian.org sid/main alpha 2010-12-02-0815.49.pdiff [225 B]
+Get:35 http://ftp.de.debian.org sid/main alpha 2010-12-02-0815.49.pdiff [225 B]
+Get:36 http://ftp.de.debian.org sid/main alpha 2010-12-02-1418.14.pdiff [26.1 kB]
+Get:37 http://ftp.de.debian.org sid/main alpha 2010-12-02-1418.14.pdiff [26.1 kB]
+Get:38 http://ftp.de.debian.org sid/main alpha 2010-12-02-1418.14.pdiff [26.1 kB]
+Get:39 http://ftp.de.debian.org sid/main alpha 2010-12-02-2015.37.pdiff [35.1 kB]
+Get:40 http://ftp.de.debian.org sid/main alpha 2010-12-02-2015.37.pdiff [35.1 kB]
+Get:41 http://ftp.de.debian.org sid/main alpha 2010-12-02-2015.37.pdiff [35.1 kB]
+Get:42 http://ftp.de.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
+Get:43 http://ftp.de.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
+Get:44 http://ftp.de.debian.org sid/main alpha 2010-12-03-0208.36.pdiff [10.1 kB]
+Get:45 http://ftp.de.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
+Get:46 http://ftp.de.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
+Get:47 http://ftp.de.debian.org sid/main alpha 2010-12-03-0810.19.pdiff [798 B]
+Fetched 485 kB in 42s (11.5 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -106,138 +88,59 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (334 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.0.0
+debhelper: already installed (8.0.0 >= 8 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 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:
- 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
- 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
-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]
+ cdbs libncurses5-dev zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-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) ...
+0 upgraded, 3 newly installed, 0 to remove and 46 not upgraded.
+Need to get 0 B/3121 kB of archives.
+After this operation, 9556 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
+(Reading database ... 13765 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) ...
-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) ...
+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-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
+Kernel: Linux 2.6.26-2-alpha-generic alpha (alpha)
+Toolchain package versions: libc6.1-dev_2.11.2-7 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-27 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.8 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_4.4.5-10 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_4.4.5-10 gcc_4:4.4.5-1 gcc-4.3_4.3.5-3 gcc-4.3-base_4.3.5-3 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 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_2.11.2-7 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_4.8.30-3 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_1:4.4.5-10 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_4.4.5-10 libgpg-error0_1.6-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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-3 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 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 libxml2-utils_2.7.7.dfsg-4 libxslt1.1_1.1.26-6 linux-libc-dev_2.6.32-27 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_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16 python_2.6.6-3+squeeze2 python-minimal_2.6.6-3+squeeze2 python2.6_2.6.6-7 python2.6-minimal_2.6.6-7 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -249,12 +152,12 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -269,34 +172,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
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
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
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
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
@@ -316,8 +220,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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
@@ -328,10 +232,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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
@@ -348,24 +252,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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
@@ -375,14 +279,14 @@ 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_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/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_0.1.10-1-alpha-o4KeS3/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
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-alpha-o4KeS3/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -395,8 +299,8 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtoo
[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
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq1...
+../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
@@ -404,21 +308,22 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtoo
[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
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
+../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
<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_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/examples'
-touch debian/stamp-makefile-check
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/examples'
/usr/bin/fakeroot debian/rules binary-arch
+touch debian/stamp-makefile-check
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -443,8 +348,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -468,7 +373,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-alpha-o4KeS3/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -482,66 +387,69 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_alpha.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_alpha.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1201
+Build finished at 20101203-0930
-samtools_0.1.10-1_alpha.changes:
+samtools_0.1.12a-1_alpha.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: alpha
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: alpha Build Daemon (goetz) <buildd_alpha-goetz at buildd...>
+Maintainer: Debian Build Daemon <buildd_alpha-goedel 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- a1e51ad4045a416cdea105b8f4bda5335a97aba5 605070 samtools_0.1.10-1_alpha.deb
- 289158da20b96f15c5179e69a62b660494c7a34a 207186 libbam-dev_0.1.10-1_alpha.deb
+ e386da50ad8f4b31c12c471a3ee2e92af0868f6e 596686 samtools_0.1.12a-1_alpha.deb
+ ca438ab8033960703fc2010cf168bd0df1e89bb5 187896 libbam-dev_0.1.12a-1_alpha.deb
Checksums-Sha256:
- 2faa4d1455551181538b101b40c86539a286e6385e7d837c51fddddba7df5224 605070 samtools_0.1.10-1_alpha.deb
- d936b2faf2ea800c0b3d249392e328f2de9321e6b7acdb6527daeafcc902df12 207186 libbam-dev_0.1.10-1_alpha.deb
+ 9694d7c3e75170dc00a9743e3ff2a74586c122ab77940d4552d855d03c312297 596686 samtools_0.1.12a-1_alpha.deb
+ d75f2196ea5c327e83095b580dc38f8572e307b757dbd80f85cd1bae91f1d259 187896 libbam-dev_0.1.12a-1_alpha.deb
Files:
- 70f64ae69b1eb44108a3b6c5da0bad9a 605070 science optional samtools_0.1.10-1_alpha.deb
- e5c671c45e8bbb25726bd396010b1bd1 207186 libdevel optional libbam-dev_0.1.10-1_alpha.deb
+ ccd175cc94346c4fca39c74db4373826 596686 science optional samtools_0.1.12a-1_alpha.deb
+ 844a3e6973cc5cb3b9a1a2ba51319355 187896 libdevel optional libbam-dev_0.1.12a-1_alpha.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_alpha.deb
-───────────────────────────
+samtools_0.1.12a-1_alpha.deb
+────────────────────────────
new debian package, version 2.0.
- size 605070 bytes: control archive= 1796 bytes.
- 794 bytes, 16 lines control
+ size 596686 bytes: control archive= 1796 bytes.
+ 795 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: alpha
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1128
+ Installed-Size: 1132
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -554,69 +462,69 @@ samtools_0.1.10-1_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 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 126609 2010-11-17 11:56 ./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 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
+-rw-r--r-- root/root 126609 2010-12-03 09:24 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-12-03 09:29 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 09:29 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 09:29 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 12567 2010-12-02 16:41 ./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 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 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 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 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
-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
-─────────────────────────────
+-rwxr-xr-x root/root 5778 2010-12-03 09:29 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/bin/
+-rwxr-xr-x root/root 111048 2010-12-03 09:29 ./usr/bin/bcftools
+-rwxr-xr-x root/root 31568 2010-12-03 09:29 ./usr/bin/razip
+-rwxr-xr-x root/root 410632 2010-12-03 09:29 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/lib/samtools/
+-rwxr-xr-x root/root 22296 2010-12-03 09:29 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9728 2010-12-03 09:29 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 9728 2010-12-03 09:29 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 15320 2010-12-03 09:29 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 11136 2010-12-03 09:29 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2010-12-03 09:29 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_alpha.deb
+──────────────────────────────
new debian package, version 2.0.
- size 207186 bytes: control archive= 894 bytes.
- 674 bytes, 15 lines control
+ size 187896 bytes: control archive= 895 bytes.
+ 675 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: alpha
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 616
@@ -630,23 +538,23 @@ libbam-dev_0.1.10-1_alpha.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/lib/
+-rw-r--r-- root/root 475670 2010-12-03 09:29 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:29 ./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
-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
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -655,10 +563,14 @@ drwxr-xr-x root/root 0 2010-11-17 12:01 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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
+Purging /var/lib/schroot/mount/sid-alpha-sbuild-8c0a09a0-0453-4a03-9ecf-2d62cbdb7eda/build/buildd-samtools_0.1.12a-1-alpha-NKtcft
+(Reading database ... 14898 files and directories currently installed.)
+Removing libncurses5-dev ...
+Removing cdbs ...
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1201
-Build needed 00:08:01, 11400k disc space
+Finished at 20101203-0930
+Build needed 00:08:29, 11404k 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 daf806c..7fd5195 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_0.1.10-1/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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/armel received Fri Dec 3 09:28:30 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=armel">armel</a> >> Fri Dec 3 09:28:30 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on arnold.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (armel) 17 Nov 2010 11:52 ║
+║ samtools 0.1.12a-1 (armel) 03 Dec 2010 09:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: armel
-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
+Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-933fddaf-1beb-4ac8-bf61-db1837fff3ba/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0
+Start Time: 20101203-0922
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://ftp.uk.debian.org unstable/main Sources [4061kB]
-Get:4 http://incoming.debian.org unstable Release.gpg [835B]
+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://ftp.uk.debian.org unstable/main Sources [4071kB]
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 [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 [15.1kB]
-Get:18 http://incoming.debian.org Packages [227kB]
-Fetched 22.4MB in 50s (448kB/s)
+Get:8 http://incoming.debian.org unstable/main Sources [4071kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib Sources [38.7kB]
+Get:10 http://ftp.uk.debian.org unstable/non-free Sources [83.8kB]
+Get:11 http://ftp.uk.debian.org unstable/main armel Packages [6754kB]
+Get:12 http://incoming.debian.org unstable/contrib Sources [38.7kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [83.8kB]
+Get:14 http://incoming.debian.org unstable/main armel Packages [6754kB]
+Get:15 http://ftp.uk.debian.org unstable/contrib armel Packages [49.6kB]
+Get:16 http://incoming.debian.org unstable/contrib armel Packages [49.6kB]
+Get:17 http://incoming.debian.org Sources [8014B]
+Get:18 http://incoming.debian.org Packages [169kB]
+Fetched 22.4MB in 50s (440kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -56,18 +56,18 @@ 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 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)
+Need to get 364kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337B]
+Fetched 364kB in 1s (279kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -100,12 +100,12 @@ 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 49 not upgraded.
+2 upgraded, 19 newly installed, 0 to remove and 61 not upgraded.
Need to get 12.0MB of archives.
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 8.0.16 [204kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.0.17 [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]
@@ -125,18 +125,18 @@ 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 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) ...
+Fetched 12.0MB in 9s (1325kB/s)
+(Reading database ... 9961 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.7+20100313-2 (using .../ncurses-bin_5.7+20100313-4_armel.deb) ...
Unpacking replacement ncurses-bin ...
Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 10006 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-3 (using .../libncurses5_5.7+20100313-4_armel.deb) ...
+(Reading database ... 9961 files and directories currently installed.)
+Preparing to replace libncurses5 5.7+20100313-2 (using .../libncurses5_5.7+20100313-4_armel.deb) ...
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_8.0.16_armel.deb) ...
+(Reading database ... 9961 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_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.
@@ -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 (8.0.16) ...
+Setting up bsdmainutils (8.0.17) ...
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) ...
@@ -198,8 +198,8 @@ Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32 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_8.0.16 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
+Toolchain package versions: libc6-dev_2.11.2-5 dpkg-dev_1.15.8.4 linux-libc-dev_2.6.32-21 gcc-4.4_4.4.4-13 g++-4.4_4.4.4-13 binutils_2.20.1-14 libstdc++6-4.4-dev_4.4.4-13 libstdc++6_4.4.4-13
+Package versions: apt_0.8.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-14 bsdmainutils_8.0.17 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_4.4.4-13 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_1.15.8.4 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_4.4.4-13 gcc_4:4.4.4-2 gcc-4.4_4.4.4-13 gcc-4.4-base_4.4.4-13 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_2.11.2-5 libc-dev-bin_2.11.2-5 libc6_2.11.2-5 libc6-dev_2.11.2-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.4 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-13 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-13 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_1.1.1-4 libpam-runtime_1.1.1-4 libpam0g_1.1.1-4 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_4.4.4-13 libstdc++6-4.4-dev_4.4.4-13 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_2.7.8.dfsg-1 linux-libc-dev_2.6.32-21 login_1:4.1.4.2-1+b2 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+b2 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+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-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
┌──────────────────────────────────────────────────────────────────────────────┐
│ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -231,34 +231,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
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
@@ -284,8 +285,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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
@@ -296,10 +297,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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
@@ -316,24 +317,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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
@@ -343,31 +344,31 @@ 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_0.1.10-1-armel-EP8FwK/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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_0.1.10-1-armel-EP8FwK/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
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-armel-EP8FwK/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/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_0.1.10-1-armel-EP8FwK/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1158
+Build finished at 20101203-0928
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-3065dfec-037e-4cdb-a2aa-531dc5b60773/build/buildd-samtools_0.1.10-1-armel-EP8FwK
+Purging /var/lib/schroot/mount/sid-armel-sbuild-933fddaf-1beb-4ac8-bf61-db1837fff3ba/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1158
-Build needed 00:06:04, 4960k disc space
+Finished at 20101203-0928
+Build needed 00:06:06, 4988k 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 9c9359c..133daf2 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_0.1.10-1_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
+<html><head><title>File `log' in samtools_0.1.12a-1_armhf (Dec 3 16:39)</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_0.1.12a-1_armhf (Dec 3 16:39)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=armhf">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=armhf">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=armhf&stamp=1291394381">Dec 3 16:39</a> >> log</td></tr></table><p><pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on efikamx04.lan
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (armhf) 17 Nov 2010 19:03 ║
+║ samtools 0.1.12a-1 (armhf) 03 Dec 2010 19:37 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: armhf
-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
+Chroot Build Dir: /var/lib/schroot/mount/sid-armhf-sbuild-bee06c27-7dcb-4954-ac4b-1e6de6af9d42/build/buildd-samtools_0.1.12a-1-armhf-bIURqR
+Start Time: 20101203-1937
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
@@ -29,11 +29,11 @@ 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
+Ign http://www.freevec.org/repository/ unstable/main Translation-en
Hit http://ftp.debian-ports.org unreleased Release.gpg
Ign http://ftp.debian-ports.org/debian/ unreleased/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
+Hit http://ftp.gr.debian.org unstable/main Sources/DiffIndex
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
@@ -43,8 +43,8 @@ Ign http://www.freevec.org unstable/main armhf Packages
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
Hit http://ftp.debian-ports.org unstable/main armhf Packages
+Hit http://www.freevec.org unstable/main armhf Packages
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,18 +77,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 0s (812 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
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
@@ -131,12 +131,51 @@ 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
-debhelper: already installed (8.0.0 >= 7 is satisfied)
-cdbs: already installed (0.4.89)
+debhelper: already installed (8.0.0 >= 8 is satisfied)
+cdbs: missing
libncurses5-dev: already installed (5.7+20100313-4)
zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for source dependency conflicts...
-Installing positive dependencies:
+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
+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
+Installing positive dependencies: cdbs
+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
+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
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 ttf-dejavu-core mime-support x11proto-kb-dev whiptail
+ libgpg-error-dev x11proto-xinerama-dev comerr-dev x11proto-render-dev
+ texlive-common m4 python-minimal xtrans-dev udev x11proto-core-dev
+ x11proto-scrnsaver-dev x11proto-randr-dev qt4-qmake x11proto-input-dev
+ libtext-format-perl libgpg-error0 adduser tcl ucf x11proto-print-dev tcl-dev
+ uuid-dev libnewt0.52 tsconf x11-common x11proto-xf86vidmode-dev sgml-data
+ libstreams0 libgc1c2 texlive-doc-base wx2.8-headers libreadline5 tex-common
+Use 'apt-get autoremove' to remove them.
+Suggested packages:
+ doc-base
+Recommended packages:
+ autotools-dev
+The following NEW packages will be installed:
+ cdbs
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 12 not upgraded.
+Need to get 0 B/1240 kB of archives.
+After this operation, 1696 kB of additional disk space will be used.
+Selecting previously deselected package cdbs.
+(Reading database ... 16417 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Processing triggers for man-db ...
+Setting up cdbs (0.4.89) ...
Removing negative dependencies:
Checking correctness of source dependencies...
W: line 6 [sid-armhf-sbuild]: Deprecated key 'run-setup-scripts' used
@@ -146,29 +185,11 @@ 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_2.11.2-7 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_0.8.8 autoconf_2.67-2 autoconf-archive_20090426-1 autoconf2.13_2.13-60 automake_1:1.11.1-1 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 bc_1.06.95-2 binutils_2.20.51.20101009-1+armhf bison_1:2.4.1.dfsg-3 blt_2.4z-4.2 blt-dev_2.4z-4.2 bsdmainutils_8.0.15 bsdutils_1:2.17.2-3.1+armhf build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 ccache_3.1.1-1 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_4:4.4.5-1 cpp-4.4_4.4.5-5+armhf 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 dejagnu_1.4.4.git20080407-1.1 dh-buildinfo_0.9 dh-ocaml_0.9.6 diffstat_1.53-1 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 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 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_0.2.41-8 expect_5.44.1.15-4 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 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-5+armhf gcc-4.4-base_4.4.5-5+armhf gconf2_2.28.1-6 gconf2-common_2.28.1-6 gdb_7.2-1+armhf gdbserver_7.2-1+armhf gettext_0.18.1.1-1+armhf gettext-base_0.18.1.1-1+armhf gir-repository-dev_0.6.5-6 gir1.0-freedesktop_0.6.14-1 gir1.0-glib-2.0_0.6.14-1 gir1.0-gtk-2.0_0.6.5-6 gnome-common_2.28.0-1 gnome-doc-utils_0.20.1-1 gnome-icon-theme_2.30.3-2 gnome-mime-data_2.18.0-1 gnome-pkg-tools_0.16.3 gnupg_1.4.10-4 gobject-
- introspection_0.6.14-1 gpgv_1.4.10-4 graphviz_2.26.3-5 grep_2.6.3-3 groff_1.20.1-10 groff-base_1.20.1-10 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gtk-doc-tools_1.15-2 gvfs_1.6.4-2 gzip_1.3.12-9 hardening-wrapper_1.29 hicolor-icon-theme_0.12-1 highlight_2.16-1 highlight-common_2.16-1 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 iso-codes_3.22-1 jade_1.2.1-47 jadetex_3.13-12 krb5-multidev_1.8.3+dfsg-2 ladspa-sdk_1.13-1 lam4-dev_7.1.2-2 liba52-0.7.4_0.7.4-14 libaa1_1.4p5-38 libaa1-dev_1.4p5-38 libacl1_2.2.49-4 libacl1-dev_2.2.49-4 libalien-wxwidgets-perl_0.50+dfsg-1 libao-common_1.0.0-5 libao-dev_1.0.0-5 libao4_1.0.0-5 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 libaspell15_0.60.6-4 libasyncns0_0.3-1 libatasmart4_0.17+git20100219-2 libatk
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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
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.4+armhf linux-libc-dev_2.6.35~rc6-1+armhf~experimental.2 gcc-4.4_4.4.5-9 g++-4.4_4.4.5-9 binutils_2.20.51.20101009-1+armhf libstdc++6-4.4-dev_4.4.5-9 libstdc++6_4.4.5-9
+Package versions: adduser_3.112+nmu2 apt_0.8.9 autotools-dev_20100122.1 base-files_5.10 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.51.20101009-1+armhf bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.1+armhf build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 comerr-dev_2.1-1.41.12-2 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-9 dash_0.5.5.1-7.3 debconf_1.5.37 debconf-i18n_1.5.37 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2010.06.16 debianutils_3.4.2 devscripts_2.10.69 diffutils_1:3.0-1 dmsetup_2:1.02.48-4 dpkg_1.15.8.4+armhf dpkg-dev_1.15.8.4+armhf e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-2 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.5-1 g++-4.4_4.4.5-9 gcc_4:4.4.5-1 gcc-4.4_4.4.5-9 gcc-4.4-base_4.4.5-9 gettext_0.18.1.1-1+armhf gettext-base_0.18.1.1-1+armhf 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_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 lib
+ acl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.1+armhf libbsd-dev_0.2.0-1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libbz2-dev_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_4.7.25-10 libdb4.8_4.8.30-3 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.4+armhf libffi-dev_3.0.9-2+armhf libffi5_3.0.9-2+armhf libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-9 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-9 libgpg-error-dev_1.6-1 libgpg-error0_1.6-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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 libncursesw5-dev_5.7+20100313-4 libnewt0.52_0.52.11-2 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 libpopt0_1.16-1 libreadline5_5.2-7 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 l
+ ibssl0.9.8_0.9.8o-3 libstdc++6_4.4.5-9 libstdc++6-4.4-dev_4.4.5-9 libstreams0_0.7.2-1 libtext-charwidth-perl_0.04-6 libtext-format-perl_0.52-21 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_2.17.2-3.1+armhf libxml2_2.7.8.dfsg-1 libzzip-0-13_0.13.56-1 libzzip-dev_0.13.56-1 linux-libc-dev_2.6.35~rc6-1+armhf~experimental.2 llvm-2.7-priv-dev_2.7-6 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mime-support_3.51-1 mount_2.17.2-3.1+armhf nano_2.2.5-1 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 patchutils_0.3.1-2 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 pkg-kde-tools_0.9.3 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 python-minimal_2.6.6-3+squeeze2 python2.6-minimal_2.6.6-7 qt4-qmake_4:4.6.3-3+armhf readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sgm
+ l-base_1.26+nmu1 sgml-data_2.0.4 sudo_1.7.4p4-4 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.25-2 tcl_8.4.16-2 tcl-dev_8.4.16-2 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 tex-common_2.08 texinfo_4.13a.dfsg.1-6 texlive-common_2009-11 texlive-doc-base_2009-2 tsconf_1.0-7 ttf-dejavu-core_2.31-1 tzdata_2010o-1 ucf_3.0025+nmu1 udev_164-2 unzip_6.0-4 util-linux_2.17.2-3.1+armhf uuid-dev_2.17.2-3.1+armhf whiptail_0.52.11-2 wx2.8-headers_2.8.10.1-3 x11-common_1:7.5+8+armhf x11proto-core-dev_7.0.19-1 x11proto-input-dev_2.0.1-1 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-scrnsaver-dev_1.2.1-1 x11proto-xf86vidmode-dev_2.3-2 x11proto-xinerama-dev_1.2-2 xml-core_0.13 xtrans-dev_1.2.6-1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -186,12 +207,12 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -212,34 +233,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
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
@@ -265,8 +287,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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 +299,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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
@@ -297,24 +319,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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
@@ -324,14 +346,14 @@ 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_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/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_0.1.10-1-armhf-XV65Zs/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a'
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-armhf-XV65Zs/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -344,8 +366,8 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtoo
[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'
@@ -360,7 +382,7 @@ 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_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -368,6 +390,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -391,11 +414,9 @@ dh_installudev -psamtools
dh_lintian -psamtools
dh_install -psamtools
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_0.1.10-1-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -414,14 +435,12 @@ dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
-dh_buildinfo -plibbam-dev
-Use of uninitialized value within @essentials in string ne at /usr/bin/dh_buildinfo line 164.
dh_installmime -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-armhf-XV65Zs/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-armhf-bIURqR/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -435,63 +454,66 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_armhf.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_armhf.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1907
+Build finished at 20101203-1942
-samtools_0.1.10-1_armhf.changes:
+samtools_0.1.12a-1_armhf.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: armhf
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: armhf Build Daemon (efikamx01) <buildd_armhf-efikamx01 at debian-ports...>
+Maintainer: armhf Build Daemon (efikamx04) <buildd_armhf-efikamx04 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 03ebf695f57f22bd957ba5787921d1a471f9d129 579454 samtools_0.1.10-1_armhf.deb
- 2fe18e561bfb58a81916041adc5bd963c5d9898d 168048 libbam-dev_0.1.10-1_armhf.deb
+ 76d314c62b90686808137f9226997b31f8546a1f 585164 samtools_0.1.12a-1_armhf.deb
+ 5cda0c9d27be475906b6a2b722d74a0676d9627c 168644 libbam-dev_0.1.12a-1_armhf.deb
Checksums-Sha256:
- caed4d43993d218c0136b0b20e330f039e17033d5c4acc8da8bc7d44516b67cd 579454 samtools_0.1.10-1_armhf.deb
- 69188112d39b43a99b52108cf8273d41c96273217b1c3cd73ac1fffe02222264 168048 libbam-dev_0.1.10-1_armhf.deb
+ e971e4844cd355f0d49db34d6104a19ee0c168feb9529fd47f08f94dc23779dc 585164 samtools_0.1.12a-1_armhf.deb
+ 1807791a96b5502d0ed9939288c27c3c72948c63f3db5bb9301d714719916023 168644 libbam-dev_0.1.12a-1_armhf.deb
Files:
- 62d563fddd970fa6b3d795c129276ccc 579454 science optional samtools_0.1.10-1_armhf.deb
- 1085dd86de4b06ff411167948cd4873f 168048 libdevel optional libbam-dev_0.1.10-1_armhf.deb
+ f9a15338d032e195e5056ad4edf9f6da 585164 science optional samtools_0.1.12a-1_armhf.deb
+ c8fee737c0e6f9642b1c0ecb9618dff8 168644 libdevel optional libbam-dev_0.1.12a-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_armhf.deb
-───────────────────────────
+samtools_0.1.12a-1_armhf.deb
+────────────────────────────
new debian package, version 2.0.
- size 579454 bytes: control archive= 1828 bytes.
- 791 bytes, 16 lines control
- 2587 bytes, 39 lines md5sums
+ size 585164 bytes: control archive= 1793 bytes.
+ 792 bytes, 16 lines control
+ 2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 888
@@ -507,73 +529,72 @@ samtools_0.1.10-1_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 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/bin/
+-rwxr-xr-x root/root 68536 2010-12-03 19:42 ./usr/bin/bcftools
+-rwxr-xr-x root/root 20364 2010-12-03 19:42 ./usr/bin/razip
+-rwxr-xr-x root/root 259436 2010-12-03 19:42 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/samtools/
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.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 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 5778 2010-12-03 19:42 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-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
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 126609 2010-12-03 19:41 ./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 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
-─────────────────────────────
+-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 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1966 2010-12-03 19:42 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2010-12-03 19:42 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-12-03 19:42 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/lib/samtools/
+-rwxr-xr-x root/root 5828 2010-12-03 19:42 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 5828 2010-12-03 19:42 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7052 2010-12-03 19:42 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 15356 2010-12-03 19:42 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 10132 2010-12-03 19:42 ./usr/lib/samtools/md5fa
+lrwxrwxrwx root/root 0 2010-12-03 19:42 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_armhf.deb
+──────────────────────────────
new debian package, version 2.0.
- size 168048 bytes: control archive= 928 bytes.
- 674 bytes, 15 lines control
- 690 bytes, 11 lines md5sums
+ size 168644 bytes: control archive= 896 bytes.
+ 675 bytes, 15 lines control
+ 618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 352
+ Installed-Size: 348
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -584,24 +605,23 @@ libbam-dev_0.1.10-1_armhf.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./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 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
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./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 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2010-12-03 19:42 ./usr/lib/
+-rw-r--r-- root/root 205838 2010-12-03 19:42 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -610,16 +630,25 @@ drwxr-xr-x root/root 0 2010-11-17 19:07 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-ae55037d-2fca-4bcb-92dd-9b7bd9142996/build/buildd-samtools_0.1.10-1-armhf-XV65Zs
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-bee06c27-7dcb-4954-ac4b-1e6de6af9d42/build/buildd-samtools_0.1.12a-1-armhf-bIURqR
+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
+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
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
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
+(Reading database ... 16473 files and directories currently installed.)
+Removing cdbs ...
+Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1907
-Build needed 00:04:45, 8232k disc space
+Finished at 20101203-1942
+Build needed 00:04:49, 8256k disc space
</pre>
<p>
diff --git a/hppa.build b/hppa.build
index 50b080b..94f526d 100644
--- a/hppa.build
+++ b/hppa.build
@@ -1,39 +1,51 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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>
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/hppa received Fri Dec 3 09:25:30 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=hppa">hppa</a> >> Fri Dec 3 09:25:30 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on penalosa.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (hppa) 18 Nov 2010 12:24 ║
+║ samtools 0.1.12a-1 (hppa) 03 Dec 2010 09:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: hppa
-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
+Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-6f59b41d-9d09-44f5-adc7-d30a4b15c4ec/build/buildd-samtools_0.1.12a-1-hppa-luOI2H
+Start Time: 20101203-0921
+Get:1 http://spohr.debian.org sid Release.gpg [835 B]
Ign http://spohr.debian.org/debian/ sid/contrib Translation-en
Ign http://spohr.debian.org/debian/ sid/main Translation-en
-Hit http://spohr.debian.org sid Release
-Hit http://spohr.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid Release.gpg
+Get:2 http://spohr.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
-Get:1 http://incoming.debian.org Release.gpg [835 B]
+Get:4 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
+Get:5 http://incoming.debian.org sid Release [104 kB]
+Get:6 http://spohr.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:7 http://incoming.debian.org Release [1604 B]
Hit http://spohr.debian.org sid/contrib Sources/DiffIndex
-Hit http://spohr.debian.org sid/main hppa Packages/DiffIndex
+Get:8 http://spohr.debian.org sid/main hppa Packages/DiffIndex [2038 B]
Hit http://spohr.debian.org sid/contrib hppa 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
+Get:9 http://spohr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:10 http://spohr.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
+Get:11 http://spohr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:12 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:13 http://spohr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:14 http://spohr.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main hppa Packages/DiffIndex
+Get:15 http://incoming.debian.org sid/main hppa Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib hppa Packages/DiffIndex
-Hit http://incoming.debian.org Sources
-Get:3 http://incoming.debian.org Packages [261 kB]
-Fetched 263 kB in 13s (19.1 kB/s)
+Get:16 http://incoming.debian.org Sources [8014 B]
+Get:17 http://incoming.debian.org Packages [169 kB]
+Get:18 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:19 http://spohr.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
+Get:20 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:21 http://incoming.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
+Get:22 http://incoming.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
+Get:23 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:24 http://incoming.debian.org sid/main hppa 2010-12-03-0810.19.pdiff [798 B]
+Fetched 399 kB in 16s (23.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,103 +66,35 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (356 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.0.0
-cdbs: missing
+debhelper: already installed (8.0.0 >= 8 is satisfied)
+cdbs: already installed (0.4.89)
libncurses5-dev: already installed (5.7+20100313-4)
-zlib1g-dev: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for source dependency conflicts...
-Installing positive dependencies: debhelper cdbs zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libpcre3 libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- 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:
- cdbs debhelper gettext gettext-base groff-base html2text intltool-debian
- 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 17 not upgraded.
-Need to get 0 B/9891 kB of archives.
-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) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_hppa.deb) ...
-Selecting previously deselected package gettext-base.
-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_2.7.8.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.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_hppa.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hppa.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hppa.deb) ...
-Selecting previously deselected package gettext.
-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+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hppa.deb) ...
-Setting up groff-base (1.20.1-10) ...
-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 (2.7.8.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 zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Installing positive dependencies:
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-5-parisc64 hppa (parisc64)
-Toolchain package versions: libc6-dev_2.11.2-7 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
+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_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+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 bison_1:2.4.1.dfsg-3 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_4.4.5-10 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 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 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-10 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_4.4.5-10 gcc-4.4-base_4.4.5-10 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_4.8.30-3 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.5 libextutils-parsexs-perl_2.220600-1 libffi-dev_3.0.9-3 libffi5_3.0.9-3 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-10 libgdbm-dev_1.8.3-9 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 libice-dev_2:1.0.7-1 libice6_2:1.0.7-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline5_5.2-7 libreadline5-dev_5.2-7 libreadline6_6.1-3 libruby1.8_1.8.7.302-2 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4+b1 libsm-dev_2:1.2.0-1 libsm6_2:1.2.0-1 libss2_1.41.12-2 libssl-dev_0.9.8o-3 libssl0.9.8_0.9.8o-3 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 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 libx11-6_2:1.3.3-4 libx11-data_2:1.3.3-4 libx11-dev_2:1.3.3-4 libxau-dev_1:1.0.6-1 libxau6_1:1.0.6-1 libxcb1_1.6-1 libxcb1-dev_1.6-1 libxdmcp-dev_1:1.1.0-1 libxdmcp6_1:1.1.0-1 libxml2_2.7.8.dfsg-1 libxt-dev_1:1.0.7-1 libxt6_1:1.0.7-1 libyaml-0-2_0.1.3-1 libyaml-dev_0.1.3-1 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 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 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 quilt_0.48-7 readline-common_6.1-3 ruby1.8_1.8.7.302-2 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 tcl8.4-dev_8.4.19-4 tk8.4_8.4.19-4 tk8.4-dev_8.4.19-4 tzdata_2010m-1 util-linux_2.17.2-3.3 x11-common_1:7.5+8 x11proto-core-dev_7.0.19-1 x11proto-input-dev_2.0.1-1 x11proto-kb-dev_1.0.5-1 xtrans-dev_1.2.6-1 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 │
@@ -162,12 +106,12 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -182,34 +126,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-hppa-94wyup/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-hppa-94wyup/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
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
@@ -235,8 +180,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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
@@ -247,10 +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.. -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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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
@@ -267,24 +212,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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
@@ -294,14 +239,14 @@ 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_0.1.10-1-hppa-94wyup/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/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_0.1.10-1-hppa-94wyup/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
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-hppa-94wyup/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -330,7 +275,7 @@ 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_0.1.10-1-hppa-94wyup/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -338,6 +283,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -362,8 +308,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -387,7 +333,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-hppa-94wyup/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -401,28 +347,28 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_hppa.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_hppa.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101118-1229
+Build finished at 20101203-0925
-samtools_0.1.10-1_hppa.changes:
+samtools_0.1.12a-1_hppa.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hppa
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
Maintainer: hppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd...>
@@ -431,36 +377,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 0546d72c9390e268b68c3957fd64008aa56c9055 582760 samtools_0.1.10-1_hppa.deb
- febadcfa15aaeabf2bfffb52dccb3245486743e3 177016 libbam-dev_0.1.10-1_hppa.deb
+ 38a0581663a751865211c666d624f338d134be58 563494 samtools_0.1.12a-1_hppa.deb
+ aedbae40c00f4a206d289e25de9d512220153045 166206 libbam-dev_0.1.12a-1_hppa.deb
Checksums-Sha256:
- bccaccda20ff9787c8bfaba5c8dfe0f8425fb7c050f90506af64fe8d0f964338 582760 samtools_0.1.10-1_hppa.deb
- a1fd673ac2dcbd2f402f47c300409d46abe5b77373507c6a82f38775b0c8e1aa 177016 libbam-dev_0.1.10-1_hppa.deb
+ 37423289380391653718ec54186e2da7732f45d156f73fb63920c34ec1dc2c59 563494 samtools_0.1.12a-1_hppa.deb
+ 5c3ec027e567c144274ef99667fa00e40b66dc5d4afa1a4a2dc98de2c418cce4 166206 libbam-dev_0.1.12a-1_hppa.deb
Files:
- 1e5983b5cfbad6eaabfd17df7fdb73b8 582760 science optional samtools_0.1.10-1_hppa.deb
- 3486c8c2cf602b4e9506540e978a1ce9 177016 libdevel optional libbam-dev_0.1.10-1_hppa.deb
+ bf86cb9d32756635a4a69f3af457aca2 563494 science optional samtools_0.1.12a-1_hppa.deb
+ e89a9ebbcc3c3116d0ef46cbd839a6ba 166206 libdevel optional libbam-dev_0.1.12a-1_hppa.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_hppa.deb
-──────────────────────────
+samtools_0.1.12a-1_hppa.deb
+───────────────────────────
new debian package, version 2.0.
- size 582760 bytes: control archive= 1794 bytes.
- 792 bytes, 16 lines control
+ size 563494 bytes: control archive= 1792 bytes.
+ 793 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: hppa
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1020
+ Installed-Size: 1024
Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -473,48 +422,48 @@ samtools_0.1.10-1_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 2010-11-18 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/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/bin/
+-rwxr-xr-x root/root 93004 2010-12-03 09:24 ./usr/bin/bcftools
+-rwxr-xr-x root/root 341032 2010-12-03 09:24 ./usr/bin/samtools
+-rwxr-xr-x root/root 26556 2010-12-03 09:24 ./usr/bin/razip
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11744 2010-12-03 09:24 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7880 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 18492 2010-12-03 09:24 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8744 2010-12-03 09:24 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7880 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-short
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2010-12-03 09:24 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 126609 2010-12-03 09:24 ./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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./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/
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 09:24 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 09:24 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 5778 2010-12-03 09:24 ./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 12567 2010-12-02 16:41 ./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
@@ -523,19 +472,19 @@ drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/share/samtools/
-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
+lrwxrwxrwx root/root 0 2010-12-03 09:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.10-1_hppa.deb
-────────────────────────────
+libbam-dev_0.1.12a-1_hppa.deb
+─────────────────────────────
new debian package, version 2.0.
- size 177016 bytes: control archive= 898 bytes.
- 673 bytes, 15 lines control
+ size 166206 bytes: control archive= 899 bytes.
+ 674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: hppa
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 416
@@ -549,22 +498,22 @@ libbam-dev_0.1.10-1_hppa.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-18 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/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
+-rw-r--r-- root/root 270726 2010-12-03 09:24 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
@@ -574,33 +523,9 @@ drwxr-xr-x root/root 0 2010-11-18 12:29 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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 ...
-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 ...
+Purging /var/lib/schroot/mount/sid-hppa-sbuild-6f59b41d-9d09-44f5-adc7-d30a4b15c4ec/build/buildd-samtools_0.1.12a-1-hppa-luOI2H
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101118-1229
-Build needed 00:04:25, 9008k disc space
+Finished at 20101203-0925
+Build needed 00:03:25, 9004k 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 44af809..050b682 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_0.1.10-1/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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/hurd-i386 received Fri Dec 3 09:52:18 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=hurd-i386">hurd-i386</a> >> Fri Dec 3 09:52:18 2010<pre>
+sbuild (Debian sbuild) 0.59.1 (31 Jan 2010) on bach.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (hurd-i386) 17 nov. 2010 12:20 ║
+║ samtools 0.1.12a-1 (hurd-i386) 03 déc. 2010 09:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz
-Start Time: 20101117-1220
+Chroot Build Dir: /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq
+Start Time: 20101203-0924
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -30,34 +30,94 @@ 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
+Get:1 http://ftp.debian-ports.org unreleased Release.gpg [835 B]
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]
+Get:2 http://ftp.debian-ports.org unreleased Release [17.4 kB]
+Get:3 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:2 http://incoming.debian.org Release [1604B]
+Get:4 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
+Ign http://ftp.uk.debian.org/debian/ sid/non-free Translation-en
+Get:5 http://incoming.debian.org Release [1604 B]
+Get:6 http://ftp.uk.debian.org sid Release [104 kB]
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)
+Get:7 http://incoming.debian.org Sources [8014 B]
+Get:8 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:9 http://ftp.uk.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:10 http://incoming.debian.org Packages [169 kB]
+Get:11 http://ftp.uk.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:12 http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
+Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Get:13 http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex [2023 B]
+Get:14 http://ftp.uk.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
+Get:15 http://ftp.uk.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
+Get:16 http://ftp.uk.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
+Get:17 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-01-1412.04.pdiff [2228 B]
+Get:18 http://ftp.uk.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
+Get:19 http://ftp.uk.debian.org sid/non-free hurd-i386 2010-12-01-1412.04.pdiff [257 B]
+Get:20 http://ftp.uk.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
+Get:21 http://ftp.uk.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
+Get:22 http://ftp.uk.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
+Get:23 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-01-1412.04.pdiff [2228 B]
+Get:24 http://ftp.uk.debian.org sid/non-free hurd-i386 2010-12-01-1412.04.pdiff [257 B]
+Get:25 http://ftp.uk.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
+Get:26 http://ftp.uk.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
+Get:27 http://ftp.uk.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
+Get:28 http://ftp.uk.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
+Get:29 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-01-1412.04.pdiff [2228 B]
+Get:30 http://ftp.uk.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
+Get:31 http://ftp.uk.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
+Get:32 http://ftp.uk.debian.org sid/non-free hurd-i386 2010-12-01-1412.04.pdiff [257 B]
+Get:33 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-01-2014.11.pdiff [32.5 kB]
+Get:34 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-01-2014.11.pdiff [32.5 kB]
+Get:35 http://ftp.uk.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
+Get:36 http://ftp.uk.debian.org sid/non-free hurd-i386 2010-12-02-2015.37.pdiff [529 B]
+Get:37 http://ftp.uk.debian.org sid/non-free hurd-i386 2010-12-02-2015.37.pdiff [529 B]
+Get:38 http://ftp.uk.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
+Get:39 http://ftp.uk.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
+Get:40 http://ftp.uk.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
+Get:41 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-01-2014.11.pdiff [32.5 kB]
+Get:42 http://ftp.uk.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
+Get:43 http://ftp.uk.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
+Get:44 http://ftp.uk.debian.org sid/non-free hurd-i386 2010-12-02-2015.37.pdiff [529 B]
+Get:45 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0209.58.pdiff [6767 B]
+Get:46 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0209.58.pdiff [6767 B]
+Get:47 http://ftp.uk.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
+Get:48 http://ftp.uk.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
+Get:49 http://ftp.uk.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
+Get:50 http://ftp.uk.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
+Get:51 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0209.58.pdiff [6767 B]
+Get:52 http://ftp.uk.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
+Get:53 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0815.49.pdiff [225 B]
+Get:54 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0815.49.pdiff [225 B]
+Get:55 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-0815.49.pdiff [225 B]
+Get:56 http://ftp.uk.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
+Get:57 http://ftp.uk.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
+Get:58 http://ftp.uk.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
+Get:59 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-1418.14.pdiff [7365 B]
+Get:60 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-1418.14.pdiff [7365 B]
+Get:61 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-1418.14.pdiff [7365 B]
+Get:62 http://ftp.uk.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
+Get:63 http://ftp.uk.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
+Get:64 http://ftp.uk.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
+Get:65 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-2015.37.pdiff [1050 B]
+Get:66 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-2015.37.pdiff [1050 B]
+Get:67 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-02-2015.37.pdiff [1050 B]
+Get:68 http://ftp.uk.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:69 http://ftp.uk.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:70 http://ftp.uk.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:71 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0208.36.pdiff [1801 B]
+Get:72 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0208.36.pdiff [1801 B]
+Get:73 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0208.36.pdiff [1801 B]
+Get:74 http://ftp.uk.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:75 http://ftp.uk.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:76 http://ftp.uk.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:77 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0810.19.pdiff [797 B]
+Get:78 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0810.19.pdiff [797 B]
+Get:79 http://ftp.uk.debian.org sid/main hurd-i386 2010-12-03-0810.19.pdiff [797 B]
+Fetched 395 kB in 16min 11s (407 B/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
@@ -68,62 +128,64 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (191 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: already installed (8.0.0 >= 7 is satisfied)
+debhelper: already installed (8.0.0 >= 8 is satisfied)
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: cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- libwrap0 libcwidget3 libsigc++-2.0-0c2a libxapian15 libboost-iostreams1.42.0
- adduser libsysfs2
+ libpopt0 libwrap0 adduser libsysfs2 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
Suggested packages:
devscripts doc-base
Recommended packages:
autotools-dev
The following NEW packages will be installed:
- cdbs libncurses5-dev
-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.
+ cdbs libncurses5-dev zlib1g-dev
+0 upgraded, 3 newly installed, 0 to remove and 34 not upgraded.
+Need to get 0 B/2996 kB of archives.
+After this operation, 8770 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs libncurses5-dev
+ cdbs libncurses5-dev zlib1g-dev
Authentication warning overridden.
Selecting previously deselected package cdbs.
-(Reading database ... 14206 files and directories currently installed.)
+(Reading database ... 11907 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) ...
+Selecting previously deselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
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: GNU 0.3 hurd-i386 (i686-AT386)
-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
+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_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: adduser_3.112+nmu1 apt_0.8.8 apt-utils_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_1:2.16.2-0 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_4.4.5-10 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_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 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 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 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 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.2-2.1 libgcc1_1:4.4.5-10 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_4.4.5-10 libgpg-error0_1.6-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-3 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 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-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-8 libxml2_2.7.8.dfsg-1 lsb-base_3.2-25 make_3.81-8 man-db_2.5.7-4 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 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-bitstream-vera_1.10-8 ttf-dejavu-core_2.31-1 ttf-freefont_20090104-7 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 │
@@ -135,12 +197,12 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -154,46 +216,47 @@ 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-source --before-build samtools-0.1.12a
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
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_0.1.10-1-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'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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_0.1.10-1-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
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
debian/rules build
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
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_0.1.10-1-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'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
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
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
bam_import.c: In function 'append_text':
bam_import.c:179: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
+gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
@@ -208,8 +271,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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
@@ -220,10 +283,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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
@@ -240,24 +303,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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
@@ -267,16 +330,16 @@ 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_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/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_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
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_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
+[sam_header_read2] 2 sequences loaded.
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
@@ -294,8 +357,8 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-hurd-i386-ft_Rcz/sa
[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
+<mpileup> Set max per-sample depth to 8000
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
@@ -303,7 +366,7 @@ 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_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -311,6 +374,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -335,8 +399,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -360,7 +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_0.1.10-1-hurd-i386-ft_Rcz/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -374,66 +438,69 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_hurd-i386.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_hurd-i386.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1228
+Build finished at 20101203-0951
-samtools_0.1.10-1_hurd-i386.changes:
+samtools_0.1.12a-1_hurd-i386.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd...>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-bach 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- effd906208110c35f1d8377d3bb7e0317d9a358b 555002 samtools_0.1.10-1_hurd-i386.deb
- e9693a3eceb7a39813280f3398d8bca06dd40e1f 164884 libbam-dev_0.1.10-1_hurd-i386.deb
+ fc6e365d7c892b4387863d76ea111b7472b3c561 547110 samtools_0.1.12a-1_hurd-i386.deb
+ 44e8ea42aae8953667c17f5ae653bab19787b73f 157814 libbam-dev_0.1.12a-1_hurd-i386.deb
Checksums-Sha256:
- abe7170f8bd8a6cdaa58cd503271d98ee1f21c1dfb72d29432a5500cfabedba6 555002 samtools_0.1.10-1_hurd-i386.deb
- f01bc8713b1acff855c43ba1323bc89af7d9b0ed6fc66ee795c4e58bfdc84318 164884 libbam-dev_0.1.10-1_hurd-i386.deb
+ a8ed8afefbcae83803779faab971bc7c5bc61f39b7bf0ce3c43b418a61d172fa 547110 samtools_0.1.12a-1_hurd-i386.deb
+ ba7fdaf7613cb931823565aae39623efcc209dd80631393f62ecc333d9cf0efc 157814 libbam-dev_0.1.12a-1_hurd-i386.deb
Files:
- 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
+ 6627d972decf32161f0019456b9e585a 547110 science optional samtools_0.1.12a-1_hurd-i386.deb
+ 35fb52d023b0d946c4bdf2b5418b1b75 157814 libdevel optional libbam-dev_0.1.12a-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_hurd-i386.deb
-───────────────────────────────
+samtools_0.1.12a-1_hurd-i386.deb
+────────────────────────────────
new debian package, version 2.0.
- size 555002 bytes: control archive= 1803 bytes.
- 798 bytes, 16 lines control
+ size 547110 bytes: control archive= 1801 bytes.
+ 799 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 972
+ Installed-Size: 976
Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -446,33 +513,33 @@ samtools_0.1.10-1_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 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:48 ./
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:48 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./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/
+-rw-r--r-- root/root 126609 2010-12-03 09:47 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-12-03 09:49 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:48 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 09:48 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 09:48 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:50 ./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 12567 2010-12-02 16:41 ./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
@@ -484,31 +551,31 @@ drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 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
-─────────────────────────────────
+-rwxr-xr-x root/root 5778 2010-12-03 09:50 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/bin/
+-rwxr-xr-x root/root 80068 2010-12-03 09:49 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23788 2010-12-03 09:49 ./usr/bin/razip
+-rwxr-xr-x root/root 313996 2010-12-03 09:49 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17488 2010-12-03 09:49 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6336 2010-12-03 09:49 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6320 2010-12-03 09:49 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10084 2010-12-03 09:49 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6920 2010-12-03 09:49 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_hurd-i386.deb
+──────────────────────────────────
new debian package, version 2.0.
- size 164884 bytes: control archive= 901 bytes.
- 678 bytes, 15 lines control
+ size 157814 bytes: control archive= 904 bytes.
+ 679 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 388
@@ -522,19 +589,19 @@ libbam-dev_0.1.10-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:50 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:50 ./usr/lib/
+-rw-r--r-- root/root 243684 2010-12-03 09:50 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:49 ./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
@@ -547,13 +614,14 @@ drwxr-xr-x root/root 0 2010-11-17 12:27 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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.)
+Purging /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq
+(Reading database ... 13045 files and directories currently installed.)
Removing libncurses5-dev ...
Removing cdbs ...
+Removing zlib1g-dev ...
Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1228
-Build needed 00:08:37, 8412k disc space
+Finished at 20101203-0951
+Build needed 00:27:27, 8428k 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 26d83cf..ddecfd3 100644
--- a/i386.build
+++ b/i386.build
@@ -1,41 +1,41 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/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>
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/i386 received Fri Dec 3 09:22:26 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=i386">i386</a> >> Fri Dec 3 09:22:26 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (i386) 17 Nov 2010 11:52 ║
+║ samtools 0.1.12a-1 (i386) 03 Dec 2010 09:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: i386
-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
+Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-844f11ba-9f87-46e7-97e1-8ee812a9f6ca/build/buildd-samtools_0.1.12a-1-i386-61mbY2
+Start Time: 20101203-0920
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:3 http://ftp.gr.debian.org unstable/main Sources [4071 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]
+Get:5 http://ftp.gr.debian.org unstable/contrib Sources [38.7 kB]
+Get:6 http://ftp.gr.debian.org unstable/non-free Sources [83.8 kB]
+Get:7 http://ftp.gr.debian.org unstable/main i386 Packages [6931 kB]
+Get:8 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-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:9 http://incoming.debian.org unstable Release [104 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:12 http://incoming.debian.org unstable/main Sources [4071 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [38.7 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.8 kB]
+Get:15 http://incoming.debian.org unstable/main i386 Packages [6931 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)
+Get:17 http://incoming.debian.org Sources [8014 B]
+Get:18 http://incoming.debian.org Packages [169 kB]
+Fetched 22.8 MB in 17s (1287 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -56,18 +56,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (253 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -98,10 +98,10 @@ 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.
+0 upgraded, 19 newly installed, 0 to remove and 40 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:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.0.17 [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]
@@ -121,10 +121,10 @@ 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
-Fetched 11.4 MB in 1s (6628 kB/s)
+Fetched 11.4 MB in 1s (7238 kB/s)
Selecting previously deselected package bsdmainutils.
(Reading database ... 10160 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_i386.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_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.
@@ -161,7 +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 (8.0.16) ...
+Setting up bsdmainutils (8.0.17) ...
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) ...
@@ -187,7 +187,7 @@ Removing negative dependencies:
Checking correctness of source dependencies...
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
+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_8.0.17 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 │
@@ -199,12 +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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -219,34 +219,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
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
@@ -272,8 +273,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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
@@ -284,10 +285,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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
@@ -304,24 +305,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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
@@ -331,14 +332,14 @@ 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_0.1.10-1-i386-QHg1ix/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/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_0.1.10-1-i386-QHg1ix/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
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-i386-QHg1ix/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -367,7 +368,7 @@ 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_0.1.10-1-i386-QHg1ix/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -375,6 +376,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -399,8 +401,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -424,7 +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_0.1.10-1-i386-QHg1ix/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -438,28 +440,28 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_i386.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_i386.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1154
+Build finished at 20101203-0922
-samtools_0.1.10-1_i386.changes:
+samtools_0.1.12a-1_i386.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd...>
@@ -468,36 +470,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 7ec4ab2b401a198129224cc9ff0cf624ace52448 553262 samtools_0.1.10-1_i386.deb
- c985e110c32555e807b6a5de6e3a3a71555a2b45 163630 libbam-dev_0.1.10-1_i386.deb
+ 8bbc22fe2849d2f019694e26cdec4c5897b6403f 546556 samtools_0.1.12a-1_i386.deb
+ 3100d9b3b95c7d5cf63da6695e5184ab2fb0022a 157736 libbam-dev_0.1.12a-1_i386.deb
Checksums-Sha256:
- 53eda7de0acec9a9cb60c7a1162d981fa7b0ec7c4c353a9da0d5967bdf41f279 553262 samtools_0.1.10-1_i386.deb
- 7ecd7eacded918d932bba0ceafd1753508265cb57dc72d504fd1b4a404efd42f 163630 libbam-dev_0.1.10-1_i386.deb
+ d71ed16a874a920a546e1e9f59ac0654b81ec25aec236b666e66608efb8b0c1f 546556 samtools_0.1.12a-1_i386.deb
+ 941cd899a521e70c7c16d194c3ef695ba41aaebfe8f430ac54d9ab5afd6fa34e 157736 libbam-dev_0.1.12a-1_i386.deb
Files:
- d08facd99b849089792ca3bc5f64e390 553262 science optional samtools_0.1.10-1_i386.deb
- 8f39f35c1864f497f184a7135484b4bb 163630 libdevel optional libbam-dev_0.1.10-1_i386.deb
+ 62d7a4320ab6b1e376f9457fe30067fd 546556 science optional samtools_0.1.12a-1_i386.deb
+ e3ea536c41192f0320873286684eda1d 157736 libdevel optional libbam-dev_0.1.12a-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_i386.deb
-──────────────────────────
+samtools_0.1.12a-1_i386.deb
+───────────────────────────
new debian package, version 2.0.
- size 553262 bytes: control archive= 1798 bytes.
- 790 bytes, 16 lines control
+ size 546556 bytes: control archive= 1793 bytes.
+ 791 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 972
+ Installed-Size: 976
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -510,49 +515,49 @@ samtools_0.1.10-1_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 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/samtools/
+-rwxr-xr-x root/root 6680 2010-12-03 09:22 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6176 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6160 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9908 2010-12-03 09:22 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17224 2010-12-03 09:22 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/bin/
+-rwxr-xr-x root/root 80068 2010-12-03 09:22 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23692 2010-12-03 09:22 ./usr/bin/razip
+-rwxr-xr-x root/root 313964 2010-12-03 09:22 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./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 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./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 126609 2010-12-03 09:22 ./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
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2010-12-03 09:22 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2010-12-03 09:22 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-12-03 09:22 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/samtools/
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./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 5778 2010-12-03 09:22 ./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
@@ -560,19 +565,19 @@ drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/share/samtools/
-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
+lrwxrwxrwx root/root 0 2010-12-03 09:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.10-1_i386.deb
-────────────────────────────
+libbam-dev_0.1.12a-1_i386.deb
+─────────────────────────────
new debian package, version 2.0.
- size 163630 bytes: control archive= 898 bytes.
- 673 bytes, 15 lines control
+ size 157736 bytes: control archive= 897 bytes.
+ 674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 388
@@ -586,19 +591,19 @@ libbam-dev_0.1.10-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
+-rw-r--r-- root/root 243680 2010-12-03 09:22 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./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 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./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
@@ -611,10 +616,10 @@ drwxr-xr-x root/root 0 2010-11-17 11:53 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-i386-sbuild-a53f9891-43dc-45dc-bad2-44f8a89de5da/build/buildd-samtools_0.1.10-1-i386-QHg1ix
+Purging /var/lib/schroot/mount/sid-i386-sbuild-844f11ba-9f87-46e7-97e1-8ee812a9f6ca/build/buildd-samtools_0.1.12a-1-i386-61mbY2
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1154
-Build needed 00:01:54, 8412k disc space
+Finished at 20101203-0922
+Build needed 00:01:48, 8432k 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 621c772..228f1d3 100644
--- a/ia64.build
+++ b/ia64.build
@@ -1,39 +1,51 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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>
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/ia64 received Fri Dec 3 09:24:25 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=ia64">ia64</a> >> Fri Dec 3 09:24:25 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on caballero.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (ia64) 17 Nov 2010 11:54 ║
+║ samtools 0.1.12a-1 (ia64) 03 Dec 2010 09:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: ia64
-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
+Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-ec894d00-3834-4b0f-8e8c-e53553a07378/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc
+Start Time: 20101203-0922
+Get:1 http://mirror.positive-internet.com sid Release.gpg [835 B]
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
+Get:2 http://mirror.positive-internet.com sid Release [104 kB]
+Get:3 http://mirror.positive-internet.com sid/main Sources/DiffIndex [2038 B]
+Get:4 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
-Get:1 http://incoming.debian.org Release.gpg [835 B]
+Get:5 http://incoming.debian.org Release.gpg [835 B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
Hit http://mirror.positive-internet.com sid/contrib Sources/DiffIndex
-Hit http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex
+Get:6 http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex [2038 B]
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
+Get:7 http://mirror.positive-internet.com sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:8 http://incoming.debian.org sid Release [104 kB]
+Get:9 http://incoming.debian.org Release [1604 B]
+Get:10 http://mirror.positive-internet.com sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:11 http://mirror.positive-internet.com sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:12 http://mirror.positive-internet.com sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
+Get:13 http://mirror.positive-internet.com sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
+Get:14 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main ia64 Packages/DiffIndex
+Get:15 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [2038 B]
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)
+Get:16 http://incoming.debian.org Sources [8014 B]
+Get:17 http://incoming.debian.org Packages [169 kB]
+Get:18 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:19 http://mirror.positive-internet.com sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
+Get:20 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:21 http://incoming.debian.org sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
+Get:22 http://incoming.debian.org sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
+Get:23 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:24 http://incoming.debian.org sid/main ia64 2010-12-03-0810.19.pdiff [798 B]
+Fetched 399 kB in 11s (36.2 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,18 +66,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 0s (445 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -96,11 +108,11 @@ The following NEW packages will be installed:
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
-0 upgraded, 16 newly installed, 0 to remove and 30 not upgraded.
+0 upgraded, 16 newly installed, 0 to remove and 35 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.)
+(Reading database ... 10388 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) ...
@@ -152,8 +164,8 @@ 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_2.11.2-7 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
+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_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+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_4.4.5-10 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_4.4.5-10 gcc_4:4.4.5-1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 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_4.8.30-3 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 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 │
@@ -165,12 +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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -185,34 +197,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
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
@@ -232,8 +245,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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
@@ -244,10 +257,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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
@@ -264,24 +277,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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 +304,14 @@ 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_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
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-ia64-Ufuuiu/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -327,7 +340,7 @@ 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_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -335,6 +348,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -359,8 +373,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/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 +398,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-ia64-Ufuuiu/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -398,28 +412,28 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_ia64.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_ia64.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1156
+Build finished at 20101203-0924
-samtools_0.1.10-1_ia64.changes:
+samtools_0.1.12a-1_ia64.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd...>
@@ -428,36 +442,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 78b7c1852767f71d9874d899f520318e4ae0f0a3 709634 samtools_0.1.10-1_ia64.deb
- 6c4403d37577f8b7c299c44ecb1b09cec3b5da4b 228678 libbam-dev_0.1.10-1_ia64.deb
+ a3f0377809cbc0f8d1f1f8218392d666dbca7257 691894 samtools_0.1.12a-1_ia64.deb
+ c650b494bdef80cf7bcdb93d5b2bf550ecdd1022 207066 libbam-dev_0.1.12a-1_ia64.deb
Checksums-Sha256:
- cafae5c3f5e09ec061533831e3871c1253bebcf7d5f58189dacafe4f625f8793 709634 samtools_0.1.10-1_ia64.deb
- 34845a981de99feb539e5b0477de26aaf1fa6f202b627e55951de34db513437d 228678 libbam-dev_0.1.10-1_ia64.deb
+ a9e74b2485999044dbf3025354617b13e5844054a013f840d37ee0f6a1c302fa 691894 samtools_0.1.12a-1_ia64.deb
+ c3033101dbd1ae9b7da5b6996a0894fad18ed3a41809e685e998a124e89e2f57 207066 libbam-dev_0.1.12a-1_ia64.deb
Files:
- cfe3ca029cce695f6512f81a33c1d1de 709634 science optional samtools_0.1.10-1_ia64.deb
- 63b504f33daffefe126f731236f23a8d 228678 libdevel optional libbam-dev_0.1.10-1_ia64.deb
+ 3c80dbac2bcc0a5e51eafb62fdb31c86 691894 science optional samtools_0.1.12a-1_ia64.deb
+ 8615cef0efb0fbe67b778596950e8533 207066 libdevel optional libbam-dev_0.1.12a-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_ia64.deb
-──────────────────────────
+samtools_0.1.12a-1_ia64.deb
+───────────────────────────
new debian package, version 2.0.
- size 709634 bytes: control archive= 1792 bytes.
- 793 bytes, 16 lines control
+ size 691894 bytes: control archive= 1791 bytes.
+ 794 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1560
+ Installed-Size: 1564
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -470,33 +487,33 @@ samtools_0.1.10-1_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 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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/
+-rw-r--r-- root/root 126609 2010-12-03 09:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-12-03 09:24 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 09:24 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 09:24 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 12567 2010-12-02 16:41 ./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
@@ -508,31 +525,31 @@ drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 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
-────────────────────────────
+-rwxr-xr-x root/root 5778 2010-12-03 09:24 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/bin/
+-rwxr-xr-x root/root 206648 2010-12-03 09:24 ./usr/bin/bcftools
+-rwxr-xr-x root/root 52520 2010-12-03 09:24 ./usr/bin/razip
+-rwxr-xr-x root/root 707816 2010-12-03 09:24 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30712 2010-12-03 09:24 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13360 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13296 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 22384 2010-12-03 09:24 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2010-12-03 09:24 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2010-12-03 09:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_ia64.deb
+─────────────────────────────
new debian package, version 2.0.
- size 228678 bytes: control archive= 894 bytes.
- 673 bytes, 15 lines control
+ size 207066 bytes: control archive= 894 bytes.
+ 674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 660
@@ -546,19 +563,19 @@ libbam-dev_0.1.10-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
+-rw-r--r-- root/root 521254 2010-12-03 09:24 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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
@@ -571,8 +588,8 @@ drwxr-xr-x root/root 0 2010-11-17 11:56 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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.)
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-ec894d00-3834-4b0f-8e8c-e53553a07378/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc
+(Reading database ... 12621 files and directories currently installed.)
Removing libncurses5-dev ...
Removing zlib1g-dev ...
Removing cdbs ...
@@ -598,7 +615,7 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1156
-Build needed 00:02:06, 12692k disc space
+Finished at 20101203-0924
+Build needed 00:02:10, 12688k 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 0ea1f96..78c9c3c 100644
--- a/kfreebsd-amd64.build
+++ b/kfreebsd-amd64.build
@@ -1,39 +1,46 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/kfreebsd-amd64 received Fri Dec 3 10:18:06 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=kfreebsd-amd64">kfreebsd-amd64</a> >> Fri Dec 3 10:18:06 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on fasch.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (kfreebsd-amd64) 17 Nov 2010 21:06 ║
+║ samtools 0.1.12a-1 (kfreebsd-amd64) 03 Dec 2010 10:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: kfreebsd-amd64
-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
-Get:1 http://incoming.debian.org sid Release.gpg [835 B]
+Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2
+Start Time: 20101203-1014
+Hit http://ftp.gr.debian.org sid Release.gpg
+Ign http://ftp.gr.debian.org/debian/ sid/contrib Translation-en
+Ign http://ftp.gr.debian.org/debian/ sid/main Translation-en
+Ign http://ftp.gr.debian.org/debian/ sid/non-free Translation-en
+Hit http://ftp.gr.debian.org sid Release
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://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
-Ign http://ftp.ca.debian.org/debian/ sid/main Translation-en
Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Get:2 http://incoming.debian.org Release.gpg [835 B]
+Hit http://incoming.debian.org Release.gpg
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:3 http://incoming.debian.org sid Release [104 kB]
-Hit http://ftp.ca.debian.org sid Release
-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://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
+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/non-free Sources/DiffIndex
+Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-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 Sources
+Hit http://incoming.debian.org Packages
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Fetched 424 kB in 5s (82.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,18 +61,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (194 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -96,11 +103,11 @@ 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 18 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 3 not upgraded.
Need to get 0 B/11.8 MB of archives.
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.)
+(Reading database ... 13308 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-amd64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-amd64.deb) ...
@@ -158,8 +165,8 @@ 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_4.4.5-8 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
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.6 libstdc++6_4.4.5-9 gcc-4.4_4.4.5-9 g++-4.4_4.4.5-9 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-9 libc0.1-dev_2.11.2-7 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.9 base-files_5.10 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 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_4.4.5-9 dash_0.5.5.1-7.3 debconf_1.5.37 debconf-i18n_1.5.37 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.2 diffutils_1:3.0-1 dpkg_1.15.8.6 dpkg-dev_1.15.8.6 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_4.4.5-9 gcc_4:4.4.5-1 gcc-4.4_4.4.5-9 gcc-4.4-base_4.4.5-9 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_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13 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_4.7.25-10 libdb4.8_4.8.30-3 libdpkg-perl_1.15.8.6 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-9 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_4.4.5-9 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 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_4.4.5-9 libstdc++6-4.4-dev_4.4.5-9 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_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-4 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.23-3 type-handling_0.2.23 tzdata_2010o-1 ufsutils_7.3-1+b1 util-linux_2.17.2-3.3 vim_2:7.3.035+hg~8fdc12103333-1 vim-common_2:7.3.035+hg~8fdc12103333-1 vim-runtime_2:7.3.035+hg~8fdc12103333-1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -171,12 +178,12 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -191,34 +198,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-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'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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_0.1.10-1-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-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'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
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
@@ -238,8 +246,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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
@@ -250,10 +258,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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
@@ -270,24 +278,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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
@@ -297,14 +305,14 @@ 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_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/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_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
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-kfreebsd-amd64-thNSJN/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -333,7 +341,7 @@ 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_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -341,6 +349,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -365,8 +374,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -390,7 +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_0.1.10-1-kfreebsd-amd64-thNSJN/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -404,66 +413,69 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_kfreebsd-amd64.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_kfreebsd-amd64.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-2107
+Build finished at 20101203-1017
-samtools_0.1.10-1_kfreebsd-amd64.changes:
+samtools_0.1.12a-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd...>
+Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- ca5e0c3e1f7735d05ec237ba58ed833513a38b2c 556548 samtools_0.1.10-1_kfreebsd-amd64.deb
- 334801d9cb0d75cf144e5107ba852f5f6b06dd65 164026 libbam-dev_0.1.10-1_kfreebsd-amd64.deb
+ e9571bc72c8ddd5a2972a340e923f3def5591768 553904 samtools_0.1.12a-1_kfreebsd-amd64.deb
+ cbd8d3ca435ec22efad48117cbc24b09e7d9efe9 155700 libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
Checksums-Sha256:
- f770b722aec7a55776eaeb314fdefb74fdaa80c5595598cfdcdd977b313dbb7b 556548 samtools_0.1.10-1_kfreebsd-amd64.deb
- d697257fba7f6e5f910a107ed18028eeed8d8566b55d87ec60edab3804da7630 164026 libbam-dev_0.1.10-1_kfreebsd-amd64.deb
+ 2baa21df0016f17cb370b589b73a3ea3d85113fdf97ed83de975a1c33e04ea35 553904 samtools_0.1.12a-1_kfreebsd-amd64.deb
+ ee66327cf310e59d1a5430ef2be8591b0c9fe481c705a96b80b86567fd57bc8b 155700 libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
Files:
- 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
+ e9cc7f82a9df7d162d8c21a1f88c5cbb 553904 science optional samtools_0.1.12a-1_kfreebsd-amd64.deb
+ 8f0652d453338d28eff781fcc85ee532 155700 libdevel optional libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_kfreebsd-amd64.deb
-────────────────────────────────────
+samtools_0.1.12a-1_kfreebsd-amd64.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 556548 bytes: control archive= 1803 bytes.
- 802 bytes, 16 lines control
+ size 553904 bytes: control archive= 1800 bytes.
+ 803 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 936
+ Installed-Size: 942
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -476,33 +488,33 @@ samtools_0.1.10-1_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 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./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/
+-rw-r--r-- root/root 126609 2010-12-03 10:16 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-12-03 10:17 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 10:17 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 10:17 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./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 12567 2010-12-02 16:41 ./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
@@ -514,34 +526,34 @@ drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 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
-──────────────────────────────────────
+-rwxr-xr-x root/root 5778 2010-12-03 10:17 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/bin/
+-rwxr-xr-x root/root 85384 2010-12-03 10:17 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24864 2010-12-03 10:17 ./usr/bin/razip
+-rwxr-xr-x root/root 318672 2010-12-03 10:17 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19248 2010-12-03 10:17 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8248 2010-12-03 10:17 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8200 2010-12-03 10:17 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11712 2010-12-03 10:17 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8520 2010-12-03 10:17 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
+───────────────────────────────────────
new debian package, version 2.0.
- size 164026 bytes: control archive= 900 bytes.
- 683 bytes, 15 lines control
+ size 155700 bytes: control archive= 902 bytes.
+ 684 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 434
+ Installed-Size: 438
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -552,19 +564,19 @@ libbam-dev_0.1.10-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/lib/
+-rw-r--r-- root/root 295222 2010-12-03 10:17 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 10:17 ./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
@@ -577,8 +589,8 @@ drwxr-xr-x root/root 0 2010-11-17 21:07 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.10-1-kfreebsd-amd64-thNSJN
-(Reading database ... 14036 files and directories currently installed.)
+Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2
+(Reading database ... 15570 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -607,7 +619,7 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-2107
-Build needed 00:01:17, 9682k disc space
+Finished at 20101203-1017
+Build needed 00:02:21, 9698k 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 7f31a8c..847b191 100644
--- a/kfreebsd-i386.build
+++ b/kfreebsd-i386.build
@@ -1,45 +1,117 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/kfreebsd-i386 received Fri Dec 3 09:27:05 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=kfreebsd-i386">kfreebsd-i386</a> >> Fri Dec 3 09:27:05 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (kfreebsd-i386) 17 Nov 2010 11:53 ║
+║ samtools 0.1.12a-1 (kfreebsd-i386) 03 Dec 2010 09:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: kfreebsd-i386
-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
+Chroot Build Dir: /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx
+Start Time: 20101203-0923
+Get:1 http://ftp.gr.debian.org sid Release.gpg [835 B]
+Ign http://ftp.gr.debian.org/debian/ sid/contrib Translation-en
+Ign http://ftp.gr.debian.org/debian/ sid/main Translation-en
+Ign http://ftp.gr.debian.org/debian/ sid/non-free Translation-en
+Get:2 http://ftp.gr.debian.org sid Release [104 kB]
+Get:3 http://ftp.gr.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:4 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/contrib Translation-en
Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Get:1 http://incoming.debian.org Release.gpg [835 B]
+Get:5 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]
-Ign http://ftp.ca.debian.org/debian/ sid/main Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Ign http://ftp.ca.debian.org/debian/ sid/non-free Translation-en
-Hit http://ftp.ca.debian.org sid Release
+Get:6 http://ftp.gr.debian.org sid/contrib Sources/DiffIndex [2023 B]
+Get:7 http://ftp.gr.debian.org sid/non-free Sources/DiffIndex [2023 B]
+Get:8 http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Get:9 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex [2023 B]
+Get:10 http://ftp.gr.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
+Get:11 http://ftp.gr.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
+Get:12 http://incoming.debian.org sid Release [104 kB]
+Get:13 http://ftp.gr.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
+Get:14 http://ftp.gr.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
+Get:15 http://ftp.gr.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
+Get:16 http://ftp.gr.debian.org sid/main 2010-12-01-1412.04.pdiff [2285 B]
+Get:17 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-1412.04.pdiff [500 B]
+Get:18 http://ftp.gr.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
+Get:19 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-01-1412.04.pdiff [257 B]
+Get:20 http://incoming.debian.org Release [1604 B]
+Get:21 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-1412.04.pdiff [500 B]
+Get:22 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-01-1412.04.pdiff [257 B]
+Get:23 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Get:24 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Get: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 [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 244 kB in 3s (70.9 kB/s)
+Get:25 http://incoming.debian.org Sources [8014 B]
+Get:26 http://ftp.gr.debian.org sid/contrib 2010-12-01-2014.11.pdiff [31 B]
+Get:27 http://ftp.gr.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
+Get:28 http://ftp.gr.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
+Get:29 http://ftp.gr.debian.org sid/non-free 2010-12-01-1412.04.pdiff [329 B]
+Get:30 http://incoming.debian.org Packages [169 kB]
+Get:31 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-1412.04.pdiff [500 B]
+Get:32 http://ftp.gr.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
+Get:33 http://ftp.gr.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
+Get:34 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:35 http://incoming.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
+Get:36 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:37 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-01-1412.04.pdiff [257 B]
+Get:38 http://incoming.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
+Get:39 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-2014.11.pdiff [20.5 kB]
+Get:40 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-2014.11.pdiff [20.5 kB]
+Get:41 http://ftp.gr.debian.org sid/main 2010-12-01-2014.11.pdiff [10.4 kB]
+Get:42 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-02-2015.37.pdiff [529 B]
+Get:43 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-02-2015.37.pdiff [529 B]
+Get:44 http://ftp.gr.debian.org sid/non-free 2010-12-02-0815.49.pdiff [238 B]
+Get:45 http://ftp.gr.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
+Get:46 http://ftp.gr.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
+Get:47 http://incoming.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:48 http://ftp.gr.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
+Get:49 http://ftp.gr.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
+Get:50 http://incoming.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
+Get:51 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-01-2014.11.pdiff [20.5 kB]
+Get:52 http://ftp.gr.debian.org sid/non-free kfreebsd-i386 2010-12-02-2015.37.pdiff [529 B]
+Get:53 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0209.58.pdiff [28.1 kB]
+Get:54 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0209.58.pdiff [28.1 kB]
+Get:55 http://ftp.gr.debian.org sid/main 2010-12-02-0209.58.pdiff [5265 B]
+Get:56 http://ftp.gr.debian.org sid/non-free 2010-12-02-2015.37.pdiff [394 B]
+Get:57 http://ftp.gr.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
+Get:58 http://ftp.gr.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
+Get:59 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0209.58.pdiff [28.1 kB]
+Get:60 http://ftp.gr.debian.org sid/main 2010-12-02-0815.49.pdiff [2245 B]
+Get:61 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0815.49.pdiff [226 B]
+Get:62 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0815.49.pdiff [226 B]
+Get:63 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-0815.49.pdiff [226 B]
+Get:64 http://ftp.gr.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
+Get:65 http://ftp.gr.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
+Get:66 http://ftp.gr.debian.org sid/main 2010-12-02-1418.14.pdiff [2470 B]
+Get:67 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-1418.14.pdiff [9688 B]
+Get:68 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-1418.14.pdiff [9688 B]
+Get:69 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-1418.14.pdiff [9688 B]
+Get:70 http://ftp.gr.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
+Get:71 http://ftp.gr.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
+Get:72 http://ftp.gr.debian.org sid/main 2010-12-02-2015.37.pdiff [2371 B]
+Get:73 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-2015.37.pdiff [406 B]
+Get:74 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-2015.37.pdiff [406 B]
+Get:75 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-02-2015.37.pdiff [406 B]
+Get:76 http://ftp.gr.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:77 http://ftp.gr.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:78 http://ftp.gr.debian.org sid/main 2010-12-03-0208.36.pdiff [3044 B]
+Get:79 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0208.36.pdiff [402 B]
+Get:80 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0208.36.pdiff [402 B]
+Get:81 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0208.36.pdiff [402 B]
+Get:82 http://ftp.gr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:83 http://ftp.gr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:84 http://ftp.gr.debian.org sid/main 2010-12-03-0810.19.pdiff [666 B]
+Get:85 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
+Get:86 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
+Get:87 http://ftp.gr.debian.org sid/main kfreebsd-i386 2010-12-03-0810.19.pdiff [796 B]
+Fetched 495 kB in 25s (19.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -60,18 +132,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (210 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -95,18 +167,18 @@ Suggested packages:
devscripts doc-base dh-make gettext-doc groff less www-browser
libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper 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, 18 newly installed, 0 to remove and 22 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 33 not upgraded.
Need to get 0 B/11.1 MB of archives.
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.)
+(Reading database ... 11720 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-i386.deb) ...
@@ -163,9 +235,9 @@ 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: GNU/kFreeBSD 8.1-1-686 kfreebsd-i386 (i686)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-8 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
+Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.5 libstdc++6_4.4.5-10 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.5-10 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 cpp_4:4.4.5-1 cpp-4.4_4.4.5-10 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_4.4.5-10 gcc_4:4.4.5-1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 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_4.8.30-3 libdpkg-perl_1.15.8.5 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 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_4.4.5-10 libgpg-error0_1.6-1 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 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_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16+nmu1 procps_1:3.2.8-9 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 │
@@ -177,12 +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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -197,34 +269,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-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'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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_0.1.10-1-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-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'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
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
@@ -250,8 +323,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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
@@ -262,10 +335,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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
@@ -282,24 +355,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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
@@ -309,14 +382,14 @@ 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_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/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_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
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-kfreebsd-i386-mWRvh5/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -345,7 +418,7 @@ 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_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -353,6 +426,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -377,8 +451,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -402,7 +476,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -416,66 +490,69 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_kfreebsd-i386.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_kfreebsd-i386.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1154
+Build finished at 20101203-0926
-samtools_0.1.10-1_kfreebsd-i386.changes:
+samtools_0.1.12a-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd...>
+Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- c437a7e820a1d824230e54b896170dafac365761 554156 samtools_0.1.10-1_kfreebsd-i386.deb
- 56dc83cc9c08a228a5752fb934451b6bcc618acd 164816 libbam-dev_0.1.10-1_kfreebsd-i386.deb
+ 164adcd56b82ee0bcf67f213f6b768cda0e37c87 546952 samtools_0.1.12a-1_kfreebsd-i386.deb
+ 35fd1a19555c60c04ccd6bc7415a68191b52fa0b 157656 libbam-dev_0.1.12a-1_kfreebsd-i386.deb
Checksums-Sha256:
- 30d7d78e6a4127808baeb2de38f9525348a0ff3f4e7ae66ef2f9b40a30417d5d 554156 samtools_0.1.10-1_kfreebsd-i386.deb
- eb3adc973590bc229b4ef3b71b4af42b7fa1e85d4a1832cd126df6a8a3bec0ea 164816 libbam-dev_0.1.10-1_kfreebsd-i386.deb
+ ed916c3a9eb8d0ede51fd39e93624daea4f232f64648a850c6272d9a16b62a0a 546952 samtools_0.1.12a-1_kfreebsd-i386.deb
+ 2bc39a07a79e3115a616b805723e76262773dca29dea0bf8565792dd2fe68456 157656 libbam-dev_0.1.12a-1_kfreebsd-i386.deb
Files:
- 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
+ b69ec10fef8c78f148be3c40055c42bd 546952 science optional samtools_0.1.12a-1_kfreebsd-i386.deb
+ 28a03f293b4a554282d54e4738f1361e 157656 libdevel optional libbam-dev_0.1.12a-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_kfreebsd-i386.deb
-───────────────────────────────────
+samtools_0.1.12a-1_kfreebsd-i386.deb
+────────────────────────────────────
new debian package, version 2.0.
- size 554156 bytes: control archive= 1797 bytes.
- 801 bytes, 16 lines control
+ size 546952 bytes: control archive= 1795 bytes.
+ 802 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 914
+ Installed-Size: 924
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -488,33 +565,33 @@ samtools_0.1.10-1_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 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 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 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./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/
+-rw-r--r-- root/root 126609 2010-12-03 09:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-12-03 09:26 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 09:26 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 09:26 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./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 12567 2010-12-02 16:41 ./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
@@ -526,34 +603,34 @@ drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 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
-─────────────────────────────────────
+-rwxr-xr-x root/root 5778 2010-12-03 09:26 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/bin/
+-rwxr-xr-x root/root 80068 2010-12-03 09:26 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23612 2010-12-03 09:26 ./usr/bin/razip
+-rwxr-xr-x root/root 313868 2010-12-03 09:26 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17296 2010-12-03 09:26 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6160 2010-12-03 09:26 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6144 2010-12-03 09:26 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9876 2010-12-03 09:26 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6632 2010-12-03 09:26 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_kfreebsd-i386.deb
+──────────────────────────────────────
new debian package, version 2.0.
- size 164816 bytes: control archive= 899 bytes.
- 682 bytes, 15 lines control
+ size 157656 bytes: control archive= 902 bytes.
+ 683 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 370
+ Installed-Size: 374
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -564,19 +641,19 @@ libbam-dev_0.1.10-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/lib/
+-rw-r--r-- root/root 243644 2010-12-03 09:26 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:26 ./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
@@ -589,8 +666,8 @@ drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.10-1-kfreebsd-i386-mWRvh5
-(Reading database ... 15628 files and directories currently installed.)
+Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx
+(Reading database ... 13982 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -619,7 +696,7 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1154
-Build needed 00:01:18, 8096k disc space
+Finished at 20101203-0926
+Build needed 00:02:38, 8120k 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 ef0a316..9a312ca 100644
--- a/mipsel.build
+++ b/mipsel.build
@@ -1,39 +1,53 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/mipsel received Fri Dec 3 09:45:45 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=mipsel">mipsel</a> >> Fri Dec 3 09:45:45 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on monteverdi.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (mipsel) 17 Nov 2010 11:55 ║
+║ samtools 0.1.12a-1 (mipsel) 03 Dec 2010 09:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: mipsel
-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]
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-a7788f0e-a45d-4a01-9fc1-0c7f0fe22793/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN
+Start Time: 20101203-0924
+Get:1 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: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]
-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)
+Get:3 http://incoming.debian.org unstable Release [104 kB]
+Get:4 http://mirror.ayous.org unstable Release.gpg [835 B]
+Ign http://mirror.ayous.org/debian/ unstable/contrib Translation-en
+Ign http://mirror.ayous.org/debian/ unstable/main Translation-en
+Get:5 http://mirror.ayous.org unstable Release [104 kB]
+Ign http://mirror.ayous.org unstable/main Sources
+Ign http://mirror.ayous.org unstable/contrib Sources
+Ign http://mirror.ayous.org unstable/non-free Sources
+Ign http://mirror.ayous.org unstable/main mipsel Packages
+Ign http://mirror.ayous.org unstable/contrib mipsel Packages
+Get:6 http://incoming.debian.org Release [1604 B]
+Get:7 http://mirror.ayous.org unstable/main Sources [5242 kB]
+Ign http://incoming.debian.org unstable/main Sources
+Ign http://incoming.debian.org unstable/contrib Sources
+Ign http://incoming.debian.org unstable/non-free Sources
+Ign http://incoming.debian.org unstable/main mipsel Packages
+Ign http://incoming.debian.org unstable/contrib mipsel Packages
+Ign http://incoming.debian.org Sources
+Ign http://incoming.debian.org Packages
+Get:8 http://incoming.debian.org unstable/main Sources [5242 kB]
+Get:9 http://mirror.ayous.org unstable/contrib Sources [46.1 kB]
+Get:10 http://mirror.ayous.org unstable/non-free Sources [101 kB]
+Get:11 http://mirror.ayous.org unstable/main mipsel Packages [8868 kB]
+Get:12 http://incoming.debian.org unstable/contrib Sources [46.1 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:14 http://incoming.debian.org unstable/main mipsel Packages [8868 kB]
+Get:15 http://mirror.ayous.org unstable/contrib mipsel Packages [62.4 kB]
+Get:16 http://incoming.debian.org unstable/contrib mipsel Packages [62.4 kB]
+Get:17 http://incoming.debian.org Sources [8378 B]
+Get:18 http://incoming.debian.org Packages [262 kB]
+Fetched 29.1 MB in 48s (600 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,62 +68,138 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 3s (99.7 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
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 package was automatically installed and is no longer required:
- 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 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 44 not upgraded.
+Need to get 11.6 MB of archives.
+After this operation, 37.2 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.0.17 [208 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.20.1-10 [1188 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.7-6 [1247 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.02-1.1 [233 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-1 [832 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.24.2-1 [1039 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.7+20100313-4 [1639 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 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.
+Fetched 11.6 MB in 2s (4941 kB/s)
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10134 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_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_2.7.8.dfsg-1_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+nmu1_all.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
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) ...
-Processing triggers for man-db ...
+Setting up bsdmainutils (8.0.17) ...
+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-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
+Kernel: Linux 2.6.33-rc7 mipsel (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_4.4.5-2 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_8.0.17 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_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_1:4.4.5-2 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 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 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 │
@@ -121,12 +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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -141,34 +231,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
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
@@ -194,8 +285,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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
@@ -206,10 +297,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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
@@ -226,24 +317,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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
@@ -253,14 +344,14 @@ 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_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/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_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
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-mipsel-pvnfQY/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -289,7 +380,7 @@ 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_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -297,6 +388,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -321,8 +413,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -346,7 +438,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-mipsel-pvnfQY/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -360,66 +452,69 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_mipsel.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_mipsel.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1159
+Build finished at 20101203-0930
-samtools_0.1.10-1_mipsel.changes:
+samtools_0.1.12a-1_mipsel.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd...>
+Maintainer: mipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- eaab4b8f1f63bec010b44d386d19f4360ba51158 586618 samtools_0.1.10-1_mipsel.deb
- 41b74aaf5f325847427b23d59315dfb3a770a26d 182386 libbam-dev_0.1.10-1_mipsel.deb
+ f29fd836ed041a1f2088c9d36c8a46ad110d0d4f 578292 samtools_0.1.12a-1_mipsel.deb
+ cd679f7269405f59939c75dfd77d99bf3d62e704 173498 libbam-dev_0.1.12a-1_mipsel.deb
Checksums-Sha256:
- 3a76a0552d7e7a6695889464f41ed8421ba8b18c7479a4c992b6dd31fb618604 586618 samtools_0.1.10-1_mipsel.deb
- a7f066c7f76e015518e0116a6572cf8feda3d5f146ff0ee80b1eee42443a0e0f 182386 libbam-dev_0.1.10-1_mipsel.deb
+ a875f6bd7b1d39080160048bf0d7711496303b61d528f637c6798bb7725611bf 578292 samtools_0.1.12a-1_mipsel.deb
+ 072b4c5f5635ddb791b86e2be2fa5e5bcb16c4fc03581aa0b181720d5671e5cf 173498 libbam-dev_0.1.12a-1_mipsel.deb
Files:
- 2f161c4ec5673172c159b692884b3ea6 586618 science optional samtools_0.1.10-1_mipsel.deb
- ca2e77036f0009b7cdccd794edbd1e83 182386 libdevel optional libbam-dev_0.1.10-1_mipsel.deb
+ 7de915c17da9a27be7c7aaeeae84489e 578292 science optional samtools_0.1.12a-1_mipsel.deb
+ 912706773b87a79e5be0c4df0c4003ec 173498 libdevel optional libbam-dev_0.1.12a-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_mipsel.deb
-────────────────────────────
+samtools_0.1.12a-1_mipsel.deb
+─────────────────────────────
new debian package, version 2.0.
- size 586618 bytes: control archive= 1793 bytes.
- 793 bytes, 16 lines control
+ size 578292 bytes: control archive= 1796 bytes.
+ 794 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1112
+ Installed-Size: 1116
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -432,69 +527,69 @@ samtools_0.1.10-1_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 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/samtools/
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./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 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 5778 2010-12-03 09:30 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.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 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 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
-──────────────────────────────
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2010-12-03 09:30 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./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 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 126609 2010-12-03 09:30 ./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 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2010-12-03 09:30 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-12-03 09:30 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/bin/
+-rwxr-xr-x root/root 410760 2010-12-03 09:30 ./usr/bin/samtools
+-rwxr-xr-x root/root 30584 2010-12-03 09:30 ./usr/bin/razip
+-rwxr-xr-x root/root 108704 2010-12-03 09:30 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/lib/samtools/
+-rwxr-xr-x root/root 13268 2010-12-03 09:30 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2010-12-03 09:30 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9768 2010-12-03 09:30 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2010-12-03 09:30 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 19944 2010-12-03 09:30 ./usr/lib/samtools/wgsim
+lrwxrwxrwx root/root 0 2010-12-03 09:30 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_mipsel.deb
+───────────────────────────────
new debian package, version 2.0.
- size 182386 bytes: control archive= 897 bytes.
- 675 bytes, 15 lines control
+ size 173498 bytes: control archive= 899 bytes.
+ 676 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 444
@@ -508,23 +603,23 @@ libbam-dev_0.1.10-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./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 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/
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./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 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
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/lib/
+-rw-r--r-- root/root 302950 2010-12-03 09:30 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -533,14 +628,10 @@ drwxr-xr-x root/root 0 2010-11-17 11:59 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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 ...
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-a7788f0e-a45d-4a01-9fc1-0c7f0fe22793/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1159
-Build needed 00:04:30, 9292k disc space
+Finished at 20101203-0930
+Build needed 00:06:40, 9296k 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 79b9da6..0eaa76a 100644
--- a/powerpc.build
+++ b/powerpc.build
@@ -1,41 +1,36 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/powerpc received Fri Dec 3 09:22:35 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=powerpc">powerpc</a> >> Fri Dec 3 09:22:35 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on praetorius.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (powerpc) 17 Nov 2010 11:52 ║
+║ samtools 0.1.12a-1 (powerpc) 03 Dec 2010 09:19 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: powerpc
-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)
+Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-f6484d4d-a7cc-4101-9c13-f7b72cf926c7/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf
+Start Time: 20101203-0919
+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 [6845kB]
+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 [4071kB]
+Get:9 http://ftp.se.debian.org unstable/contrib Sources [38.7kB]
+Get:10 http://ftp.se.debian.org unstable/non-free Sources [83.8kB]
+Get:11 http://incoming.debian.org Release [1604B]
+Get:12 http://incoming.debian.org unstable/main Packages [6845kB]
+Get:13 http://incoming.debian.org unstable/contrib Packages [50.1kB]
+Get:14 http://incoming.debian.org unstable/main Sources [4071kB]
+Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
+Get:16 http://incoming.debian.org unstable/non-free Sources [83.8kB]
+Get:17 http://incoming.debian.org Packages [169kB]
+Get:18 http://incoming.debian.org Sources [8014B]
+Fetched 22.6MB in 23s (980kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,20 +49,18 @@ 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 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)
+Need to get 364kB of source archives.
+Get:1 http://incoming.debian.org samtools 0.1.12a-1 (dsc) [1946B]
+Get:2 http://incoming.debian.org samtools 0.1.12a-1 (tar) [356kB]
+Get:3 http://incoming.debian.org samtools 0.1.12a-1 (diff) [6337B]
+Fetched 364kB in 1s (352kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -86,45 +79,57 @@ 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
+ 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
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libgpm2 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 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]
+The following packages will be upgraded:
+ libncurses5 ncurses-bin
+2 upgraded, 19 newly installed, 0 to remove and 64 not upgraded.
+Need to get 12.5MB of archives.
+After this operation, 36.2MB 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 8.0.17 [207kB]
+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 2.7.8.dfsg-1 [849kB]
+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+nmu1 [223kB]
+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]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.8 MB in 2s (4685 kB/s)
+Fetched 12.5MB in 1s (9491kB/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) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10126 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_powerpc.deb) ...
+(Reading database ... 9867 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_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.
@@ -161,7 +166,7 @@ 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 (8.0.16) ...
+Setting up bsdmainutils (8.0.17) ...
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) ...
@@ -186,8 +191,8 @@ 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_2.11.2-7 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
+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_8.0.17 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_2.7.8.dfsg-1 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+nmu1 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -199,12 +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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -213,40 +218,40 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
+dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
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_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
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
@@ -272,8 +277,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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
@@ -284,10 +289,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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
@@ -304,24 +309,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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
@@ -331,17 +336,17 @@ 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_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/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_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
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-powerpc-2RQgrp/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
+../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
@@ -367,7 +372,7 @@ 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_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -375,6 +380,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -399,8 +405,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -424,7 +430,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-powerpc-2RQgrp/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -438,66 +444,68 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_powerpc.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_powerpc.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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 20101117-1154
+Build finished at 20101203-0922
-samtools_0.1.10-1_powerpc.changes:
+samtools_0.1.12a-1_powerpc.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd...>
+Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 556f78d19102f12234c63222841fcaf9d08417ac 574438 samtools_0.1.10-1_powerpc.deb
- 54e1cd80b2fae6dddbb3f28ea831598f4724cb5f 169458 libbam-dev_0.1.10-1_powerpc.deb
+ b8ae505c9c5fa2cdf3754cfbd3432b433940abc1 560870 samtools_0.1.12a-1_powerpc.deb
+ fcf051bc2b68143cb4e792f96e74ce4d0f031dd9 162450 libbam-dev_0.1.12a-1_powerpc.deb
Checksums-Sha256:
- fe7cd01804d159d3b77895f8381170f2a5e5dd80280f819965aa59ac0369d212 574438 samtools_0.1.10-1_powerpc.deb
- 018ca127bdec9afe0eaaa81c57710710ee63497d8f70f68b2ce4572955483f72 169458 libbam-dev_0.1.10-1_powerpc.deb
+ 26ccc7ee17384c17b348c7e4327b37c51f32a93035a26fd2eb03b84aad8c7314 560870 samtools_0.1.12a-1_powerpc.deb
+ 4671231fe66c2f4a647c8b80c269088e9383d1e50bcc07ca6b912fc483d8f4f5 162450 libbam-dev_0.1.12a-1_powerpc.deb
Files:
- 98e2158975397738fc69e15422f4c400 574438 science optional samtools_0.1.10-1_powerpc.deb
- a9ab9475739c025590eff674f377c2fa 169458 libdevel optional libbam-dev_0.1.10-1_powerpc.deb
+ 028831887d836951c07eaf52b9b105b2 560870 science optional samtools_0.1.12a-1_powerpc.deb
+ ef55d1299cc1be05e27fdf90636ffbe9 162450 libdevel optional libbam-dev_0.1.12a-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_powerpc.deb
-─────────────────────────────
+samtools_0.1.12a-1_powerpc.deb
+──────────────────────────────
new debian package, version 2.0.
- size 574438 bytes: control archive= 1792 bytes.
- 794 bytes, 16 lines control
+ size 560870 bytes: control archive= 1794 bytes.
+ 795 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1016
+ Installed-Size: 1020
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -510,69 +518,69 @@ samtools_0.1.10-1_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 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/bin/
+-rwxr-xr-x root/root 93516 2010-12-03 09:22 ./usr/bin/bcftools
+-rwxr-xr-x root/root 26828 2010-12-03 09:22 ./usr/bin/razip
+-rwxr-xr-x root/root 343648 2010-12-03 09:22 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7352 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11116 2010-12-03 09:22 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 19388 2010-12-03 09:22 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7352 2010-12-03 09:22 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8008 2010-12-03 09:22 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2010-12-03 09:22 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-12-03 09:22 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2010-12-03 09:21 ./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 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 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 1966 2010-12-03 09:22 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./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 5778 2010-12-03 09:22 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.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 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.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
-───────────────────────────────
+-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 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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+lrwxrwxrwx root/root 0 2010-12-03 09:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_powerpc.deb
+────────────────────────────────
new debian package, version 2.0.
- size 169458 bytes: control archive= 896 bytes.
- 676 bytes, 15 lines control
+ size 162450 bytes: control archive= 898 bytes.
+ 677 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 404
@@ -586,23 +594,23 @@ libbam-dev_0.1.10-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/lib/
+-rw-r--r-- root/root 260866 2010-12-03 09:22 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./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
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./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 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -611,10 +619,10 @@ drwxr-xr-x root/root 0 2010-11-17 11:54 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-05b829a1-dae0-44c0-a5bc-eab137be8825/build/buildd-samtools_0.1.10-1-powerpc-2RQgrp
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-f6484d4d-a7cc-4101-9c13-f7b72cf926c7/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1154
-Build needed 00:02:22, 8908k disc space
+Finished at 20101203-0922
+Build needed 00:02:57, 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 14ccf89..3af7e2d 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_0.1.10-1_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>
+<html><head><title>File `log' in samtools_0.1.12a-1_powerpcspe (Dec 3 17:51)</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_0.1.12a-1_powerpcspe (Dec 3 17:51)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=powerpcspe">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=powerpcspe">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=powerpcspe&stamp=1291398710">Dec 3 17:51</a> >> log</td></tr></table><p><pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on baako.tec.linutronix.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (powerpcspe) 18 Nov 2010 16:35 ║
+║ samtools 0.1.12a-1 (powerpcspe) 04 Dec 2010 18:45 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: powerpcspe
-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
+Chroot Build Dir: /var/lib/schroot/mount/spestage-0fea459c-6bbb-4543-9144-91e0da2cf54a/spestage/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ
+Start Time: 20101204-1845
Hit http://merkur sid Release.gpg
Hit http://merkur sid Release.gpg
Ign http://merkur/debian/debian-ports/ sid/main Translation-en
@@ -21,20 +21,17 @@ Hit http://merkur sid Release
Hit http://merkur sid Release
Hit http://merkur unreleased Release
Hit http://merkur sid/main Sources/DiffIndex
-Get:1 http://ftp.de.debian.org sid Release.gpg [835 B]
-Get:2 http://incoming.debian-ports.org unstable Release.gpg [835 B]
+Hit http://ftp.de.debian.org sid Release.gpg
+Get:1 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
-Get:3 http://ftp.de.debian.org sid Release [104 kB]
-Get:4 http://incoming.debian-ports.org unstable Release [8817 B]
+Hit http://ftp.de.debian.org sid Release
+Get:2 http://incoming.debian-ports.org unstable Release [8817 B]
+Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian-ports.org unstable/main Sources
-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)
+Hit http://incoming.debian-ports.org unstable/main powerpcspe Packages
+Fetched 9652 B in 1s (5146 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -55,18 +52,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (206 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -97,10 +94,10 @@ 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 21 not upgraded.
+0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
Need to get 11.7 MB of archives.
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:1 http://merkur/debian/debian-ports/ sid/main bsdmainutils powerpcspe 8.0.17 [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]
@@ -120,10 +117,10 @@ 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 (15.7 MB/s)
+Fetched 11.7 MB in 0s (16.2 MB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10179 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_powerpcspe.deb) ...
+(Reading database ... 10209 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_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.
@@ -160,7 +157,7 @@ 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 (8.0.16) ...
+Setting up bsdmainutils (8.0.17) ...
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) ...
@@ -185,11 +182,11 @@ Setting up zlib1g-dev (1:1.2.3.4.dfsg-3+b110) ...
Removing negative dependencies:
Checking correctness of source dependencies...
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_8.0.16 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_2.7.8.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
+Toolchain package versions: libc6-dev_2.11.1-2+powerpcspe1 dpkg-dev_1.15.8.6 linux-libc-dev_2.6.32-27+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_0.8.10 base-files_5.10 base-passwd_3.5.22+b110 bash_4.1-3+b111 binutils_2.20.1-15 bsdmainutils_8.0.17 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_2.11-5 cpp_4:4.4.4-2+powerpcspe1 cpp-4.4_4.4.4-4+powerpcspe4.5 dash_0.5.5.1-7.3 debconf_1.5.37 debconf-i18n_1.5.37 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debian-powerpcspe-archive-keyring_2009.10.13-2 debianutils_3.4.2 diff_1:3.0-1 diffutils_1:3.0-1+b110 dmsetup_2:1.02.48-4 dpkg_1.15.8.6 dpkg-dev_1.15.8.6 e2fslibs_1.41.12-2+b100 e2fsprogs_1.41.12-2+b100 fakeroot_1.14.4-2 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_3.05 html2text_1.3.2a-15+b100 initscripts_2.88!
+ dsf-13 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_4.7.25-10 libdb4.8_4.8.30-3 libdevmapper1.02.1_2:1.02.48-4 libdpkg-perl_1.15.8.6 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_5.0.0-2 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 libte
+xt-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_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+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_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.25-2 tzdata_2010o-1 util-linux_2.17.2-3.3 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3+b110 zlib1g-dev_1:1.2.3.4.dfsg-3+b110
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -201,12 +198,12 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -221,34 +218,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
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
@@ -274,8 +272,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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
@@ -286,10 +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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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
@@ -306,24 +304,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/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_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a'
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-powerpcspe-U05unX/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -369,7 +367,7 @@ 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_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -377,6 +375,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -401,8 +400,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -426,7 +425,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-powerpcspe-U05unX/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -440,28 +439,28 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_powerpcspe.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_powerpcspe.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101118-1641
+Build finished at 20101204-1851
-samtools_0.1.10-1_powerpcspe.changes:
+samtools_0.1.12a-1_powerpcspe.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpcspe
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
Maintainer: powerpcspe Build Daemon (baako) <baako at breakpoint...>
@@ -470,36 +469,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- c4f1431d843d098b4fd19e1c7397ccb572edc516 600110 samtools_0.1.10-1_powerpcspe.deb
- cbb42a446f3c7595f902a9aaac0fd520c56898a4 166310 libbam-dev_0.1.10-1_powerpcspe.deb
+ 1520872c020f97f4567636194b16a0487e2c59c1 575364 samtools_0.1.12a-1_powerpcspe.deb
+ 291ec6c5b5a441cb73a4fac22e0875ab2ad4c3f3 159186 libbam-dev_0.1.12a-1_powerpcspe.deb
Checksums-Sha256:
- ea16d571f3fe7af2465987d5f350e2496b34270b322dbac0d884aeeab72dcd86 600110 samtools_0.1.10-1_powerpcspe.deb
- c6b176f35b08b282f677af2c95c6f2b73deb512f5e9aee445b463c37a8674acb 166310 libbam-dev_0.1.10-1_powerpcspe.deb
+ f43f8492b43496d5653d05f6c61d304d1d3e61179a2543838f0eee0433ba8f21 575364 samtools_0.1.12a-1_powerpcspe.deb
+ 3ef5a014338bcd39f6d3a8ddcbd84a6eaba024dce1d04fe7a97c3a56897fe378 159186 libbam-dev_0.1.12a-1_powerpcspe.deb
Files:
- a635ecd3626ac563933ab62caf55989f 600110 science optional samtools_0.1.10-1_powerpcspe.deb
- 6d392128f0107d0946a0ea87538b519c 166310 libdevel optional libbam-dev_0.1.10-1_powerpcspe.deb
+ f3aba6c099b24d7b68fc75bf96aed0e9 575364 science optional samtools_0.1.12a-1_powerpcspe.deb
+ d2d9e4322736fa4095491f62b806876e 159186 libdevel optional libbam-dev_0.1.12a-1_powerpcspe.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_powerpcspe.deb
-────────────────────────────────
+samtools_0.1.12a-1_powerpcspe.deb
+─────────────────────────────────
new debian package, version 2.0.
- size 600110 bytes: control archive= 1800 bytes.
- 798 bytes, 16 lines control
+ size 575364 bytes: control archive= 1799 bytes.
+ 799 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: powerpcspe
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1040
+ Installed-Size: 1044
Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -512,21 +514,21 @@ samtools_0.1.10-1_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 2010-11-18 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/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/bin/
+-rwxr-xr-x root/root 340232 2010-12-04 18:51 ./usr/bin/samtools
+-rwxr-xr-x root/root 106488 2010-12-04 18:51 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24036 2010-12-04 18:51 ./usr/bin/razip
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/lib/samtools/
+-rwxr-xr-x root/root 36448 2010-12-04 18:51 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7536 2010-12-04 18:51 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 10384 2010-12-04 18:51 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6736 2010-12-04 18:51 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 6736 2010-12-04 18:51 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./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
@@ -537,44 +539,44 @@ drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/samtools/
-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 5778 2010-12-04 18:51 ./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 12567 2010-12-02 17:41 ./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
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2010-12-04 18:51 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-12-04 18:51 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 6692 2010-12-02 22:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 4927 2010-12-03 06:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2010-12-03 06:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 30752 2010-11-22 04:17 ./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 1031 2010-12-03 06:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1128 2010-12-03 06:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./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 126609 2010-12-04 18:47 ./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
+-rw-r--r-- root/root 1966 2010-12-04 18:51 ./usr/share/doc/samtools/README.bcftools
+lrwxrwxrwx root/root 0 2010-12-04 18:51 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.10-1_powerpcspe.deb
-──────────────────────────────────
+libbam-dev_0.1.12a-1_powerpcspe.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 166310 bytes: control archive= 908 bytes.
- 679 bytes, 15 lines control
+ size 159186 bytes: control archive= 903 bytes.
+ 680 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: powerpcspe
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 388
@@ -588,23 +590,23 @@ libbam-dev_0.1.10-1_powerpcspe.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-18 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/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./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
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/lib/
+-rw-r--r-- root/root 245202 2010-12-04 18:51 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-04 18:51 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 6692 2010-12-02 22:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 4927 2010-12-03 06:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 04:17 ./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
+-rw-r--r-- root/root 1128 2010-12-03 06:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -613,8 +615,8 @@ drwxr-xr-x root/root 0 2010-11-18 16:41 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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.)
+Purging /var/lib/schroot/mount/spestage-0fea459c-6bbb-4543-9144-91e0da2cf54a/spestage/build/buildd-samtools_0.1.12a-1-powerpcspe-cmP2NQ
+(Reading database ... 12586 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -645,8 +647,8 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101118-1641
-Build needed 00:05:59, 8952k disc space
+Finished at 20101204-1851
+Build needed 00:06:13, 8948k disc space
</pre>
<p>
diff --git a/s390.build b/s390.build
index 6e1ebe2..4b20c51 100644
--- a/s390.build
+++ b/s390.build
@@ -1,42 +1,41 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/s390 received Fri Dec 3 09:24:16 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=s390">s390</a> >> Fri Dec 3 09:24:16 2010<pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (s390) 17 Nov 2010 12:53 ║
+║ samtools 0.1.12a-1 (s390) 03 Dec 2010 09:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: s390
-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
-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
-Ign http://incoming.debian.org/debian/ sid/non-free Translation-en
-Hit http://incoming.debian.org Release.gpg
+Chroot Build Dir: /var/lib/schroot/mount/sid-s390-sbuild-235df352-e04a-4a75-a746-dc247b89ec10/build/buildd-samtools_0.1.12a-1-s390-zpFbOY
+Start Time: 20101203-0922
+Get:1 http://ftp.de.debian.org unstable Release.gpg [835 B]
+Ign http://ftp.de.debian.org/debian/ unstable/contrib Translation-en
+Ign http://ftp.de.debian.org/debian/ unstable/main Translation-en
+Get:2 http://ftp.de.debian.org unstable Release [104 kB]
+Get:3 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:4 http://ftp.de.debian.org unstable/main Sources [4071 kB]
+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 Sources/DiffIndex
-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
-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
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+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 [4071 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib Sources [38.7 kB]
+Get:10 http://ftp.de.debian.org unstable/non-free Sources [83.8 kB]
+Get:11 http://ftp.de.debian.org unstable/main s390 Packages [6754 kB]
+Get:12 http://ftp.de.debian.org unstable/contrib s390 Packages [48.8 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [38.7 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.8 kB]
+Get:15 http://incoming.debian.org unstable/main s390 Packages [6754 kB]
+Get:16 http://incoming.debian.org unstable/contrib s390 Packages [48.8 kB]
+Get:17 http://incoming.debian.org Sources [8014 B]
+Get:18 http://incoming.debian.org Packages [169 kB]
+Fetched 22.4 MB in 25s (866 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -57,18 +56,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 1s (264 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -99,13 +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
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 23 not upgraded.
-Need to get 0 B/11.8 MB of archives.
+0 upgraded, 19 newly installed, 0 to remove and 28 not upgraded.
+Need to get 11.8 MB of archives.
After this operation, 35.7 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.0.17 [207 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.20.1-10 [1112 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.5.7-6 [1308 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.02-1.1 [239 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-1 [872 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.24.2-1 [1140 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.7+20100313-4 [1634 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.8 MB in 5s (2352 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10966 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_s390.deb) ...
+(Reading database ... 10060 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_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.
@@ -142,7 +161,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_s390.deb) ...
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) ...
+Setting up bsdmainutils (8.0.17) ...
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) ...
@@ -166,9 +185,9 @@ 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)
+Kernel: Linux 2.6.32-bpo.5-s390x s390 (s390x)
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
+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_8.0.17 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_4.4.5-7 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_4.4.5-7 gcc_4:4.4.5-1 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 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-7 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 liblzma2_5.0.0-2 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_4.4.5-7 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 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_0.0.5 sudo_1.7.4p4-4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.25-2 tzdata_2010o-1 util-linux_2.17.2-3.3 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -179,13 +198,13 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -200,34 +219,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
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
@@ -247,8 +267,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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
@@ -259,10 +279,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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
@@ -279,24 +299,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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
@@ -306,14 +326,14 @@ 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_0.1.10-1-s390-EQyK8C/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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_0.1.10-1-s390-EQyK8C/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
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-s390-EQyK8C/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -342,7 +362,7 @@ 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_0.1.10-1-s390-EQyK8C/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -350,6 +370,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -374,8 +395,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/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 +420,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-s390-EQyK8C/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -413,66 +434,69 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_s390.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_s390.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1254
+Build finished at 20101203-0924
-samtools_0.1.10-1_s390.changes:
+samtools_0.1.12a-1_s390.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: s390 Build Daemon <buildd_s390-lxdebian at buildd...>
+Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 3545d36c6f22e6aa8d8c020440d5c0142bf97483 576734 samtools_0.1.10-1_s390.deb
- 45cae76a9077521cf580b945cfb6777cc75bd522 170246 libbam-dev_0.1.10-1_s390.deb
+ 63f318ed9acaa790b238ac22e0ac2d313b09754e 568074 samtools_0.1.12a-1_s390.deb
+ 15ccbda0b9f67f67811be5cbcaa6bcbb71bd4611 163484 libbam-dev_0.1.12a-1_s390.deb
Checksums-Sha256:
- dec401782b35283d8d15d305eaee85b4aa499cbb09debbed2caf5f498398f99c 576734 samtools_0.1.10-1_s390.deb
- fe780b1ce5e070dc1924672ce72fc3479ac3d3b4572cc465c2a38912f23415f7 170246 libbam-dev_0.1.10-1_s390.deb
+ 1f8c1fb50700acfdcddf4ae12261b0484d0226ae70a98b3432c0c65d5f36815c 568074 samtools_0.1.12a-1_s390.deb
+ fe61bcca670f8c22ad0e3531def8caa07711a97d088a47eb4239af12f204aa46 163484 libbam-dev_0.1.12a-1_s390.deb
Files:
- 0ea7c7f733c9ab9063f1bebcda25a28a 576734 science optional samtools_0.1.10-1_s390.deb
- b66bdbe36bd5b0016dade99af3e165b9 170246 libdevel optional libbam-dev_0.1.10-1_s390.deb
+ 1e960b993581b710a92f6a85a2ea1cf4 568074 science optional samtools_0.1.12a-1_s390.deb
+ ccf263db0121acdae17ea2f30ff59265 163484 libdevel optional libbam-dev_0.1.12a-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_s390.deb
-──────────────────────────
+samtools_0.1.12a-1_s390.deb
+───────────────────────────
new debian package, version 2.0.
- size 576734 bytes: control archive= 1790 bytes.
- 791 bytes, 16 lines control
+ size 568074 bytes: control archive= 1785 bytes.
+ 792 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1028
+ Installed-Size: 1032
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -485,69 +509,69 @@ samtools_0.1.10-1_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 2010-11-17 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
-────────────────────────────
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/bin/
+-rwxr-xr-x root/root 92244 2010-12-03 09:24 ./usr/bin/bcftools
+-rwxr-xr-x root/root 354472 2010-12-03 09:24 ./usr/bin/samtools
+-rwxr-xr-x root/root 27364 2010-12-03 09:24 ./usr/bin/razip
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11324 2010-12-03 09:24 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7188 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7188 2010-12-03 09:24 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7932 2010-12-03 09:24 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18572 2010-12-03 09:24 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2010-12-03 09:24 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-12-03 09:24 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/samtools/
+-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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./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 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 5778 2010-12-03 09:24 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2010-12-03 09:24 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 2010-12-03 09:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+lrwxrwxrwx root/root 0 2010-12-03 09:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_s390.deb
+─────────────────────────────
new debian package, version 2.0.
- size 170246 bytes: control archive= 891 bytes.
- 673 bytes, 15 lines control
+ size 163484 bytes: control archive= 894 bytes.
+ 674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 400
@@ -561,23 +585,23 @@ libbam-dev_0.1.10-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./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 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
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/lib/
+-rw-r--r-- root/root 256726 2010-12-03 09:24 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -586,39 +610,10 @@ drwxr-xr-x root/root 0 2010-11-17 12:54 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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 ...
-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-s390-sbuild-235df352-e04a-4a75-a746-dc247b89ec10/build/buildd-samtools_0.1.12a-1-s390-zpFbOY
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1254
-Build needed 00:00:57, 9196k disc space
+Finished at 20101203-0924
+Build needed 00:01:38, 9204k 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 855bc6f..1613501 100644
--- a/sh4.build
+++ b/sh4.build
@@ -1,17 +1,17 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<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
+<html><head><title>File `log' in samtools_0.1.12a-1_sh4 (Dec 3 19:28)</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_0.1.12a-1_sh4 (Dec 3 19:28)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=sh4">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sh4">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sh4&stamp=1291404517">Dec 3 19:28</a> >> log</td></tr></table><p><pre>
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on musashi
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (sh4) 17 Nov 2010 15:32 ║
+║ samtools 0.1.12a-1 (sh4) 03 Dec 2010 18:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: sh4
-Chroot Build Dir: /srv/chroot/sid/build/buildd-samtools_0.1.10-1-sh4-we5E9N
-Start Time: 20101117-1532
+Chroot Build Dir: /srv/chroot/sid/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq
+Start Time: 20101203-1809
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
@@ -20,23 +20,22 @@ 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
Ign http://ftp.debian-ports.org/debian/ unstable/main Translation-en
-Hit http://ftp.debian.org unstable Release.gpg
+Hit http://incoming.debian-ports.org unstable Release.gpg
Hit http://ftp.debian-ports.org unreleased Release.gpg
+Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
+Hit http://ftp.debian.org unstable Release.gpg
Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-Get:2 http://incoming.debian-ports.org unstable Release [8817 B]
Hit http://ftp.debian-ports.org unstable Release
+Hit http://incoming.debian-ports.org unstable Release
Hit http://ftp.debian.org unstable Release
Hit http://ftp.debian-ports.org unreleased Release
+Hit http://incoming.debian-ports.org unstable/main Sources
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
+Hit http://incoming.debian-ports.org unstable/main sh4 Packages
Hit http://ftp.debian-ports.org unreleased/main sh4 Packages
-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...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -65,18 +64,18 @@ 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 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)
+Need to get 364 kB of source archives.
+Get:1 http://ftp.debian.org/debian/ unstable/main samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://ftp.debian.org/debian/ unstable/main samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://ftp.debian.org/debian/ unstable/main samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 5s (61.4 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), 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
@@ -107,16 +106,17 @@ 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)
+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...
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
+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
@@ -124,24 +124,80 @@ 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 groff-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts doc-base
+ devscripts doc-base dh-make gettext-doc groff less www-browser
+ libmail-box-perl
Recommended packages:
- autotools-dev
+ autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev
+ 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 18 not upgraded.
-Need to get 0 B/2851 kB of archives.
-After this operation, 8425 kB of additional disk space will be used.
+0 upgraded, 18 newly installed, 0 to remove and 28 not upgraded.
+Need to get 0 B/11.7 MB of archives.
+After this operation, 34.5 MB of additional disk space will be used.
+Selecting previously deselected package groff-base.
+(Reading database ... 11309 files and directories currently installed.)
+Unpacking groff-base (from .../groff-base_1.20.1-10_sh4.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.7-6_sh4.deb) ...
+Selecting previously deselected package libmagic1.
+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 libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.02-1.1_sh4.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_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+nmu1_all.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
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) ...
-Processing triggers for man-db ...
+Selecting previously deselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sh4.deb) ...
+Processing triggers for install-info ...
+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...
W: line 16 [sid]: Deprecated key 'priority' used
@@ -149,8 +205,8 @@ 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_2.11.2-7 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
+Toolchain package versions: libc6-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: adduser_3.112+nmu1 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 ca-certificates_20090814+nmu2 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_0.5.5.1-7.2 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 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 g++_4:4.4.5-1 g++-4.4_4.4.5-8 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-8 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 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 install-info_4.13a.dfsg.1-6 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 libcurl3-gnutls_7.21.2-1 libdb4.6_4.6.21-16 libdb4.7_4.7.25-9 libdb4.8_4.8.30-3 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_1:4.4.5-8 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_2.8.6-1 libgomp1_4.4.5-8 libgpg-error0_1.6-1 libgpm2_1.20.4-3.3 libgssapi-krb5-2_1.8.3+dfsg-3 libidn11_1.18-1 libk5crypto3_1.8.3+dfsg-3 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-3 libkrb5support0_1.8.3+dfsg-3 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 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_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 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-3 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 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_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 make_3.81-8 makedev_2.3.1-89 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 openssl_0.9.8o-2 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 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 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 │
@@ -166,12 +222,12 @@ 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -190,34 +246,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
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_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
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
@@ -243,8 +300,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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
@@ -255,10 +312,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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
@@ -275,24 +332,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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
@@ -302,14 +359,14 @@ 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_0.1.10-1-sh4-we5E9N/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/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_0.1.10-1-sh4-we5E9N/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a'
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-sh4-we5E9N/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -338,7 +395,7 @@ 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_0.1.10-1-sh4-we5E9N/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -346,6 +403,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -370,8 +428,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -395,7 +453,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-sh4-we5E9N/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-sh4-3I2TOq/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -409,66 +467,69 @@ dh_shlibdeps -plibbam-dev
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_0.1.10-1_sh4.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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_0.1.10-1_sh4.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-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-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1646
+Build finished at 20101203-1923
-samtools_0.1.10-1_sh4.changes:
+samtools_0.1.12a-1_sh4.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: sh4
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
-Maintainer: Debian SH4 buildd <buildd-sh4-nagato at superh...>
+Maintainer: Debian SH4 buildd <buildd-sh4-musashi 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 (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 1579dfa8869ef1dd1c41f0df52a14d40f282edab 589112 samtools_0.1.10-1_sh4.deb
- b28db8e9fa96a3c0fd9ec4eaa13319734ec110ee 176392 libbam-dev_0.1.10-1_sh4.deb
+ 2d31605bfcbc8089d19e54b874ffa04b6d46575f 589182 samtools_0.1.12a-1_sh4.deb
+ b58b860721c3e454a39e7a0eff35062e65321606 174322 libbam-dev_0.1.12a-1_sh4.deb
Checksums-Sha256:
- 334bb25e4fb77f69ea5d061e822618d2f733e0c9f170e071e0eabc3b643f2fa2 589112 samtools_0.1.10-1_sh4.deb
- 985fa5597a619aa5bdf6c32933c506a31b1ac0d1313db8536d8302024439ac43 176392 libbam-dev_0.1.10-1_sh4.deb
+ 120e4f0cc10646b4843b08b0bd792bafb3ddb68b937bae7b6377350817c6dbd0 589182 samtools_0.1.12a-1_sh4.deb
+ 2ebada4a0bd2af10a4b3ab2badcdbf747a9fa37a7ab45cb2243f03647306b4da 174322 libbam-dev_0.1.12a-1_sh4.deb
Files:
- 1e07d7aca17d754ec118507b2c078a36 589112 science optional samtools_0.1.10-1_sh4.deb
- fba1e26450f9ffc2e50a50e8d9cb05e4 176392 libdevel optional libbam-dev_0.1.10-1_sh4.deb
+ 94e10ae8b21ad14bc137ba28603456ce 589182 science optional samtools_0.1.12a-1_sh4.deb
+ 4e5effd8c6ffd189dac93126aacbfd89 174322 libdevel optional libbam-dev_0.1.12a-1_sh4.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_sh4.deb
-─────────────────────────
+samtools_0.1.12a-1_sh4.deb
+──────────────────────────
new debian package, version 2.0.
- size 589112 bytes: control archive= 1801 bytes.
- 790 bytes, 16 lines control
+ size 589182 bytes: control archive= 1795 bytes.
+ 791 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: sh4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 984
+ Installed-Size: 988
Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -481,69 +542,69 @@ samtools_0.1.10-1_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 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 19:19 ./
+drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/bin/
+-rwxr-xr-x root/root 24988 2010-12-03 19:21 ./usr/bin/razip
+-rwxr-xr-x root/root 318656 2010-12-03 19:21 ./usr/bin/samtools
+-rwxr-xr-x root/root 84068 2010-12-03 19:21 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 19:19 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 19:19 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 19:19 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2010-12-03 19:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
-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 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/doc/samtools/examples/
-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 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2010-12-03 18:29 ./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 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
-───────────────────────────
+-rw-r--r-- root/root 1966 2010-12-03 19:20 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./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 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 5778 2010-12-03 19:21 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/lib/samtools/
+-rwxr-xr-x root/root 6864 2010-12-03 19:21 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 16724 2010-12-03 19:21 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6688 2010-12-03 19:21 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 9760 2010-12-03 19:21 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6624 2010-12-03 19:21 ./usr/lib/samtools/maq2sam-short
+lrwxrwxrwx root/root 0 2010-12-03 19:20 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_sh4.deb
+────────────────────────────
new debian package, version 2.0.
- size 176392 bytes: control archive= 902 bytes.
- 672 bytes, 15 lines control
+ size 174322 bytes: control archive= 897 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: sh4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 384
@@ -557,23 +618,23 @@ libbam-dev_0.1.10-1_sh4.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 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
+drwxr-xr-x root/root 0 2010-12-03 19:20 ./
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./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 2010-11-17 16:45 ./usr/lib/
--rw-r--r-- root/root 238286 2010-11-17 16:45 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 19:20 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./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 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 19:21 ./usr/lib/
+-rw-r--r-- root/root 238394 2010-12-03 19:21 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -582,7 +643,7 @@ drwxr-xr-x root/root 0 2010-11-17 16:45 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/chroot/sid/build/buildd-samtools_0.1.10-1-sh4-we5E9N
+Purging /srv/chroot/sid/build/buildd-samtools_0.1.12a-1-sh4-3I2TOq
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
@@ -591,13 +652,38 @@ 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 ...
+(Reading database ... 13572 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 libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Processing triggers for install-info ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1646
-Build needed 01:14:27, 8888k disc space
+Finished at 20101203-1923
+Build needed 01:13:51, 8912k disc space
</pre>
<p>
diff --git a/sparc.build b/sparc.build
index ee0ba82..e265982 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_0.1.10-1/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>
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/sparc received Fri Dec 3 09:29:08 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=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=sparc">sparc</a> >> Fri Dec 3 09:29:08 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on spontini.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (sparc) 17 Nov 2010 11:53 ║
+║ samtools 0.1.12a-1 (sparc) 03 Dec 2010 09:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: sparc
-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
+Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-5f94f0dc-8583-4e98-bc68-e5cff85fb5ae/build/buildd-samtools_0.1.12a-1-sparc-UAUacU
+Start Time: 20101203-0922
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://mirrors.ece.ubc.ca unstable/main Packages [6781kB]
+Get:6 http://mirrors.ece.ubc.ca unstable/main Packages [6789kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Packages [6781kB]
+Get:8 http://incoming.debian.org unstable/main Packages [6789kB]
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:10 http://mirrors.ece.ubc.ca unstable/main Sources [4071kB]
+Get:11 http://mirrors.ece.ubc.ca unstable/contrib Sources [38.7kB]
+Get:12 http://mirrors.ece.ubc.ca unstable/non-free Sources [83.8kB]
Get:13 http://incoming.debian.org unstable/contrib Packages [51.2kB]
-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)
+Get:14 http://incoming.debian.org unstable/main Sources [4071kB]
+Get:15 http://incoming.debian.org unstable/contrib Sources [38.7kB]
+Get:16 http://incoming.debian.org unstable/non-free Sources [83.8kB]
+Get:17 http://incoming.debian.org Packages [169kB]
+Get:18 http://incoming.debian.org Sources [8014B]
+Fetched 22.5MB in 53s (416kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -49,18 +49,18 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-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)
+Need to get 364kB of source archives.
+Get:1 http://incoming.debian.org samtools 0.1.12a-1 (dsc) [1946B]
+Get:2 http://incoming.debian.org samtools 0.1.12a-1 (tar) [356kB]
+Get:3 http://incoming.debian.org samtools 0.1.12a-1 (diff) [6337B]
+Fetched 364kB in 1s (352kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -93,12 +93,12 @@ 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 72 not upgraded.
+2 upgraded, 19 newly installed, 0 to remove and 73 not upgraded.
Need to get 12.3MB of archives.
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:3 http://mirrors.ece.ubc.ca unstable/main bsdmainutils 8.0.17 [203kB]
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]
@@ -118,7 +118,7 @@ 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 2s (4531kB/s)
+Fetched 12.3MB in 3s (4052kB/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 ...
@@ -129,7 +129,7 @@ Unpacking replacement libncurses5 ...
Setting up libncurses5 (5.7+20100313-4) ...
Selecting previously deselected package bsdmainutils.
(Reading database ... 10166 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_sparc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_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.
@@ -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 (8.0.16) ...
+Setting up bsdmainutils (8.0.17) ...
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) ...
@@ -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_8.0.16 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
+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_8.0.17 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 Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 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_0.1.10-1.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
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -224,33 +224,34 @@ 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 0.1.10-1
+dpkg-buildpackage: source version 0.1.12a-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_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
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
@@ -276,8 +277,8 @@ 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_reheader.c -o bam_reheader.o
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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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
@@ -288,10 +289,10 @@ 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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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
@@ -308,24 +309,24 @@ 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. 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 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[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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_0.1.10-1-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]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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
@@ -335,30 +336,30 @@ 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_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
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-sparc-gbhG2Z/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/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_0.1.10-1-sparc-gbhG2Z/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-1200
+Build finished at 20101203-0928
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-ee0cabb2-61cd-481d-a707-e4a6682674d0/build/buildd-samtools_0.1.10-1-sparc-gbhG2Z
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-5f94f0dc-8583-4e98-bc68-e5cff85fb5ae/build/buildd-samtools_0.1.12a-1-sparc-UAUacU
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-1200
-Build needed 00:06:35, 5188k disc space
+Finished at 20101203-0928
+Build needed 00:06:40, 5208k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/sparc64.build b/sparc64.build
index c80c305..e2415eb 100644
--- a/sparc64.build
+++ b/sparc64.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_sparc64 (Nov 7 18:21)</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_sparc64 (Nov 7 18:21)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=sparc64">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=sparc64">0.1.9-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.9-1&arch=sparc64&stamp=1289154100">Nov 7 18:21</a> >> log</td></tr></table><p><pre>
+<html><head><title>File `log' in samtools_0.1.12a-1_sparc64 (Dec 3 19:46)</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_0.1.12a-1_sparc64 (Dec 3 19:46)</h2></td><td align=right><a href="build.php?&pkg=samtools&arch=sparc64">samtools</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sparc64">0.1.12a-1</a> >> <a href="build.php?&pkg=samtools&ver=0.1.12a-1&arch=sparc64&stamp=1291405586">Dec 3 19:46</a> >> log</td></tr></table><p><pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on zee.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.9-1 (sparc64) 07 Nov 2010 18:18 ║
+║ samtools 0.1.12a-1 (sparc64) 03 Dec 2010 19:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.9-1
+Version: 0.1.12a-1
Architecture: sparc64
-Chroot Build Dir: /var/lib/schroot/mount/sid-sparc64-sbuild-048dc450-8991-4418-9d76-d1c039fcc785/build/buildd-samtools_0.1.9-1-sparc64-WdElZc
-Start Time: 20101107-1818
+Chroot Build Dir: /var/lib/schroot/mount/sid-sparc64-sbuild-f82f2939-8b43-40d2-a78b-433607da1db0/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb
+Start Time: 20101203-1943
Hit http://debian.oregonstate.edu sid Release.gpg
Hit http://debian.oregonstate.edu sid Release
Hit http://debian.oregonstate.edu sid/main Sources/DiffIndex
@@ -21,13 +21,13 @@ Hit http://ftp.debian-ports.org unreleased Release.gpg
Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
Hit http://incoming.debian-ports.org unstable Release.gpg
Ign http://incoming.debian-ports.org/buildd/ unstable/main Translation-en
+Hit http://incoming.debian-ports.org unstable Release
Hit http://ftp.debian-ports.org sid Release
Hit http://ftp.debian-ports.org unreleased Release
-Hit http://incoming.debian-ports.org unstable Release
-Hit http://ftp.debian-ports.org sid/main sparc64 Packages
Hit http://incoming.debian-ports.org unstable/main Sources
-Hit http://ftp.debian-ports.org unreleased/main sparc64 Packages
+Hit http://ftp.debian-ports.org sid/main sparc64 Packages
Hit http://incoming.debian-ports.org unstable/main sparc64 Packages
+Hit http://ftp.debian-ports.org unreleased/main sparc64 Packages
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -48,102 +48,56 @@ 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://debian.oregonstate.edu/debian/ sid/main samtools 0.1.9-1 (dsc) [1932 B]
-Get:2 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.9-1 (tar) [350 kB]
-Get:3 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.9-1 (diff) [6264 B]
-Fetched 358 kB in 0s (3720 kB/s)
+Need to get 364 kB of source archives.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.12a-1 (dsc) [1946 B]
+Get:2 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.12a-1 (tar) [356 kB]
+Get:3 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.12a-1 (diff) [6337 B]
+Fetched 364 kB in 0s (3728 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.0.0
+debhelper: already installed (8.0.0 >= 8 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
+Installing positive dependencies: cdbs libncurses5-dev
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 9 not upgraded.
-Need to get 0 B/8873 kB of archives.
-After this operation, 28.6 MB of additional disk space will be used.
-Selecting previously deselected package libmagic1.
-(Reading database ... 10787 files and directories currently installed.)
-Unpacking libmagic1 (from .../libmagic1_5.04-5_sparc64.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5_sparc64.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc64.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_sparc64.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_sparc64.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_sparc64.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc64.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_sparc64.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_sparc64.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 34 not upgraded.
+Need to get 0 B/2873 kB of archives.
+After this operation, 8733 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
+(Reading database ... 31276 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_sparc64.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc64.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 (2.7.8.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 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-bpo.5-sparc64-smp sparc64 (sparc64)
-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+b1 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+b1 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_4.4.5-5 dash_0.5.5.1-7.1 debconf_1.5.36 debconf-english_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 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_4.4.5-5 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 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~sparc64 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 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 libgpm2_1.20.4-3.3 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_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libpng12-0_1.2.44-1 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 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 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 net-tools_1.60-23 netbase_4.43 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-12 perl-base_5.10.1-12 perl-modules_5.10.1-16 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 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 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
+Toolchain package versions: libc6-dev_2.11.2-7 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-26 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-15+b1 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: adduser_3.112+nmu2 ant1.7_1.7.1-7 ant1.7-optional_1.7.1-7 apt_0.8.8 autoconf_2.67-2 automake_1:1.11.1-1 autotools-dev_20100122.1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15+b1 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 chrpath_0.13-2 comerr-dev_2.1-1.41.12-2 coreutils_8.5-1 cpio_2.11-4 cpp_4:4.4.5-1 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.1 dbus_1.2.24-3 dbus-x11_1.2.24-3 debconf_1.5.36 debconf-english_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 debianutils_3.4.1 default-jdk_1:1.5-40 default-jre_1:1.5-40 default-jre-headless_1:1.5-40 defoma_0.11.11 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 ecj_3.5.1-1 ecj-gcj_3.5.1-1 fakeroot_1.14.4-1 fastjar_2:0.98-3 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++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcj-4.4-base_4.4.5-9 gcj-4.4-jdk_4.4.5-9 gcj-4.4-jre_4.4.5-9 gcj-4.4-jre-headless_4.4.5-9 gcj-4.4-jre-lib_4.4.5-9 gcj-jdk_4:4.4.5-1 gcj-jre_4:4.4.5-1 gcj-jre-headless_4:4.4.5-1 gconf2_2.28.1-6 gconf2-common_2.28.1-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 ghostscript_8.71~dfsg2-6 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 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 java-common_0.40 krb5-multidev_1.8.3+dfsg-3 libacl1_2.2.49-4 libantlr-java_2.7.7-16 libasound2_1.0.23-2.1 libasound2-dev_1.0.23-2.1 libasyncns0_0.3-1.1 libatk1.0-0_1.30.0-1 libatk1.0-dev_1.30.0-1 libattr1_1:2.4.44-2 libaudit0_1.7.13-1+b2 libavahi-client-dev_0.6.27-3 libavahi-client3_0.6.27-3 libavahi-common-data_0.6.27-2 libavahi-common-dev_0.6.27-3 libavahi-common3_0.6.27-3 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libbz2-dev_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 libcairo2_1.8.10-6 libcairo2-dev_1.8.10-6 libcanberra-gtk0_0.24-1 libcanberra0_0.24-1 libcap2_1:2.19-3 libcdt4_2.26.3-5+b1 libcgraph5_2.26.3-5+b1 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcups2_1.4.4-7 libcups2-dev_1.4.4-7 libcupsimage2_1.4.4-7 libdatrie1_0.2.4-1 libdb4.7_4.7.25-9~sparc64 libdb4.8_4.8.30-3 libdbus-1-3_1.2.24-3 libdbus-1-dev_1.2.24-3 libdbus-glib-1-2_0.88-2 libdjvulibre-dev_3.5.23-3 libdjvulibre-text_3.5.23-3 libdjvulibre21_3.5.23-3 libdpkg-perl_1.15.8.5 libdrm-radeon1_2.4.21-1~squeeze3 libdrm2_2.4.21-1~squeeze3 libecj-java_3.5.1-1 libecj-java-gcj_3.5.1-1 libexif-dev_0.6.19-1 libexif12_0.6.19-1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libffi-dev_3.0.9-3 libffi5_3.0.9-3 libflac8_1.2.1-3 libfontconfig1_2.8.0-2.1 libfontconfig1-dev_2.8.0-2.1 libfontenc1_1:1.1.0-1 libfreetype6_2.4.2-2 libfreetype6-dev_2.4.2-2 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcj-bc_4.4.5-1 libgcj-common_1:4.4.5-1 libgcj10_4.4.5-9 libgcj10-awt_4.4.5-9 libgcj10-dev_4.4.5-9 libgconf2-4_2.28.1-6 libgcrypt11_1.4.5-2 libgcrypt11-dev_1.4.5-2 libgd2-noxpm_2.0.36~rc1~dfsg-5 libgdbm3_1.8.3-9 libgif-dev_4.1.6-9 libgif4_4.1.6-9 libgl1-mesa-dri_7.7.1-4 libglib2.0-0_2.24.2-1 libglib2.0-dev_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls-dev_2.8.6-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-10 libgpg-error-dev_1.6-1 libgpg-error0_1.6-1 libgpm2_1.20.4-3.3 libgraph4_2.26.3-5+b1 libgraphviz-dev_2.26.3-5+b1 libgs8_8.71~dfsg2-6 libgsf-1-114_1.14.19-2 libgsf-1-common_1.14.19-2 libgssapi-krb5-2_1.8.3+dfsg-3 libgssrpc4_1.8.3+dfsg-3 libgtk2.0-0_2.20.1-2 libgtk2.0-common_2.20.1-2 libgtk2.0-dev_2.20.1-2 libgtop2-7_2.28.1-1 libgtop2-common_2.28.1-1 libgvc5_2.26.3-5+b1 libgvpr1_2.26.3-5+b1 libhunspell-1.2-0_1.2.11-1 libice-dev_2:1.0.6-2 libice6_2:1.0.6-2 libidl0_0.8.14-0.1 libilmbase-dev_1.0.1-3 libilmbase6_1.0.1-3 libjasper-dev_1.900.1-7 libjasper1_1.900.1-7 libjaxp1.3-java_1.3.05-1 libjbig2dec0_0.11-1 libjline-java_0.9.94-5 libjpeg62_6b1-1 libjpeg62-dev_6b1-1 libk5crypto3_1.8.3+dfsg-3 libkadm5clnt-mit7_1.8.3+dfsg-3 libkadm5srv-mit7_1.8.3+dfsg-3 libkdb5-4_1.8.3+dfsg-3 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-3 libkrb5-dev_1.8.3+dfsg-3 libkrb5support0_1.8.3+dfsg-3 liblcms1_1.18.dfsg-1.2+b2 liblcms1-dev_1.18.dfsg-1.2+b2 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblqr-1-0_0.4.1-1 liblqr-1-0-dev_0.4.1-1 libltdl-dev_2.2.6b-2~sparc64 libltdl7_2.2.6b-2~sparc64 liblzma2_5.0.0-2 libmagic1_5.04-5 libmetacity-private0_1:2.30.1-3 libmozjs-dev_1.9.1.12-2+sparc64 libmozjs2d_1.9.1.12-2+sparc64 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libncursesw5_5.7+20100313-4 libnewt0.52_0.52.11-2 libnotify1_0.5.0-2 libnspr4-0d_4.8.6-1 libnspr4-dev_4.8.6-1 libnss3-1d_3.12.8-1 libnss3-dev_3.12.8-1 libogg0_1.2.0~dfsg-1 libopenexr-dev_1.6.1-4.1 libopenexr6_1.6.1-4.1 liborbit2_1:2.14.18-0.1 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpango1.0-0_1.28.3-1 libpango1.0-common_1.28.3-1 libpango1.0-dev_1.28.3-1 libpaper1_1.1.24 libpathplan4_2.26.3-5+b1 libpcre3_8.02-1.1 libperl-dev_5.10.1-12 libperl5.10_5.10.1-12 libpixman-1-0_0.16.4-1 libpixman-1-dev_0.16.4-1 libpng12-0_1.2.44-1 libpng12-dev_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libpulse-browse0_0.9.21-3 libpulse-dev_0.9.21-3 libpulse-mainloop-glib0_0.9.21-3 libpulse0_0.9.21-3 libreadline5_5.2-7 libreadline6_6.1-3 librsvg2-2_2.26.3-1 librsvg2-dev_2.26.3-1 libsasl2-2_2.1.23.dfsg1-6 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libsm-dev_2:1.2.0-1 libsm6_2:1.2.0-1 libsndfile1_1.0.23-1 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libssl0.9.8_0.9.8o-3 libstartup-notification0_0.10-1 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtasn1-3_2.7-1 libtasn1-3-dev_2.7-1 libtdb1_1.2.7+git20101021-1 libthai-data_0.1.14-2 libthai0_0.1.14-2 libtiff4_3.9.4-5 libtiff4-dev_3.9.4-5 libtiffxx0c2_3.9.4-5 libtimedate-perl_1.2000-1 libtool_2.2.6b-2~sparc64 libudev0_164-2 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 libvorbisfile3_1.3.1-1 libwmf-dev_0.2.8.4-6.1 libwmf0.2-7_0.2.8.4-6.1 libwrap0_7.6.q-19 libx11-6_2:1.3.3-3 libx11-data_2:1.3.3-3 libx11-dev_2:1.3.3-3 libxalan2-java_2.7.1-5 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_1:1.1.0-1 libxdmcp6_1:1.1.0-1 libxdot4_2.26.3-5+b1 libxerces2-java_2.9.1-4.1 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_2:1.1.1-1 libxinerama1_2:1.1.1-1 libxkbfile1_1:1.0.7-1 libxml2_2.7.8.dfsg-1 libxml2-dev_2.7.8.dfsg-1 libxml2-utils_2.7.8.dfsg-1 libxmu-dev_2:1.1.0-1 libxmu-headers_2:1.1.0-1 libxmu6_2:1.1.0-1 libxmuu1_2:1.1.0-1 libxp-dev_1:1.0.0.xsf1-2 libxp6_1:1.0.0.xsf1-2 libxpm-dev_1:3.5.9-1 libxpm4_1:3.5.9-1 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 libxt-dev_1:1.0.7-1 libxt6_1:1.0.7-1 libxtst-dev_2:1.2.0-1 libxtst6_2:1.2.0-1 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lsb-release_3.2-26 m4_1.4.14-3 make_3.81-8 man-db_2.5.7-6 mauve_20090924-1 mawk_1.3.3-15 metacity_1:2.30.1-3 metacity-common_1:2.30.1-3 mime-support_3.51-1 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 net-tools_1.60-23 netbase_4.43 ocaml-base-nox_3.11.2-2 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-12 perl-base_5.10.1-12 perl-modules_5.10.1-16 pkg-config_0.25-1.1 po-debconf_1.0.16 procps_1:3.2.8-9 psmisc_22.13-1 python_2.6.6-3+squeeze2 python-minimal_2.6.6-3+squeeze2 python-support_1.0.11 python2.6_2.6.6-7 python2.6-minimal_2.6.6-7 readline-common_6.1-3 rhino_1.7R2-4 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-4 sharutils_1:4.9-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 time_1.7-23.1 ttf-dejavu-core_2.31-1 tzdata_2010o-1 ucf_3.0025+nmu1 unzip_6.0-4 util-linux_2.17.2-3.3 wget_1.12-2.1 whiptail_0.52.11-2 x11-common_1:7.5+8 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_2.0.1-1 x11proto-kb-dev_1.0.5-1 x11proto-print-dev_1.0.3.xsf1-1 x11proto-randr-dev_1.3.2-1 x11proto-record-dev_1.14.1-1 x11proto-render-dev_2:0.11.1-1 x11proto-xext-dev_7.1.2-1 x11proto-xinerama-dev_1.2-2 xauth_1:1.0.5-1 xfonts-base_1:1.0.3 xfonts-encodings_1:1.0.4-1 xfonts-utils_1:7.6~1 xkb-data_1.8-2 xserver-common_2:1.7.7-9 xtrans-dev_1.2.5-1 xulrunner-1.9.1_1.9.1.12-2+sparc64 xulrunner-dev_1.9.1.12-2+sparc64 xvfb_2:1.7.7-9 xz-utils_4.999.9beta+20100810-1 zenity_2.30.0-1 zip_3.0-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -155,12 +109,12 @@ 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 Fri Dec 3 06:37:23 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_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -175,34 +129,35 @@ 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 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture sparc64
/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-sparc64-WdElZc/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
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-sparc64-WdElZc/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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-sparc64-WdElZc/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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-sparc64-WdElZc/samtools-0.1.9/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/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-sparc64-WdElZc/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
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
@@ -220,9 +175,10 @@ 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-sparc64-WdElZc/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/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_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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
@@ -233,10 +189,10 @@ 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-sparc64-WdElZc/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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
@@ -249,27 +205,28 @@ 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-sparc64-WdElZc/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/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_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/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-sparc64-WdElZc/samtools-0.1.9'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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-sparc64-WdElZc/samtools-0.1.9/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.9-1-sparc64-WdElZc/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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
@@ -279,53 +236,34 @@ 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-sparc64-WdElZc/samtools-0.1.9/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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-sparc64-WdElZc/samtools-0.1.9'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a'
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-sparc64-WdElZc/samtools-0.1.9/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/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-sparc64-WdElZc/samtools-0.1.9/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb/samtools-0.1.12a/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101107-1821
+Build finished at 20101203-1946
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc64-sbuild-048dc450-8991-4418-9d76-d1c039fcc785/build/buildd-samtools_0.1.9-1-sparc64-WdElZc
-(Reading database ... 12673 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-sparc64-sbuild-f82f2939-8b43-40d2-a78b-433607da1db0/build/buildd-samtools_0.1.12a-1-sparc64-IIstEb
+(Reading database ... 32383 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 20101107-1821
-Build needed 00:02:58, 6104k disc space
+Finished at 20101203-1946
+Build needed 00:02:55, 6420k disc space
</pre>
<p>
--
Processing of sequence alignments in SAM and BAM formats.
More information about the debian-med-commit
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