[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. b9dfdadb88e2d82f0cc4fcf29dc7d0c590629179
Charles Plessy
plessy at debian.org
Mon Mar 28 01:25:04 UTC 2011
The following commit has been merged in the meta branch:
commit b9dfdadb88e2d82f0cc4fcf29dc7d0c590629179
Author: Charles Plessy <plessy at debian.org>
Date: Mon Mar 28 10:24:03 2011 +0900
# Collected build logs for 0.1.13-1.
diff --git a/alpha.log b/alpha.log
index d5b8196..4d6e0d9 100644
--- a/alpha.log
+++ b/alpha.log
@@ -1,73 +1,63 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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>
+From buildd at goedel.debian.org Wed Mar 02 06:28:50 2011
+Return-path: <buildd at goedel.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at goedel.debian.org>)
+ id 1PufYI-0001wH-5y
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 06:28:50 +0000
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+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=goedel.debian.org, EMAIL=hostmaster at goedel.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at goedel.debian.org>)
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+Received: from buildd by goedel.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at goedel.debian.org>)
+ id 1PufYD-0002or-90; Wed, 02 Mar 2011 06:28:45 +0000
+From: buildd at goedel.debian.org
+To: kurt at roeckx.be,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on alpha (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PufYD-0002or-90 at goedel.debian.org>
+Date: Wed, 02 Mar 2011 06:28:45 +0000
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goedel.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (alpha) 03 Dec 2010 09:21 ║
+║ samtools 0.1.13-1 (alpha) 02 Mar 2011 06:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: alpha
-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.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]
+Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-14927942-aadb-44e8-aa29-895355cebfe1/build/buildd-samtools_0.1.13-1-alpha-MDqSxB
+Start Time: 20110302-0617
+Hit http://ftp.de.debian.org sid InRelease
+Hit http://ftp.de.debian.org sid/main alpha Packages/DiffIndex
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
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]
+Ign http://ftp.de.debian.org sid/contrib TranslationIndex
+Hit http://ftp.de.debian.org sid/main TranslationIndex
+Ign http://ftp.de.debian.org sid/contrib Translation-en
+Get:1 http://incoming.debian.org Release.gpg [835 B]
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
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/main alpha Packages/DiffIndex
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)
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [19.5 kB]
+Get:4 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 395 kB in 7s (53.6 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,61 +76,124 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 0s (441 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), 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 >= 8 is satisfied)
+debhelper: missing
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following extra packages will be installed:
+ bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 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
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-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.
+0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/12.7 MB of archives.
+After this operation, 39.5 MB of additional disk space will be used.
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10132 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_alpha.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-4_alpha.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_alpha.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.9-4_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_8.12-3_alpha.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_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_2.28.1-1+b1_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_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 13765 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_alpha.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_alpha.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_alpha.deb) ...
-Processing triggers for man-db ...
-Setting up cdbs (0.4.89) ...
-Setting up libncurses5-dev (5.7+20100313-4) ...
+Setting up bsdmainutils (8.2.2) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
+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 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
+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 (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.26-2-alpha-generic alpha (alpha)
-Toolchain package versions: libc6.1-dev_2.11.2-7 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
+Toolchain package versions: libc6.1-dev_2.11.2-13 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libstdc++6_4.5.2-4
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6.1_2.11.2-13 libc6.1-dev_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -151,13 +204,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -172,158 +225,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
rm -f debian/stamp-makefile-check
dh_clean
debian/rules build
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
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_0.1.12a-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
-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
-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
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_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 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
+[bam_rmdupse_core] 4666 / 6542 = 0.7132 in library 'ex1'
+[bam_rmdupse_core] 1395 / 3271 = 0.4265 in library 'ex1b'
+../samtools glfview ex1.glf | gzip > ex1.glfview.gz
[mpileup] 1 samples in 1 input files
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+../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 -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-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
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
+ /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -345,11 +400,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -366,6 +421,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -373,7 +429,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-alpha-NKtcft/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -388,69 +444,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_alpha.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_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 -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_alpha.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_alpha.deb'.
+ dpkg-genchanges -B -mDebian Build Daemon <buildd_alpha-goedel at buildd.debian.org> >../samtools_0.1.13-1_alpha.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0930
+Build finished at 20110302-0627
-samtools_0.1.12a-1_alpha.changes:
+samtools_0.1.13-1_alpha.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: alpha
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: Debian Build Daemon <buildd_alpha-goedel at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: Debian Build Daemon <buildd_alpha-goedel at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- e386da50ad8f4b31c12c471a3ee2e92af0868f6e 596686 samtools_0.1.12a-1_alpha.deb
- ca438ab8033960703fc2010cf168bd0df1e89bb5 187896 libbam-dev_0.1.12a-1_alpha.deb
+ 8579ee901338d7a0837511a07aed429d848030d6 637112 samtools_0.1.13-1_alpha.deb
+ 2ba7369eb96064e1e98b1e3613e5baf294a5fadd 193980 libbam-dev_0.1.13-1_alpha.deb
Checksums-Sha256:
- 9694d7c3e75170dc00a9743e3ff2a74586c122ab77940d4552d855d03c312297 596686 samtools_0.1.12a-1_alpha.deb
- d75f2196ea5c327e83095b580dc38f8572e307b757dbd80f85cd1bae91f1d259 187896 libbam-dev_0.1.12a-1_alpha.deb
+ 53fc211136e32a8ac58788124909b45d9599b05815124343dfefb37642e0e90a 637112 samtools_0.1.13-1_alpha.deb
+ f9c2453f5fdce4892c931421e982680885473de62a8d33dad8eb67fc76052704 193980 libbam-dev_0.1.13-1_alpha.deb
Files:
- ccd175cc94346c4fca39c74db4373826 596686 science optional samtools_0.1.12a-1_alpha.deb
- 844a3e6973cc5cb3b9a1a2ba51319355 187896 libdevel optional libbam-dev_0.1.12a-1_alpha.deb
+ 57b848558a0ce24df0daf637cc9aa6c6 637112 science optional samtools_0.1.13-1_alpha.deb
+ a4d50dc064ac6b9a9ed244a1744a6ea1 193980 libdevel optional libbam-dev_0.1.13-1_alpha.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_alpha.deb
-────────────────────────────
+samtools_0.1.13-1_alpha.deb
+───────────────────────────
new debian package, version 2.0.
- size 596686 bytes: control archive= 1796 bytes.
- 795 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 637112 bytes: control archive= 1786 bytes.
+ 794 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: alpha
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1132
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1200
+ Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -462,33 +522,33 @@ samtools_0.1.12a-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 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2010-12-03 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 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-12-03 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
+-rw-r--r-- root/root 126609 2011-03-02 06:21 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-02 06:27 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-02 06:27 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 06:27 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1229 2011-03-02 06:27 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./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
@@ -500,34 +560,33 @@ drwxr-xr-x root/root 0 2010-12-03 09:29 ./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 2010-12-03 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
-──────────────────────────────
+-rwxr-xr-x root/root 5778 2011-03-02 06:27 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/bin/
+-rwxr-xr-x root/root 127432 2011-03-02 06:27 ./usr/bin/bcftools
+-rwxr-xr-x root/root 31568 2011-03-02 06:27 ./usr/bin/razip
+-rwxr-xr-x root/root 460768 2011-03-02 06:27 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/lib/samtools/
+-rwxr-xr-x root/root 22296 2011-03-02 06:27 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9728 2011-03-02 06:27 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 9728 2011-03-02 06:27 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 15320 2011-03-02 06:27 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 11136 2011-03-02 06:27 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.13-1_alpha.deb
+─────────────────────────────
new debian package, version 2.0.
- size 187896 bytes: control archive= 895 bytes.
- 675 bytes, 15 lines control
+ size 193980 bytes: control archive= 895 bytes.
+ 674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: alpha
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 616
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 620
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -538,22 +597,22 @@ libbam-dev_0.1.12a-1_alpha.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 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 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/lib/
+-rw-r--r-- root/root 478092 2011-03-02 06:27 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./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 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -563,14 +622,40 @@ drwxr-xr-x root/root 0 2010-12-03 09:29 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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 ...
+Purging /var/lib/schroot/mount/sid-alpha-sbuild-14927942-aadb-44e8-aa29-895355cebfe1/build/buildd-samtools_0.1.13-1-alpha-MDqSxB
+(Reading database ... 12577 files and directories currently installed.)
Removing zlib1g-dev ...
-Processing triggers for man-db ...
+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 libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0930
-Build needed 00:08:29, 11404k disc space
+Finished at 20110302-0627
+Build needed 00:09:54, 12028k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/armel.log b/armel.log
index 7fd5195..fde4879 100644
--- a/armel.log
+++ b/armel.log
@@ -1,41 +1,67 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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>
+From buildd at arnold.debian.org Wed Mar 02 05:27:42 2011
+Return-path: <buildd at arnold.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at arnold.debian.org>)
+ id 1Pueb8-0002rP-JT
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:27:42 +0000
+Received: from arnold.islands.arm.com ([217.140.96.57] helo=arnold.debian.org)
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=arnold.debian.org, EMAIL=hostmaster at arnold.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at arnold.debian.org>)
+ id 1Pueb6-0001G2-F6
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:27:40 +0000
+Received: from buildd by arnold.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at arnold.debian.org>)
+ id 1Pueaj-00059Z-Li; Wed, 02 Mar 2011 05:27:17 +0000
+From: buildd on arnold <buildd at arnold.debian.org>
+To: buildd-porters at arnold.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.13-1 on armel (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1Pueaj-00059Z-Li at arnold.debian.org>
+Date: Wed, 02 Mar 2011 05:27:17 +0000
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on arnold.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (armel) 03 Dec 2010 09:22 ║
+║ samtools 0.1.13-1 (armel) 02 Mar 2011 05:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: armel
-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]
+Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-c25d4e2a-8085-46ea-a3fe-2707dc746f1c/build/buildd-samtools_0.1.13-1-armel-m5S1Vn
+Start Time: 20110302-0521
+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 [104kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
+Get:2 http://ftp.uk.debian.org unstable Release [146 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.uk.debian.org unstable/main Sources [4071kB]
-Get:5 http://incoming.debian.org Release.gpg [835B]
+Get:4 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 [104kB]
-Get:7 http://incoming.debian.org Release [1604B]
-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)
+Get:5 http://incoming.debian.org unstable Release [146 kB]
+Get:6 http://ftp.uk.debian.org unstable/main Sources [4155 kB]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://incoming.debian.org unstable/main Sources [4156 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib Sources [38.5 kB]
+Get:10 http://ftp.uk.debian.org unstable/non-free Sources [82.8 kB]
+Get:11 http://ftp.uk.debian.org unstable/main armel Packages [6831 kB]
+Get:12 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
+Get:14 http://incoming.debian.org unstable/main armel Packages [6831 kB]
+Get:15 http://ftp.uk.debian.org unstable/contrib armel Packages [50.7 kB]
+Get:16 http://incoming.debian.org unstable/contrib armel Packages [50.7 kB]
+Get:17 http://incoming.debian.org Sources [19.2 kB]
+Get:18 http://incoming.debian.org Packages [373 kB]
+Fetched 23.0 MB in 51s (446 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,20 +80,20 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (336 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -75,7 +101,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -86,61 +112,52 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 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 8.0.17 [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]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-3 [129kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.02-1.1 [234kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-1 [817kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.24.2-1 [1050kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.7+20100313-4 [1603kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190kB]
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 20 newly installed, 0 to remove and 35 not upgraded.
+Need to get 11.8 MB of archives.
+After this operation, 35.1 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.2 [205 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-4 [1082 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.1.0-1 [33.7 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.5.9-4 [976 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5 [237 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-3 [129 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-3 [258 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-2 [816 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.1-1+b1 [1516 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.7+20100313-5 [1607 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 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 ... 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) ...
+Fetched 11.8 MB in 6s (1764 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 9961 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_armel.deb) ...
+(Reading database ... 10042 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_armel.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_armel.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_armel.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_armel.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_armel.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_armel.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_armel.deb) ...
Selecting previously deselected package file.
@@ -148,13 +165,13 @@ Unpacking file (from .../archives/file_5.04-5_armel.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_armel.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_armel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_armel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_armel.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
Selecting previously deselected package libunistring0.
@@ -166,40 +183,42 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_armel.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
+Setting up bsdmainutils (8.2.2) ...
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) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
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_2.11.2-5 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
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.10.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 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_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 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 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 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 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_2:0.1.12-17 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011a-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -210,13 +229,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -231,144 +250,139 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
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_0.1.12a-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
-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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
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_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/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_0.1.12a-1-armel-F8yvZ0/samtools-0.1.12a/examples'
+make[1]: *** Deleting file `ex1.bam'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0928
+Build finished at 20110302-0527
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-933fddaf-1beb-4ac8-bf61-db1837fff3ba/build/buildd-samtools_0.1.12a-1-armel-F8yvZ0
+Purging /var/lib/schroot/mount/sid-armel-sbuild-c25d4e2a-8085-46ea-a3fe-2707dc746f1c/build/buildd-samtools_0.1.13-1-armel-m5S1Vn
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0928
-Build needed 00:06:06, 4988k disc space
+Finished at 20110302-0527
+Build needed 00:06:14, 5288k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/hppa.log b/hppa.log
index 94f526d..4b4df16 100644
--- a/hppa.log
+++ b/hppa.log
@@ -1,51 +1,71 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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>
+From buildd at penalosa.debian.org Wed Mar 02 09:37:27 2011
+Return-path: <buildd at penalosa.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at penalosa.debian.org>)
+ id 1PuiUo-0002eg-DL
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 09:37:26 +0000
+Received: from penalosa.debian.org ([192.25.206.68])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=penalosa.debian.org,
+ EMAIL=hostmaster at penalosa.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at penalosa.debian.org>)
+ id 1PuiUk-0003uT-Di; Wed, 02 Mar 2011 09:37:23 +0000
+Received: from buildd by penalosa.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at penalosa.debian.org>)
+ id 1PuiUe-0008Pe-Tn; Wed, 02 Mar 2011 09:37:17 +0000
+From: buildd on penalosa <buildd at penalosa.debian.org>
+To: dannf+buildd at dannf.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on hppa (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PuiUe-0008Pe-Tn at penalosa.debian.org>
+Date: Wed, 02 Mar 2011 09:37:16 +0000
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on penalosa.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (hppa) 03 Dec 2010 09:21 ║
+║ samtools 0.1.13-1 (hppa) 02 Mar 2011 09:33 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: hppa
-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
-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: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]
+Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-e02e2472-e461-4194-b7d0-5bc4f17318db/build/buildd-samtools_0.1.13-1-hppa-xspK0E
+Start Time: 20110302-0933
+Hit http://spohr.debian.org sid InRelease
+Hit http://spohr.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
Hit http://spohr.debian.org sid/contrib Sources/DiffIndex
-Get:8 http://spohr.debian.org sid/main hppa Packages/DiffIndex [2038 B]
+Hit http://spohr.debian.org sid/main hppa Packages/DiffIndex
Hit http://spohr.debian.org sid/contrib hppa Packages/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]
+Ign http://spohr.debian.org sid/contrib TranslationIndex
+Hit http://spohr.debian.org sid/main TranslationIndex
+Hit http://incoming.debian.org Release.gpg
+Ign http://spohr.debian.org sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:15 http://incoming.debian.org sid/main hppa Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/main hppa Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib hppa Packages/DiffIndex
-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)
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Hit http://incoming.debian.org Release
+Ign http://incoming.debian.org sid/main 2011-03-02-0827.59.pdiff
+Ign http://incoming.debian.org sid/contrib 2011-03-02-0827.59.pdiff
+Ign http://incoming.debian.org sid/main hppa 2011-03-02-0827.59.pdiff
+Hit http://incoming.debian.org sid/main
+Hit http://incoming.debian.org sid/contrib
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
+Hit http://incoming.debian.org sid/main hppa
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -64,37 +84,109 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (310 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), 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 >= 8 is satisfied)
-cdbs: already installed (0.4.89)
-libncurses5-dev: already installed (5.7+20100313-4)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+debhelper: missing
+Using default version 8.1.2
+cdbs: missing
+libncurses5-dev: already installed (5.7+20100313-5)
+zlib1g-dev: missing
Checking for source dependency conflicts...
-Installing positive dependencies:
+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 libpipeline1 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 libpipeline1 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 9 not upgraded.
+Need to get 0 B/10.3 MB of archives.
+After this operation, 27.1 MB of additional disk space will be used.
+Selecting previously deselected package groff-base.
+(Reading database ... 11588 files and directories currently installed.)
+Unpacking groff-base (from .../groff-base_1.21-4_hppa.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_hppa.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.5.9-4_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_8.12-3_hppa.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_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_2.28.1-1+b1_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_8.1.2_all.deb) ...
+Selecting previously deselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.92_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 (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
+Building database of manual pages ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
+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 (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32-5-parisc64 hppa (parisc64)
-Toolchain package versions: libc6-dev_2.11.2-7 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
+Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.11.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.48-5 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 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_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10 libc-dev-bin_2.11.2-10 libc6_2.11.2-10 libc6-dev_2.11.2-10 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.48-5 libdpkg-perl_1.15.8.10 libextutils-parsexs-perl_2.220600-1 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 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 libmodule-build-perl_0.360700-1 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-6 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.2-1 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libreadline5_5.2-7 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4+b1 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 libudev0_166-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 libyaml-perl_0.71-1 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -105,13 +197,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -126,164 +218,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
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_0.1.12a-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
-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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
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_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -305,11 +393,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -326,6 +414,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -333,7 +422,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-hppa-luOI2H/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -348,69 +437,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_hppa.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_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 -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_hppa.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_hppa.deb'.
+ dpkg-genchanges -B -mhppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd.debian.org> >../samtools_0.1.13-1_hppa.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0925
+Build finished at 20110302-0936
-samtools_0.1.12a-1_hppa.changes:
+samtools_0.1.13-1_hppa.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hppa
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: hppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: hppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- 38a0581663a751865211c666d624f338d134be58 563494 samtools_0.1.12a-1_hppa.deb
- aedbae40c00f4a206d289e25de9d512220153045 166206 libbam-dev_0.1.12a-1_hppa.deb
+ cb9201266b913e4ed094a286e11982576b85ed97 590730 samtools_0.1.13-1_hppa.deb
+ d3d9d98576fcfec2c090f56df2adfada8defe0fa 171726 libbam-dev_0.1.13-1_hppa.deb
Checksums-Sha256:
- 37423289380391653718ec54186e2da7732f45d156f73fb63920c34ec1dc2c59 563494 samtools_0.1.12a-1_hppa.deb
- 5c3ec027e567c144274ef99667fa00e40b66dc5d4afa1a4a2dc98de2c418cce4 166206 libbam-dev_0.1.12a-1_hppa.deb
+ 1f4630f35ed5ab5a470009d5a4b4f487a7298f5112afb71aa60a2daf4b31745f 590730 samtools_0.1.13-1_hppa.deb
+ 2e98a5cc4ef84cb8d43b9fcb24c97e7e4b23ec37a5210f33332fce0783bfce3a 171726 libbam-dev_0.1.13-1_hppa.deb
Files:
- bf86cb9d32756635a4a69f3af457aca2 563494 science optional samtools_0.1.12a-1_hppa.deb
- e89a9ebbcc3c3116d0ef46cbd839a6ba 166206 libdevel optional libbam-dev_0.1.12a-1_hppa.deb
+ 7a357d381c941ea9f318b88749ec858f 590730 science optional samtools_0.1.13-1_hppa.deb
+ 0de29d01bb923a4a125b4dc3e43d9e5c 171726 libdevel optional libbam-dev_0.1.13-1_hppa.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_hppa.deb
-───────────────────────────
+samtools_0.1.13-1_hppa.deb
+──────────────────────────
new debian package, version 2.0.
- size 563494 bytes: control archive= 1792 bytes.
- 793 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 590730 bytes: control archive= 1783 bytes.
+ 792 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: hppa
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1024
- Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1076
+ Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -422,48 +515,49 @@ samtools_0.1.12a-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 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/bin/
+-rwxr-xr-x root/root 104028 2011-03-02 09:36 ./usr/bin/bcftools
+-rwxr-xr-x root/root 380924 2011-03-02 09:36 ./usr/bin/samtools
+-rwxr-xr-x root/root 26564 2011-03-02 09:36 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11744 2011-03-02 09:36 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7880 2011-03-02 09:36 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 18492 2011-03-02 09:36 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8744 2011-03-02 09:36 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7880 2011-03-02 09:36 ./usr/lib/samtools/maq2sam-short
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-03-02 09:36 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./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 2010-12-03 09:24 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-02 09:36 ./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 2010-12-03 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 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 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
-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/
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/man/man1/
+-rw-r--r-- root/root 1229 2011-03-02 09:36 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-03-02 09:36 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 09:36 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./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 2010-12-03 09:24 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-03-02 09:36 ./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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./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
@@ -471,23 +565,21 @@ drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/samtools/
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
-lrwxrwxrwx root/root 0 2010-12-03 09:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.12a-1_hppa.deb
-─────────────────────────────
+libbam-dev_0.1.13-1_hppa.deb
+────────────────────────────
new debian package, version 2.0.
- size 166206 bytes: control archive= 899 bytes.
- 674 bytes, 15 lines control
+ size 171726 bytes: control archive= 894 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: hppa
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 416
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 420
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -498,22 +590,22 @@ libbam-dev_0.1.12a-1_hppa.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./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 2010-12-03 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 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/lib/
+-rw-r--r-- root/root 271240 2011-03-02 09:36 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
@@ -523,9 +615,34 @@ drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-hppa-sbuild-6f59b41d-9d09-44f5-adc7-d30a4b15c4ec/build/buildd-samtools_0.1.12a-1-hppa-luOI2H
+Purging /var/lib/schroot/mount/sid-hppa-sbuild-e02e2472-e461-4194-b7d0-5bc4f17318db/build/buildd-samtools_0.1.13-1-hppa-xspK0E
+(Reading database ... 12843 files and directories currently installed.)
+Removing zlib1g-dev ...
+Removing cdbs ...
+Removing debhelper ...
+Removing po-debconf ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing intltool-debian ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing gettext ...
+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 libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0925
-Build needed 00:03:25, 9004k disc space
+Finished at 20110302-0936
+Build needed 00:03:48, 9412k 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.log b/hurd-i386.log
index 050b682..7d4891c 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,17 +1,66 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+From buildd at rossini.debian.net Sun Mar 06 06:00:11 2011
+Return-path: <buildd at rossini.debian.net>
+Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at rossini.debian.net>)
+ id 1Pw70k-0002lI-He
+ for logs at buildd.debian.org; Sun, 06 Mar 2011 06:00:10 +0000
+Received: from hurd.ethz.ch ([192.33.98.55] helo=rossini.debian.net)
+ by io.debian.net with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
+ id 1Pw70f-000DSP-EB; Sun, 06 Mar 2011 07:00:05 +0100
+Received: from buildd by rossini.debian.net with local (Exim 4.72)
+ (envelope-from <buildd at rossini.debian.net>)
+ id 1Pw70f-0002ks-1O; Sun, 06 Mar 2011 06:00:05 +0000
+Date: Sun, 06 Mar 2011 06:00:05 +0000
+Message-Id: <E1Pw70f-0002ks-1O at rossini.debian.net>
+From: Build Daemon <buildd at rossini.debian.net>
+To: samuel.thibault at labri.fr, mbanck at debian.org, logs at debian-ports.org,
+ logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
+Subject: Log for attempted build of samtools_0.1.13-1 on hurd-i386 (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rossini.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (hurd-i386) 03 déc. 2010 09:24 ║
+║ samtools 0.1.13-1 (hurd-i386) 06 Mar 2011 05:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq
-Start Time: 20101203-0924
+Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-gNFKIo
+Start Time: 20110306-0556
+Ign file: ./ InRelease
+Ign file: ./ Release.gpg
+Ign file: ./ Release
+Ign file: ./ Translation-en
+Ign http://ftp.debian-ports.org unreleased InRelease
+Hit http://ftp.fr.debian.org unstable InRelease
+Hit http://ftp.fr.debian.org experimental InRelease
+Hit http://ftp.debian-ports.org unreleased Release.gpg
+Ign http://incoming.debian.org InRelease
+Hit http://ftp.debian-ports.org unreleased Release
+Get:1 http://incoming.debian.org Release.gpg [835 B]
+Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
+Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
+Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
+Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
+Hit http://ftp.fr.debian.org unstable/main TranslationIndex
+Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
+Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
+Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
+Get:3 http://incoming.debian.org Sources [36.0 kB]
+Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Get:4 http://incoming.debian.org Packages [200 kB]
+Ign http://incoming.debian.org Translation-en
+Fetched 239 kB in 1min 4s (3715 B/s)
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -23,101 +72,256 @@ Check APT
Checking available source versions...
-Update APT
+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 374 kB of source archives.
+Get:1 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (325 kB/s)
+Download complete and in download only mode
+
+Check arch
──────────
+** Using build dependencies supplied by package:
+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 8.1.2
+cdbs: missing
+libncurses5-dev: missing
+zlib1g-dev: missing
+Checking for source dependency conflicts...
+Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+debconf: delaying package configuration, since apt-utils is not installed
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libident liblzo2-2
+Use 'apt-get autoremove' to remove them.
+The following extra packages will be installed:
+ file gettext gettext-base html2text intltool-debian libcroco3 libexpat1
+ libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
+Suggested packages:
+ devscripts doc-base dh-make gettext-doc libmail-box-perl
+Recommended packages:
+ autotools-dev 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 html2text intltool-debian libcroco3
+ libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2
+ po-debconf zlib1g-dev
+0 upgraded, 16 newly installed, 0 to remove and 20 not upgraded.
+Need to get 0 B/9452 kB of archives.
+After this operation, 28.8 MB of additional disk space will be used.
+WARNING: The following packages cannot be authenticated!
+ libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3
+ libexpat1 libunistring0 gettext intltool-debian po-debconf debhelper cdbs
+ libncurses5-dev zlib1g-dev
+Authentication warning overridden.
+Selecting previously deselected package libmagic1.
+(Reading database ... 11608 files and directories currently installed.)
+Unpacking libmagic1 (from .../libmagic1_5.03-5+b1_hurd-i386.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../file_5.03-5+b1_hurd-i386.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hurd-i386.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hurd-i386.deb) ...
+Selecting previously deselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
+Selecting previously deselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_hurd-i386.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
+Selecting previously deselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hurd-i386.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_hurd-i386.deb) ...
+Selecting previously deselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously deselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Selecting previously deselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Selecting previously deselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5+b1_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 ...
+Processing triggers for install-info ...
+Setting up libmagic1 (5.03-5+b1) ...
+Setting up file (5.03-5+b1) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libexpat1 (2.0.1-7) ...
+Setting up libunistring0 (0.9.3-3) ...
+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 (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5+b1) ...
+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_2.11.2-13 dpkg-dev_1.15.8.10 hurd-dev_20110303-1~0 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
+Package versions: adduser_3.112+nmu2 apt_0.8.11.5+b1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.6-2 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15+b1 hurd_20110303-1~0 hurd-dev_20110303-1~0 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.1 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 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_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.3-1+hurd.1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libident_0.22-3 libidn11_1.20-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 liblzo2-2_2.04-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5+b1 libncurses5-dev_5.7+20100313-5+b1 libncursesw5_5.7+20100313-5+b1 libnewt0.52_0.52.11-2 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.2-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.1.0-1 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.dfsg1-7 libsasl2-modules_2.1.23.dfsg1-7 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-2 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-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-8 libxml2_2.7.8.dfsg-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5+b1 netbase_4.45 netcat-traditional_1.10-39 openssl_0.9.8o-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-2 tzdata_2011a-1 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+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 Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+
+Check disc space
+────────────────
+
+
+dpkg-buildpackage
+─────────────────
+
+/usr/sbin/chroot: failed to run command `/bin/su': Computer bought the farm
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20110306-0559
+FAILED [dpkg-buildpackage died]
+────────────────────────────────────────────────────────────────────────────────
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-gNFKIo
+(Reading database ... 13552 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 ...
+Purging configuration files for file ...
+Removing libexpat1 ...
+Purging configuration files for libexpat1 ...
+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 ...
+Processing triggers for install-info ...
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110306-0559
+Build needed 00:03:24, 1576k disc space
+
+From buildd at rossini.debian.net Wed Mar 09 11:43:32 2011
+Return-path: <buildd at rossini.debian.net>
+Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at rossini.debian.net>)
+ id 1PxHnf-00083q-FL
+ for logs at buildd.debian.org; Wed, 09 Mar 2011 11:43:32 +0000
+Received: from hurd.ethz.ch ([192.33.98.55] helo=rossini.debian.net)
+ by io.debian.net with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
+ id 1PxHnb-000PI7-EW; Wed, 09 Mar 2011 12:43:27 +0100
+Received: from buildd by rossini.debian.net with local (Exim 4.72)
+ (envelope-from <buildd at rossini.debian.net>)
+ id 1PxHnf-0007Qh-OJ; Wed, 09 Mar 2011 11:43:31 +0000
+Date: Wed, 09 Mar 2011 11:43:31 +0000
+Message-Id: <E1PxHnf-0007Qh-OJ at rossini.debian.net>
+From: Build Daemon <buildd at rossini.debian.net>
+To: samuel.thibault at labri.fr, mbanck at debian.org, logs at debian-ports.org,
+ logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on hurd-i386 (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rossini.debian.net
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 0.1.13-1 (hurd-i386) 09 Mar 2011 11:32 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.13-1
+Architecture: hurd-i386
+Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn
+Start Time: 20110309-1132
+Ign file: ./ InRelease
Ign file: ./ Release.gpg
-Ign file:/build/local-debs/ ./ Translation-en
Ign file: ./ Release
-Ign file: ./ Packages
-Get:1 http://ftp.debian-ports.org unreleased Release.gpg [835 B]
-Ign http://ftp.debian-ports.org/debian/ unreleased/main Translation-en
-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: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]
+Ign file: ./ Translation-en
+Ign http://ftp.debian-ports.org unreleased InRelease
+Hit http://ftp.fr.debian.org unstable InRelease
+Hit http://ftp.fr.debian.org experimental InRelease
+Hit http://ftp.debian-ports.org unreleased Release.gpg
+Ign http://incoming.debian.org InRelease
+Hit http://ftp.debian-ports.org unreleased Release
+Hit http://incoming.debian.org Release.gpg
+Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
+Hit http://incoming.debian.org Release
+Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
+Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
+Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.fr.debian.org unstable/main TranslationIndex
+Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
+Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
+Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-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)
+Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
+Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
+Ign http://incoming.debian.org Translation-en
Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
Checking available source versions...
Download source files with APT
@@ -126,66 +330,114 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (279 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), 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 >= 8 is satisfied)
+debhelper: missing
+Using default version 8.1.2
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
+debconf: delaying package configuration, since apt-utils is not installed
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libwrap0 adduser libsysfs2 libusb-0.1-4p
-Use 'apt-get autoremove' to remove them.
+The following extra packages will be installed:
+ file gettext gettext-base html2text intltool-debian libcroco3 libexpat1
+ libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- devscripts doc-base
+ devscripts doc-base dh-make gettext-doc ncurses-doc 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 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.
+ cdbs debhelper file gettext gettext-base html2text intltool-debian libcroco3
+ libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2
+ po-debconf zlib1g-dev
+0 upgraded, 16 newly installed, 0 to remove and 25 not upgraded.
+Need to get 0 B/8347 kB of archives.
+After this operation, 23.5 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs libncurses5-dev zlib1g-dev
+ libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3
+ libexpat1 libunistring0 gettext intltool-debian po-debconf debhelper cdbs
+ libncurses5-dev zlib1g-dev
Authentication warning overridden.
+Selecting previously deselected package libmagic1.
+(Reading database ... 11608 files and directories currently installed.)
+Unpacking libmagic1 (from .../libmagic1_5.03-5+b1_hurd-i386.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../file_5.03-5+b1_hurd-i386.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hurd-i386.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hurd-i386.deb) ...
+Selecting previously deselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
+Selecting previously deselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_hurd-i386.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
+Selecting previously deselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hurd-i386.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_hurd-i386.deb) ...
+Selecting previously deselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously deselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 11907 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_hurd-i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8-1_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) ...
+Processing triggers for install-info ...
+Setting up libmagic1 (5.03-5+b1) ...
+Setting up file (5.03-5+b1) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libexpat1 (2.0.1-7) ...
+Setting up libunistring0 (0.9.3-3) ...
+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 (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.8-1) ...
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_4.4.5-10 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
+Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.15.8.10 hurd-dev_20110303-1~1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
+Package versions: adduser_3.112+nmu2 apt_0.8.11.5+b1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.6-2 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15+b1 hurd_20110303-1~1 hurd-dev_20110303-1~1 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.1 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 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_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.3-1+hurd.1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libident_0.22-3 libidn11_1.20-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 liblzo2-2_2.04-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-7 libncurses5_5.8-1 libncurses5-dev_5.8-1 libncursesw5_5.8-1 libnewt0.52_0.52.11-2 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.2-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.1.0-1 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.dfsg1-7 libsasl2-modules_2.1.23.dfsg1-7 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-2 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-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-8 libxml2_2.7.8.dfsg-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.8-1 netbase_4.45 netcat-traditional_1.10-39 openssl_0.9.8o-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-2 tzdata_2011a-1 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -196,13 +448,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -213,168 +465,164 @@ dpkg-buildpackage
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
+ dpkg-source --before-build samtools-0.1.13
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 0.1.12a-1
+dpkg-buildpackage: source version 0.1.13-1
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_0.1.12a-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'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
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
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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_0.1.12a-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
-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
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_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/examples'
-../samtools faidx ex1.fa
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
[sam_header_read2] 2 sequences loaded.
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/examples'
+../samtools faidx ex1.fa
../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
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
[samopen] SAM header is present: 2 sequences.
+../samtools index ex1.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
[bam_rmdup_core] processing reference seq1...
-[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'
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-[mpileup] 1 samples in 1 input files
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-<mpileup> Set max per-sample depth to 8000
+[bam_rmdup_core] processing reference seq2...
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
+[mpileup] 1 samples in 1 input files
+../samtools glfview ex1.glf | gzip > ex1.glfview.gz
+<mpileup> Set max per-sample depth to 8000
+../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/examples'
-touch debian/stamp-makefile-check
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -396,11 +644,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -417,6 +665,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -424,7 +673,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -439,69 +688,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_hurd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_hurd-i386.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mhurd-i386 Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../samtools_0.1.13-1_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0951
+Build finished at 20110309-1142
-samtools_0.1.12a-1_hurd-i386.changes:
+samtools_0.1.13-1_hurd-i386.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: hurd-i386 Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- fc6e365d7c892b4387863d76ea111b7472b3c561 547110 samtools_0.1.12a-1_hurd-i386.deb
- 44e8ea42aae8953667c17f5ae653bab19787b73f 157814 libbam-dev_0.1.12a-1_hurd-i386.deb
+ 63e225a0aa19088164afcc1621327058a2123ea4 573676 samtools_0.1.13-1_hurd-i386.deb
+ 66010e2872537411b1ac3e423585fdec17b1dcba 163446 libbam-dev_0.1.13-1_hurd-i386.deb
Checksums-Sha256:
- a8ed8afefbcae83803779faab971bc7c5bc61f39b7bf0ce3c43b418a61d172fa 547110 samtools_0.1.12a-1_hurd-i386.deb
- ba7fdaf7613cb931823565aae39623efcc209dd80631393f62ecc333d9cf0efc 157814 libbam-dev_0.1.12a-1_hurd-i386.deb
+ ebe68e1457e38485a77b1c39a5225231a3fe6fc80928e7598b2792eb77c811ac 573676 samtools_0.1.13-1_hurd-i386.deb
+ f13e62fad0d97eb6bbc33b4ab42265d8ba45211de96b62b66b96caca33173c98 163446 libbam-dev_0.1.13-1_hurd-i386.deb
Files:
- 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
+ ab0f5cbe484b78c9d29559f3fd5239ce 573676 science optional samtools_0.1.13-1_hurd-i386.deb
+ 313550a03c4c714b2c750bfdbd672cdb 163446 libdevel optional libbam-dev_0.1.13-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_hurd-i386.deb
-────────────────────────────────
+samtools_0.1.13-1_hurd-i386.deb
+───────────────────────────────
new debian package, version 2.0.
- size 547110 bytes: control archive= 1801 bytes.
- 799 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 573676 bytes: control archive= 1797 bytes.
+ 793 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: hurd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 976
- Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1028
+ Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -513,33 +766,33 @@ samtools_0.1.12a-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 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-09 11:40 ./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 2010-12-03 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 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-09 11:40 ./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 2010-12-03 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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rw-r--r-- root/root 126609 2011-03-09 11:38 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-09 11:39 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-09 11:39 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-09 11:39 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1229 2011-03-09 11:39 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-09 11:41 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./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
@@ -551,34 +804,33 @@ drwxr-xr-x root/root 0 2010-12-03 09:50 ./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 2010-12-03 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
-──────────────────────────────────
+-rwxr-xr-x root/root 5778 2011-03-09 11:41 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/bin/
+-rwxr-xr-x root/root 88260 2011-03-09 11:40 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23788 2011-03-09 11:40 ./usr/bin/razip
+-rwxr-xr-x root/root 353772 2011-03-09 11:40 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17488 2011-03-09 11:40 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6336 2011-03-09 11:40 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6320 2011-03-09 11:40 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10084 2011-03-09 11:40 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6920 2011-03-09 11:40 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.13-1_hurd-i386.deb
+─────────────────────────────────
new debian package, version 2.0.
- size 157814 bytes: control archive= 904 bytes.
- 679 bytes, 15 lines control
+ size 163446 bytes: control archive= 903 bytes.
+ 678 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: hurd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 388
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 392
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -589,22 +841,22 @@ libbam-dev_0.1.12a-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./
+drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-09 11:41 ./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 09:50 ./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 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-09 11:41 ./usr/lib/
+-rw-r--r-- root/root 245022 2011-03-09 11:41 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./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 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -614,14 +866,35 @@ drwxr-xr-x root/root 0 2010-12-03 09:49 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-unstable/build/buildd-samtools_0.1.12a-1-hurd-i386-baH8wq
-(Reading database ... 13045 files and directories currently installed.)
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn
+(Reading database ... 12544 files and directories currently installed.)
Removing libncurses5-dev ...
-Removing cdbs ...
Removing zlib1g-dev ...
+Removing cdbs ...
+Removing debhelper ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing file ...
+Purging configuration files for file ...
+Removing libexpat1 ...
+Purging configuration files for libexpat1 ...
+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 ...
+Processing triggers for install-info ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0951
-Build needed 00:27:27, 8428k disc space
+Finished at 20110309-1142
+Build needed 00:10:57, 8808k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/i386.log b/i386.log
index ddecfd3..6fc8f91 100644
--- a/i386.log
+++ b/i386.log
@@ -1,41 +1,67 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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>
+From buildd at biber.debian.org Wed Mar 02 05:23:36 2011
+Return-path: <buildd at biber.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at biber.debian.org>)
+ id 1PueXA-0001wG-7m
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:23:36 +0000
+Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at biber.debian.org>)
+ id 1PueX7-0001A0-VK; Wed, 02 Mar 2011 05:23:34 +0000
+Received: from buildd by biber.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at biber.debian.org>)
+ id 1PueX6-0002pc-BM; Wed, 02 Mar 2011 05:23:32 +0000
+From: buildd on biber <buildd at biber.debian.org>
+To: kurt at roeckx.be,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on i386 (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PueX6-0002pc-BM at biber.debian.org>
+Date: Wed, 02 Mar 2011 05:23:32 +0000
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (i386) 03 Dec 2010 09:20 ║
+║ samtools 0.1.13-1 (i386) 02 Mar 2011 05:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: i386
-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 [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 [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: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 [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 [8014 B]
-Get:18 http://incoming.debian.org Packages [169 kB]
-Fetched 22.8 MB in 17s (1287 kB/s)
+Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-0ea7fe83-726a-4c1d-a06d-ec5b060e0a7e/build/buildd-samtools_0.1.13-1-i386-TcVkK4
+Start Time: 20110302-0520
+Get:1 http://ftp.gr.debian.org unstable InRelease [147 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [4156 kB]
+Get:3 http://incoming.debian.org unstable InRelease [147 kB]
+Get:4 http://ftp.gr.debian.org unstable/contrib Sources [38.5 kB]
+Get:5 http://ftp.gr.debian.org unstable/non-free Sources [82.8 kB]
+Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [6999 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [61.0 kB]
+Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
+Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2232 B]
+Ign http://ftp.gr.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org InRelease
+Get:9 http://incoming.debian.org Release.gpg [835 B]
+Get:10 http://incoming.debian.org unstable/main Sources [4156 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [6999 kB]
+Get:14 http://incoming.debian.org unstable/contrib i386 Packages [61.0 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [19.2 kB]
+Get:18 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 23.4 MB in 20s (1141 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,20 +80,20 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (229 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -75,7 +101,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -86,8 +112,8 @@ 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 libpcre3 libpipeline1 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
@@ -97,38 +123,41 @@ Recommended packages:
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 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 8.0.17 [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]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.02-1.1 [231 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-1 [827 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.24.2-1 [1029 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.0.0 [454 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.89 [1240 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.7+20100313-4 [1601 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
+Need to get 11.8 MB of archives.
+After this operation, 35.2 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.2 [200 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-4 [1130 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.1.0-1 [35.2 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.5.9-4 [980 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2 [827 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.1-1+b1 [1487 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.7+20100313-5 [1597 kB]
+Get:20 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 (7238 kB/s)
+Fetched 11.8 MB in 1s (9326 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10160 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_i386.deb) ...
+(Reading database ... 10235 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_i386.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_i386.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_i386.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_i386.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_i386.deb) ...
Selecting previously deselected package file.
@@ -136,13 +165,13 @@ Unpacking file (from .../archives/file_5.04-5_i386.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_i386.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
Selecting previously deselected package libunistring0.
@@ -154,40 +183,42 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
+Setting up bsdmainutils (8.2.2) ...
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) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
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-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_8.0.17 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
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-2 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libstdc++6_4.5.2-4
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,13 +229,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -219,164 +250,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
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_0.1.12a-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
-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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-i386-61mbY2/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
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_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -398,11 +425,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -419,6 +446,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -426,7 +454,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-i386-61mbY2/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -441,69 +469,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_i386.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.13-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0922
+Build finished at 20110302-0523
-samtools_0.1.12a-1_i386.changes:
+samtools_0.1.13-1_i386.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- 8bbc22fe2849d2f019694e26cdec4c5897b6403f 546556 samtools_0.1.12a-1_i386.deb
- 3100d9b3b95c7d5cf63da6695e5184ab2fb0022a 157736 libbam-dev_0.1.12a-1_i386.deb
+ ade2eb3236c4b6ac7d3e591c1ce6a35ef3a0398c 572508 samtools_0.1.13-1_i386.deb
+ 99f19933e954aa396f16555d1e01476cc49cd590 163322 libbam-dev_0.1.13-1_i386.deb
Checksums-Sha256:
- d71ed16a874a920a546e1e9f59ac0654b81ec25aec236b666e66608efb8b0c1f 546556 samtools_0.1.12a-1_i386.deb
- 941cd899a521e70c7c16d194c3ef695ba41aaebfe8f430ac54d9ab5afd6fa34e 157736 libbam-dev_0.1.12a-1_i386.deb
+ 664b163f71501b9fa3e8e9d8d4e980d4fbe8fa17001ec70084cc6c35ada4aacd 572508 samtools_0.1.13-1_i386.deb
+ 575d0af686c6327c19fbd7cddd9b3022bb396da31f83c63e24bff45c55af9067 163322 libbam-dev_0.1.13-1_i386.deb
Files:
- 62d7a4320ab6b1e376f9457fe30067fd 546556 science optional samtools_0.1.12a-1_i386.deb
- e3ea536c41192f0320873286684eda1d 157736 libdevel optional libbam-dev_0.1.12a-1_i386.deb
+ 225ee85994601154b340e480a74716ab 572508 science optional samtools_0.1.13-1_i386.deb
+ b6ace1ccf9f7e0448af80832ab0fb930 163322 libdevel optional libbam-dev_0.1.13-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_i386.deb
-───────────────────────────
+samtools_0.1.13-1_i386.deb
+──────────────────────────
new debian package, version 2.0.
- size 546556 bytes: control archive= 1793 bytes.
+ size 572508 bytes: control archive= 1783 bytes.
791 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 976
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1028
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -515,72 +547,71 @@ samtools_0.1.12a-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 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/lib/samtools/
+-rwxr-xr-x root/root 6680 2011-03-02 05:23 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6176 2011-03-02 05:23 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6160 2011-03-02 05:23 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9908 2011-03-02 05:23 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17224 2011-03-02 05:23 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/bin/
+-rwxr-xr-x root/root 88260 2011-03-02 05:23 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23692 2011-03-02 05:23 ./usr/bin/razip
+-rwxr-xr-x root/root 353772 2011-03-02 05:23 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./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 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 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./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 2010-12-03 09:22 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-02 05:23 ./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 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 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
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-03-02 05:23 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/man/man1/
+-rw-r--r-- root/root 1229 2011-03-02 05:23 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 05:23 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-02 05:23 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./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 2010-12-03 09:22 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-03-02 05:23 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
-lrwxrwxrwx root/root 0 2010-12-03 09:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.12a-1_i386.deb
-─────────────────────────────
+libbam-dev_0.1.13-1_i386.deb
+────────────────────────────
new debian package, version 2.0.
- size 157736 bytes: control archive= 897 bytes.
- 674 bytes, 15 lines control
+ size 163322 bytes: control archive= 899 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 388
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 392
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -591,21 +622,21 @@ libbam-dev_0.1.12a-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/lib/
+-rw-r--r-- root/root 245070 2011-03-02 05:23 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./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 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 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/include/
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./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
@@ -616,10 +647,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-i386-sbuild-844f11ba-9f87-46e7-97e1-8ee812a9f6ca/build/buildd-samtools_0.1.12a-1-i386-61mbY2
+Purging /var/lib/schroot/mount/sid-i386-sbuild-0ea7fe83-726a-4c1d-a06d-ec5b060e0a7e/build/buildd-samtools_0.1.13-1-i386-TcVkK4
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0922
-Build needed 00:01:48, 8432k disc space
+Finished at 20110302-0523
+Build needed 00:02:56, 8808k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/ia64.log b/ia64.log
index 228f1d3..b4ef90e 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,51 +1,68 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+From buildd at alkman.debian.org Wed Mar 02 05:28:59 2011
+Return-path: <buildd at alkman.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at alkman.debian.org>)
+ id 1PuecM-00030H-RA
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:28:59 +0000
+Received: from alkman.debian.org ([192.25.206.63])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at alkman.debian.org>)
+ id 1Puebx-0006DF-P5
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:28:55 +0000
+Received: from buildd by alkman.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at alkman.debian.org>)
+ id 1Puebq-0001dc-6B; Wed, 02 Mar 2011 05:28:26 +0000
+From: buildd on alkman <buildd at alkman.debian.org>
+To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on ia64 (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1Puebq-0001dc-6B at alkman.debian.org>
+Date: Wed, 02 Mar 2011 05:28:26 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (ia64) 03 Dec 2010 09:22 ║
+║ samtools 0.1.13-1 (ia64) 02 Mar 2011 05:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: ia64
-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
-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: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
-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
-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
-Get:15 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
-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)
+Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-921a377a-9305-4edc-bc84-5d1036145ce6/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK
+Start Time: 20110302-0524
+Get:1 http://spohr.debian.org unstable InRelease [147 kB]
+Get:2 http://incoming.debian.org unstable InRelease [147 kB]
+Get:3 http://spohr.debian.org unstable/main Sources [4156 kB]
+Get:4 http://spohr.debian.org unstable/contrib Sources [38.5 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [82.8 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [6790 kB]
+Ign http://incoming.debian.org InRelease
+Get:7 http://incoming.debian.org Release.gpg [835 B]
+Get:8 http://incoming.debian.org unstable/main Sources [4156 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [51.4 kB]
+Ign http://spohr.debian.org unstable/contrib TranslationIndex
+Get:10 http://spohr.debian.org unstable/main TranslationIndex [2232 B]
+Ign http://spohr.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [6790 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [51.4 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [19.2 kB]
+Get:18 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 22.9 MB in 20s (1104 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -64,20 +81,20 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 0s (419 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -85,7 +102,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -95,37 +112,67 @@ 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
+ bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff less www-browser
- libmail-box-perl
+ 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
The following NEW packages will be installed:
- cdbs debhelper gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libncurses5-dev libpcre3 libunistring0 libxml2 man-db
- po-debconf zlib1g-dev
+ bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 20 newly installed, 0 to remove and 19 not upgraded.
+Need to get 14.0 MB of archives.
+After this operation, 47.4 MB of additional disk space will be used.
+Get:1 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.2 [236 kB]
+Get:2 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-4 [1400 kB]
+Get:3 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.1.0-1 [46.5 kB]
+Get:4 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.5.9-4 [1154 kB]
+Get:5 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.04-5 [263 kB]
+Get:6 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5 [51.9 kB]
+Get:7 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-3 [174 kB]
+Get:8 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-3 [316 kB]
+Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-2 [1181 kB]
+Get:10 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
+Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.1-1+b1 [1963 kB]
+Get:12 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
+Get:13 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-3 [469 kB]
+Get:14 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-3 [2453 kB]
+Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:19 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.7+20100313-5 [1716 kB]
+Get:20 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-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.
+Fetched 14.0 MB in 4s (3116 kB/s)
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10123 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_ia64.deb) ...
Selecting previously deselected package groff-base.
-(Reading database ... 10388 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.20.1-10_ia64.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_ia64.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_ia64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_ia64.deb) ...
+Selecting previously deselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.04-5_ia64.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../archives/file_5.04-5_ia64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_ia64.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_ia64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_ia64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_ia64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
Selecting previously deselected package libunistring0.
@@ -137,35 +184,42 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_ia64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_ia64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up bsdmainutils (8.2.2) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
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_4.4.5-10 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
+Toolchain package versions: libc6.1-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
+Package versions: apt_0.8.11.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 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_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6.1_2.11.2-11 libc6.1-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 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+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.2-2 libpam0g_1.1.1-6.1 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 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 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -176,13 +230,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -197,158 +251,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
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_0.1.12a-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
-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
-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
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_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -370,11 +426,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -391,6 +447,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -398,7 +455,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-ia64-gr6cnc/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -413,69 +470,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_ia64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_ia64.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.13-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0924
+Build finished at 20110302-0528
-samtools_0.1.12a-1_ia64.changes:
+samtools_0.1.13-1_ia64.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- a3f0377809cbc0f8d1f1f8218392d666dbca7257 691894 samtools_0.1.12a-1_ia64.deb
- c650b494bdef80cf7bcdb93d5b2bf550ecdd1022 207066 libbam-dev_0.1.12a-1_ia64.deb
+ 1084bf1f41cc43c6da647f501e5413c710f7b67e 713526 samtools_0.1.13-1_ia64.deb
+ ed2687461eba5fcb36c546914e1a1d9cf9068707 212932 libbam-dev_0.1.13-1_ia64.deb
Checksums-Sha256:
- a9e74b2485999044dbf3025354617b13e5844054a013f840d37ee0f6a1c302fa 691894 samtools_0.1.12a-1_ia64.deb
- c3033101dbd1ae9b7da5b6996a0894fad18ed3a41809e685e998a124e89e2f57 207066 libbam-dev_0.1.12a-1_ia64.deb
+ ee7d12486e7e6805716ee2f650ac832ab98b50bb8b97b4714a1f4b5b72576b5c 713526 samtools_0.1.13-1_ia64.deb
+ ec80d4dd8147f85363109220ee897f195a3f984ac518f57f6849c10500fd238d 212932 libbam-dev_0.1.13-1_ia64.deb
Files:
- 3c80dbac2bcc0a5e51eafb62fdb31c86 691894 science optional samtools_0.1.12a-1_ia64.deb
- 8615cef0efb0fbe67b778596950e8533 207066 libdevel optional libbam-dev_0.1.12a-1_ia64.deb
+ f53a25adc191c81783e610278f9c6c9f 713526 science optional samtools_0.1.13-1_ia64.deb
+ c6592ca4b578749b158f4ae1c0bc29d2 212932 libdevel optional libbam-dev_0.1.13-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_ia64.deb
-───────────────────────────
+samtools_0.1.13-1_ia64.deb
+──────────────────────────
new debian package, version 2.0.
- size 691894 bytes: control archive= 1791 bytes.
- 794 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 713526 bytes: control archive= 1789 bytes.
+ 793 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: ia64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1564
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1936
+ Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -487,72 +548,71 @@ samtools_0.1.12a-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 2010-12-03 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 2010-12-03 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 2010-12-03 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 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
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30712 2011-03-02 05:28 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13360 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13296 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 22384 2011-03-02 05:28 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2011-03-02 05:28 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/bin/
+-rwxr-xr-x root/root 226632 2011-03-02 05:28 ./usr/bin/bcftools
+-rwxr-xr-x root/root 52520 2011-03-02 05:28 ./usr/bin/razip
+-rwxr-xr-x root/root 792192 2011-03-02 05:28 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-03-02 05:28 ./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 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
-─────────────────────────────
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 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 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 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/man1/
+-rw-r--r-- root/root 1229 2011-03-02 05:28 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-03-02 05:28 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 05:28 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-02 05:28 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2011-03-02 05:28 ./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 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+
+
+libbam-dev_0.1.13-1_ia64.deb
+────────────────────────────
new debian package, version 2.0.
- size 207066 bytes: control archive= 894 bytes.
- 674 bytes, 15 lines control
+ size 212932 bytes: control archive= 895 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: ia64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 660
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 752
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -563,23 +623,23 @@ libbam-dev_0.1.12a-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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 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
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/include/
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
+-rw-r--r-- root/root 521844 2011-03-02 05:28 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -588,34 +648,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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 ...
-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-ia64-sbuild-921a377a-9305-4edc-bc84-5d1036145ce6/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK
+Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0924
-Build needed 00:02:10, 12688k disc space
+Finished at 20110302-0528
+Build needed 00:03:35, 15492k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/info b/info
new file mode 100644
index 0000000..ab88a03
--- /dev/null
+++ b/info
@@ -0,0 +1,14 @@
+s390~1299043371~sid~successful
+i386~1299043417~sid~successful
+powerpc~1299043539~sid~successful
+sparc~1299043573~sid~failed
+armel~1299043663~sid~failed
+ia64~1299043739~sid~successful
+kfreebsd-i386~1299043749~sid~successful
+mipsel~1299044792~sid~successful
+alpha~1299047331~sid~successful
+mips~1299054657~sid~successful
+hppa~1299058650~sid~successful
+kfreebsd-amd64~1299139939~sid~successful
+hurd-i386~1299391211~sid~failed
+hurd-i386~1299671012~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 78c9c3c..ad9474c 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,46 +1,66 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+From buildd at fano.debian.org Thu Mar 03 08:12:19 2011
+Return-path: <buildd at fano.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at fano.debian.org>)
+ id 1Pv3dy-0002f4-Q8
+ for logs at buildd.debian.org; Thu, 03 Mar 2011 08:12:19 +0000
+Received: from fano.debian.org ([206.12.19.110])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at fano.debian.org>)
+ id 1Pv3dv-0003M1-RA; Thu, 03 Mar 2011 08:12:16 +0000
+Received: from buildd by fano.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fano.debian.org>)
+ id 1Pv3dp-0002mV-Pp; Thu, 03 Mar 2011 08:12:09 +0000
+Date: Thu, 03 Mar 2011 08:12:09 +0000
+Message-Id: <E1Pv3dp-0002mV-Pp at fano.debian.org>
+From: buildd on fano <buildd at fano.debian.org>
+To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
+Subject: Log for successful build of samtools_0.1.13-1 on kfreebsd-amd64
+ (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (kfreebsd-amd64) 03 Dec 2010 10:14 ║
+║ samtools 0.1.13-1 (kfreebsd-amd64) 03 Mar 2011 08:10 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: kfreebsd-amd64
-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://incoming.debian.org/debian/ sid/non-free Translation-en
+Chroot Build Dir: /var/lib/schroot/mount/sid-ka-sbuild-1299139834-9072/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd
+Start Time: 20110303-0810
+Hit http://ftp.ca.debian.org sid InRelease
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Hit http://ftp.ca.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org Release.gpg
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-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://ftp.ca.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.ca.debian.org sid/main TranslationIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Ign http://incoming.debian.org sid/non-free TranslationIndex
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
Hit http://incoming.debian.org Sources
Hit http://incoming.debian.org Packages
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org sid/non-free Translation-en
+Ign http://incoming.debian.org Translation-en
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -59,20 +79,20 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (318 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -80,7 +100,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -91,7 +111,8 @@ 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
+ libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
devscripts doc-base dh-make gettext-doc groff less www-browser
libmail-box-perl
@@ -101,16 +122,18 @@ Recommended packages:
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
+ libpipeline1 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 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.
+0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/12.0 MB of archives.
+After this operation, 33.7 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 13308 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-amd64.deb) ...
+(Reading database ... 11844 files and directories currently installed.)
+Unpacking groff-base (from .../groff-base_1.21-4_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-amd64.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-amd64.deb) ...
Selecting previously deselected package file.
@@ -118,13 +141,13 @@ Unpacking file (from .../file_5.04-5_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-amd64.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libunistring0.
@@ -136,37 +159,39 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_kfreebsd-amd64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_kfreebsd-amd64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-amd64.deb) ...
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
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_1.15.8.6 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
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.5.2-4 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libc0.1-dev_2.11.2-13 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1+b1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 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_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.5-1 libgomp1_4.5.2-4 libgpg-error0_1.10-0.3 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_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 libtasn1-3_2.9-2 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011b-2 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -177,13 +202,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -198,158 +223,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-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'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
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_0.1.12a-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
-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
-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
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_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -371,11 +398,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -392,6 +419,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -399,7 +427,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -414,69 +442,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_kfreebsd-amd64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_kfreebsd-amd64.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.13-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-1017
+Build finished at 20110303-0811
-samtools_0.1.12a-1_kfreebsd-amd64.changes:
+samtools_0.1.13-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- e9571bc72c8ddd5a2972a340e923f3def5591768 553904 samtools_0.1.12a-1_kfreebsd-amd64.deb
- cbd8d3ca435ec22efad48117cbc24b09e7d9efe9 155700 libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
+ fe45b44e2603d5ef8c612bd631a2d8afc65e2db0 582914 samtools_0.1.13-1_kfreebsd-amd64.deb
+ f8b231d35ce6fe977645a4cf67fd466365886700 161392 libbam-dev_0.1.13-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 2baa21df0016f17cb370b589b73a3ea3d85113fdf97ed83de975a1c33e04ea35 553904 samtools_0.1.12a-1_kfreebsd-amd64.deb
- ee66327cf310e59d1a5430ef2be8591b0c9fe481c705a96b80b86567fd57bc8b 155700 libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
+ 80b584d252e31830bbcb68be5ffb8aae03261c18c95b9dc2ca72e92da19dc6d4 582914 samtools_0.1.13-1_kfreebsd-amd64.deb
+ 9d98b0214ffbd8be51eb703fb31a0d515592b7c414ecfe68b38b6f4620abb073 161392 libbam-dev_0.1.13-1_kfreebsd-amd64.deb
Files:
- 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
+ f37e340d80c90e52c0a535ab32f235a4 582914 science optional samtools_0.1.13-1_kfreebsd-amd64.deb
+ 3b32618835f90c4680bf7354661b61cd 161392 libdevel optional libbam-dev_0.1.13-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_kfreebsd-amd64.deb
-─────────────────────────────────────
+samtools_0.1.13-1_kfreebsd-amd64.deb
+────────────────────────────────────
new debian package, version 2.0.
- size 553904 bytes: control archive= 1800 bytes.
- 803 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 582914 bytes: control archive= 1791 bytes.
+ 802 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: kfreebsd-amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 942
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 984
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -488,33 +520,33 @@ samtools_0.1.12a-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 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./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 2010-12-03 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 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./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 2010-12-03 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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rw-r--r-- root/root 126609 2011-03-03 08:11 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-03 08:11 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-03 08:11 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-03 08:11 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1229 2011-03-03 08:11 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./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 +558,33 @@ drwxr-xr-x root/root 0 2010-12-03 10:17 ./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 2010-12-03 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
-───────────────────────────────────────
+-rwxr-xr-x root/root 5778 2011-03-03 08:11 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/bin/
+-rwxr-xr-x root/root 93576 2011-03-03 08:11 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24864 2011-03-03 08:11 ./usr/bin/razip
+-rwxr-xr-x root/root 356560 2011-03-03 08:11 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19248 2011-03-03 08:11 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8248 2011-03-03 08:11 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8200 2011-03-03 08:11 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11712 2011-03-03 08:11 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8520 2011-03-03 08:11 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.13-1_kfreebsd-amd64.deb
+──────────────────────────────────────
new debian package, version 2.0.
- size 155700 bytes: control archive= 902 bytes.
- 684 bytes, 15 lines control
+ size 161392 bytes: control archive= 901 bytes.
+ 683 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: kfreebsd-amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 438
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 440
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -564,22 +595,22 @@ libbam-dev_0.1.12a-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./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 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 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/lib/
+-rw-r--r-- root/root 296260 2011-03-03 08:11 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./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 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -589,8 +620,8 @@ drwxr-xr-x root/root 0 2010-12-03 10:17 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-amd64-RqAos2
-(Reading database ... 15570 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1299139834-9072/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd
+(Reading database ... 14181 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -612,6 +643,8 @@ Removing libcroco3 ...
Purging configuration files for libcroco3 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
Removing libglib2.0-0 ...
@@ -619,7 +652,6 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-1017
-Build needed 00:02:21, 9698k disc space
+Finished at 20110303-0811
+Build needed 00:01:22, 10174k 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.log b/kfreebsd-i386.log
index 847b191..e1505ea 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,117 +1,74 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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>
+From buildd at field.debian.org Wed Mar 02 05:29:08 2011
+Return-path: <buildd at field.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at field.debian.org>)
+ id 1PuecW-00031Q-Ad
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:29:08 +0000
+Received: from field.debian.org ([194.177.211.210])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at field.debian.org>)
+ id 1PuecS-0001IA-Ri; Wed, 02 Mar 2011 05:29:05 +0000
+Received: from buildd by field.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at field.debian.org>)
+ id 1PuecR-0007eK-81; Wed, 02 Mar 2011 05:29:03 +0000
+Date: Wed, 02 Mar 2011 05:29:03 +0000
+Message-Id: <E1PuecR-0007eK-81 at field.debian.org>
+From: buildd on field <buildd at field.debian.org>
+To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
+Subject: Log for successful build of samtools_0.1.13-1 on kfreebsd-i386
+ (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (kfreebsd-i386) 03 Dec 2010 09:23 ║
+║ samtools 0.1.13-1 (kfreebsd-i386) 02 Mar 2011 05:25 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: kfreebsd-i386
-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://incoming.debian.org/debian/ sid/non-free Translation-en
-Get:5 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-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]
+Chroot Build Dir: /var/lib/schroot/mount/sid-ki-sbuild-1299043555-27708/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx
+Start Time: 20110302-0525
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-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://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
+Get:1 http://incoming.debian.org Release.gpg [835 B]
+Ign http://ftp.gr.debian.org sid/contrib Translation-en
+Ign http://ftp.gr.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:24 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Get: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)
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Ign http://incoming.debian.org sid/non-free TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [19.2 kB]
+Get:4 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org sid/non-free Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 395 kB in 4s (81.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -130,20 +87,20 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (197 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -151,7 +108,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -162,7 +119,8 @@ 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
+ libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
devscripts doc-base dh-make gettext-doc groff less www-browser
libmail-box-perl
@@ -172,16 +130,18 @@ Recommended packages:
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
+ libpipeline1 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 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.
+0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/11.5 MB of archives.
+After this operation, 32.1 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 11720 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.20.1-10_kfreebsd-i386.deb) ...
+(Reading database ... 11789 files and directories currently installed.)
+Unpacking groff-base (from .../groff-base_1.21-4_kfreebsd-i386.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-i386.deb) ...
Selecting previously deselected package file.
@@ -189,13 +149,13 @@ Unpacking file (from .../file_5.04-5_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_kfreebsd-i386.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_kfreebsd-i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libunistring0.
@@ -207,37 +167,39 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_kfreebsd-i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_kfreebsd-i386.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
-Setting up groff-base (1.20.1-10) ...
-Setting up man-db (2.5.7-6) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
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-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
+Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.5.2-4 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libc0.1-dev_2.11.2-13 kfreebsd-kernel-headers_0.53
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1+b1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 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_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.5-1 libgomp1_4.5.2-4 libgpg-error0_1.10-0.3 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_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 libtasn1-3_2.9-2 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011b-2 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -248,13 +210,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -269,164 +231,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-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'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
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_0.1.12a-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
-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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
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_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -448,11 +406,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -469,6 +427,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -476,7 +435,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -491,69 +450,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_kfreebsd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_kfreebsd-i386.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.13-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0926
+Build finished at 20110302-0528
-samtools_0.1.12a-1_kfreebsd-i386.changes:
+samtools_0.1.13-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- 164adcd56b82ee0bcf67f213f6b768cda0e37c87 546952 samtools_0.1.12a-1_kfreebsd-i386.deb
- 35fd1a19555c60c04ccd6bc7415a68191b52fa0b 157656 libbam-dev_0.1.12a-1_kfreebsd-i386.deb
+ 428bb527c130930bd9664c727b920e5cec99b126 572384 samtools_0.1.13-1_kfreebsd-i386.deb
+ 377f032405891e1669dcc434ecf3abe268dce306 163380 libbam-dev_0.1.13-1_kfreebsd-i386.deb
Checksums-Sha256:
- ed916c3a9eb8d0ede51fd39e93624daea4f232f64648a850c6272d9a16b62a0a 546952 samtools_0.1.12a-1_kfreebsd-i386.deb
- 2bc39a07a79e3115a616b805723e76262773dca29dea0bf8565792dd2fe68456 157656 libbam-dev_0.1.12a-1_kfreebsd-i386.deb
+ 8c5b32ef9c0d5f660ec13b2aab72bbbf402abdd02f9f40afd2949b3d5ec449f6 572384 samtools_0.1.13-1_kfreebsd-i386.deb
+ e975100d3d3596af04c618ef3ea436e5a2c6df72596849d491d01a0dcfff65a3 163380 libbam-dev_0.1.13-1_kfreebsd-i386.deb
Files:
- 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
+ f227797b77fab3d79c5d11a62274ce31 572384 science optional samtools_0.1.13-1_kfreebsd-i386.deb
+ 6fc6111d6f389e43b3df8d4c33e14937 163380 libdevel optional libbam-dev_0.1.13-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_kfreebsd-i386.deb
-────────────────────────────────────
+samtools_0.1.13-1_kfreebsd-i386.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 546952 bytes: control archive= 1795 bytes.
- 802 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 572384 bytes: control archive= 1791 bytes.
+ 801 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: kfreebsd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 924
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 966
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -565,33 +528,33 @@ samtools_0.1.12a-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 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./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 2010-12-03 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 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./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 2010-12-03 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 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rw-r--r-- root/root 126609 2011-03-02 05:28 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-02 05:28 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-02 05:28 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 05:28 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1229 2011-03-02 05:28 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./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
@@ -603,34 +566,33 @@ drwxr-xr-x root/root 0 2010-12-03 09:26 ./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 2010-12-03 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
-──────────────────────────────────────
+-rwxr-xr-x root/root 5778 2011-03-02 05:28 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/bin/
+-rwxr-xr-x root/root 88260 2011-03-02 05:28 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23612 2011-03-02 05:28 ./usr/bin/razip
+-rwxr-xr-x root/root 353772 2011-03-02 05:28 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17296 2011-03-02 05:28 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6160 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6144 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9876 2011-03-02 05:28 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6632 2011-03-02 05:28 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.13-1_kfreebsd-i386.deb
+─────────────────────────────────────
new debian package, version 2.0.
- size 157656 bytes: control archive= 902 bytes.
- 683 bytes, 15 lines control
+ size 163380 bytes: control archive= 900 bytes.
+ 682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: kfreebsd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 374
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 376
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -641,22 +603,22 @@ libbam-dev_0.1.12a-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 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 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
+-rw-r--r-- root/root 245054 2011-03-02 05:28 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./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 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -666,8 +628,8 @@ drwxr-xr-x root/root 0 2010-12-03 09:26 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /srv/home/buildd/chroots/sid/build/buildd-samtools_0.1.12a-1-kfreebsd-i386-Yc8cGx
-(Reading database ... 13982 files and directories currently installed.)
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1299043555-27708/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx
+(Reading database ... 14126 files and directories currently installed.)
Removing zlib1g-dev ...
Removing cdbs ...
Removing debhelper ...
@@ -689,6 +651,8 @@ Removing libcroco3 ...
Purging configuration files for libcroco3 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
Removing libglib2.0-0 ...
@@ -696,7 +660,6 @@ Purging configuration files for libglib2.0-0 ...
Removing libpcre3 ...
Purging configuration files for libpcre3 ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0926
-Build needed 00:02:38, 8120k disc space
+Finished at 20110302-0528
+Build needed 00:02:29, 8490k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/mips.log b/mips.log
index 946901a..1983aa9 100644
--- a/mips.log
+++ b/mips.log
@@ -1,41 +1,67 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/mips received Sat Dec 4 07:50:05 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=mips">mips</a> >> Sat Dec 4 07:50:05 2010<pre>
+From buildd at ball.debian.org Wed Mar 02 08:30:56 2011
+Return-path: <buildd at ball.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at ball.debian.org>)
+ id 1PuhSS-0002Mt-4Z
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 08:30:56 +0000
+Received: from ball.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d09])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=ball.debian.org, EMAIL=hostmaster at ball.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at ball.debian.org>)
+ id 1PuhSO-0001pk-MY
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 08:30:52 +0000
+Received: from buildd by ball.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at ball.debian.org>)
+ id 1PuhSN-000452-Px; Wed, 02 Mar 2011 08:30:51 +0000
+From: buildd on ball <buildd at ball.debian.org>
+To: logs at buildd.debian.org,buildd-porters at ball.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on mips (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PuhSN-000452-Px at ball.debian.org>
+Date: Wed, 02 Mar 2011 08:30:51 +0000
+Delivered-To: logs at buildd.debian.org
+
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on ball.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (mips) 04 Dec 2010 07:42 ║
+║ samtools 0.1.13-1 (mips) 02 Mar 2011 08:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: mips
-Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-f75c9a7d-199d-45ad-ba56-a30973cbabf2/build/buildd-samtools_0.1.12a-1-mips-QwKHhy
-Start Time: 20101204-0742
+Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-e12386c2-4fa2-477c-a347-07dc3227f8c5/build/buildd-samtools_0.1.13-1-mips-vcsZoS
+Start Time: 20110302-0823
Get:1 http://debian.netcologne.de unstable Release.gpg [835B]
Ign http://debian.netcologne.de/debian/ unstable/contrib Translation-en
Ign http://debian.netcologne.de/debian/ unstable/main Translation-en
-Get:2 http://debian.netcologne.de unstable Release [104kB]
+Get:2 http://debian.netcologne.de unstable Release [146kB]
Get:3 http://incoming.debian.org unstable Release.gpg [835B]
Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
Ign http://incoming.debian.org/debian/ unstable/main Translation-en
Get:4 http://incoming.debian.org Release.gpg [835B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://debian.netcologne.de unstable/main Sources [4073kB]
+Get:5 http://incoming.debian.org unstable Release [146kB]
+Get:6 http://debian.netcologne.de unstable/main Sources [4155kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4071kB]
-Get:9 http://debian.netcologne.de unstable/contrib Sources [38.7kB]
-Get:10 http://debian.netcologne.de unstable/non-free Sources [83.8kB]
-Get:11 http://debian.netcologne.de unstable/main mips Packages [6730kB]
+Get:8 http://debian.netcologne.de unstable/contrib Sources [38.5kB]
+Get:9 http://debian.netcologne.de unstable/non-free Sources [82.8kB]
+Get:10 http://incoming.debian.org unstable/main Sources [4156kB]
+Get:11 http://debian.netcologne.de unstable/main mips Packages [6811kB]
Get:12 http://debian.netcologne.de unstable/contrib mips Packages [51.5kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [83.8kB]
-Get:15 http://incoming.debian.org unstable/main mips Packages [6731kB]
-Get:16 http://incoming.debian.org unstable/contrib mips Packages [51.5kB]
-Get:17 http://incoming.debian.org Sources [10.0kB]
-Get:18 http://incoming.debian.org Packages [110kB]
-Fetched 22.3MB in 46s (478kB/s)
+Get:13 http://incoming.debian.org unstable/contrib Sources [38.5kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [82.8kB]
+Get:15 http://incoming.debian.org unstable/main mips Packages [6812kB]
+Get:16 http://incoming.debian.org unstable/contrib mips Packages [51.4kB]
+Get:17 http://incoming.debian.org Sources [19.5kB]
+Get:18 http://incoming.debian.org Packages [373kB]
+Fetched 23.0MB in 46s (495kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -53,20 +79,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 364kB of source archives.
-Get:1 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (dsc) [1946B]
-Get:2 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (tar) [356kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (diff) [6337B]
-Fetched 364kB in 0s (1758kB/s)
+Need to get 374kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523B]
+Fetched 374kB in 0s (402kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -74,7 +100,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -84,8 +110,8 @@ Reading package lists...
Building dependency tree...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1
+ 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
@@ -95,50 +121,53 @@ Recommended packages:
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
+ libpipeline1 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 54 not upgraded.
-Need to get 12.3MB of archives.
-After this operation, 37.2MB of additional disk space will be used.
-Get:1 http://debian.netcologne.de/debian/ unstable/main ncurses-bin mips 5.7+20100313-4 [317kB]
-Get:2 http://debian.netcologne.de/debian/ unstable/main libncurses5 mips 5.7+20100313-4 [349kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mips 8.0.17 [208kB]
-Get:4 http://debian.netcologne.de/debian/ unstable/main groff-base mips 1.20.1-10 [1190kB]
-Get:5 http://debian.netcologne.de/debian/ unstable/main man-db mips 2.5.7-6 [1251kB]
-Get:6 http://debian.netcologne.de/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
-Get:7 http://debian.netcologne.de/debian/ unstable/main file mips 5.04-5 [49.7kB]
-Get:8 http://debian.netcologne.de/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
-Get:9 http://debian.netcologne.de/debian/ unstable/main libpcre3 mips 8.02-1.1 [232kB]
-Get:10 http://debian.netcologne.de/debian/ unstable/main libxml2 mips 2.7.8.dfsg-1 [836kB]
-Get:11 http://debian.netcologne.de/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
-Get:12 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 mips 2.24.2-1 [1043kB]
-Get:13 http://debian.netcologne.de/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
-Get:14 http://debian.netcologne.de/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
-Get:15 http://debian.netcologne.de/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
-Get:16 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:17 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
-Get:18 http://debian.netcologne.de/debian/ unstable/main debhelper all 8.0.0 [454kB]
-Get:19 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.89 [1240kB]
-Get:20 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev mips 5.7+20100313-4 [1643kB]
-Get:21 http://debian.netcologne.de/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
+2 upgraded, 20 newly installed, 0 to remove and 64 not upgraded.
+Need to get 12.7MB of archives.
+After this operation, 38.0MB of additional disk space will be used.
+Get:1 http://debian.netcologne.de/debian/ unstable/main ncurses-bin mips 5.7+20100313-5 [317kB]
+Get:2 http://debian.netcologne.de/debian/ unstable/main libncurses5 mips 5.7+20100313-5 [349kB]
+Get:3 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mips 8.2.2 [210kB]
+Get:4 http://debian.netcologne.de/debian/ unstable/main groff-base mips 1.21-4 [1203kB]
+Get:5 http://debian.netcologne.de/debian/ unstable/main libpipeline1 mips 1.1.0-1 [35.1kB]
+Get:6 http://debian.netcologne.de/debian/ unstable/main man-db mips 2.5.9-4 [997kB]
+Get:7 http://debian.netcologne.de/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
+Get:8 http://debian.netcologne.de/debian/ unstable/main file mips 5.04-5 [49.7kB]
+Get:9 http://debian.netcologne.de/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
+Get:10 http://debian.netcologne.de/debian/ unstable/main libpcre3 mips 8.12-3 [262kB]
+Get:11 http://debian.netcologne.de/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2 [837kB]
+Get:12 http://debian.netcologne.de/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
+Get:13 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 mips 2.28.1-1+b1 [1501kB]
+Get:14 http://debian.netcologne.de/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
+Get:15 http://debian.netcologne.de/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
+Get:16 http://debian.netcologne.de/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
+Get:17 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
+Get:18 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
+Get:19 http://debian.netcologne.de/debian/ unstable/main debhelper all 8.1.2 [553kB]
+Get:20 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.92 [1268kB]
+Get:21 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev mips 5.7+20100313-5 [1643kB]
+Get:22 http://debian.netcologne.de/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.3MB in 2s (4710kB/s)
+Fetched 12.7MB in 3s (3230kB/s)
(Reading database ... 10123 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-4_mips.deb) ...
+Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-5_mips.deb) ...
Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-4) ...
+Setting up ncurses-bin (5.7+20100313-5) ...
(Reading database ... 10123 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-3 (using .../libncurses5_5.7+20100313-4_mips.deb) ...
+Preparing to replace libncurses5 5.7+20100313-3 (using .../libncurses5_5.7+20100313-5_mips.deb) ...
Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
+Setting up libncurses5 (5.7+20100313-5) ...
Selecting previously deselected package bsdmainutils.
(Reading database ... 10123 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_mips.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mips.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_mips.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_mips.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_mips.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_mips.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_mips.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_mips.deb) ...
Selecting previously deselected package file.
@@ -146,13 +175,13 @@ Unpacking file (from .../archives/file_5.04-5_mips.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_mips.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_mips.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_mips.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_mips.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
Selecting previously deselected package libunistring0.
@@ -164,40 +193,42 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_mips.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_mips.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
-Setting up bsdmainutils (8.0.17) ...
+Setting up bsdmainutils (8.2.2) ...
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) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32.2-dsa-mips-swarm mips (mips64)
Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.4-15 g++-4.4_4.4.4-15 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-15 libstdc++6_4.4.4-15
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-15 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-15 gcc_4:4.4.4-2 gcc-4.4_4.4.4-15 gcc-4.4-base_4.4.4-15 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-15 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-15 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-15 libstdc++6-4.4-dev_4.4.4-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+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_8.2.2 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-15 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-15 gcc_4:4.4.4-2 gcc-4.4_4.4.4-15 gcc-4.4-base_4.4.4-15 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-15 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-15 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-15 libstdc++6-4.4-dev_4.4.4-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-1 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -208,13 +239,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -229,164 +260,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
dpkg-buildpackage: host architecture mips
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/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_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/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_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
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_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-mips-QwKHhy/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/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-mips-QwKHhy/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/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_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-1-mips-QwKHhy/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_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
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_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -408,11 +435,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -429,6 +456,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -436,7 +464,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -451,69 +479,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_mips.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_mips.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_mips.deb'.
+ dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../samtools_0.1.13-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101204-0749
+Build finished at 20110302-0830
-samtools_0.1.12a-1_mips.changes:
+samtools_0.1.13-1_mips.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: Debian Build Daemon <buildd_mips-ball at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: Debian Build Daemon <buildd_mips-ball at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- 819ca6a39882f43c04698bc7aaaa06631ed10e0b 574528 samtools_0.1.12a-1_mips.deb
- 67683aff48ff5b969fe894fb62879a6a270e2a1d 172934 libbam-dev_0.1.12a-1_mips.deb
+ 19429914145f75322b5ea497e562d8671cfffd9a 612004 samtools_0.1.13-1_mips.deb
+ c4f35b4344a0bacedecefe1346d9e10ca97f7b9a 178466 libbam-dev_0.1.13-1_mips.deb
Checksums-Sha256:
- 0558c06b947bd330216871469e3921cc71144f216eba89a26325ff9e62e8efdb 574528 samtools_0.1.12a-1_mips.deb
- 2fff24c10a6abce81214d6eb3c3973b8a01659ce2a4cbba55edb565f84f96049 172934 libbam-dev_0.1.12a-1_mips.deb
+ 9886d680a19a3f8facf21a093f195b501fdb3160397a08af91e5696c3c8f3fb8 612004 samtools_0.1.13-1_mips.deb
+ 1c8b1ec23abcf52f0e22274329742c43c6fd065437637cdd8e5a50a8303d77c7 178466 libbam-dev_0.1.13-1_mips.deb
Files:
- ad86bf07ab4b83c8e247ce25aa58ce23 574528 science optional samtools_0.1.12a-1_mips.deb
- 713b2da1c6a306a68ca29dd52f92c7b8 172934 libdevel optional libbam-dev_0.1.12a-1_mips.deb
+ 7c9aaf4dba7f011e454956aca53f312e 612004 science optional samtools_0.1.13-1_mips.deb
+ 726c409ca321426acfbf088e4afada7b 178466 libdevel optional libbam-dev_0.1.13-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_mips.deb
-───────────────────────────
+samtools_0.1.13-1_mips.deb
+──────────────────────────
new debian package, version 2.0.
- size 574528 bytes: control archive= 1790 bytes.
- 792 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 612004 bytes: control archive= 1787 bytes.
+ 791 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: mips
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1116
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1180
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -525,31 +557,32 @@ samtools_0.1.12a-1_mips.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/samtools/
--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 1966 2010-12-04 07:49 ./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 2011-03-02 08:30 ./
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-02 08:30 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./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 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 2010-12-04 07:49 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./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 2010-12-04 07:48 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-02 08:29 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/man/man1/
--rw-r--r-- root/root 7546 2010-12-04 07:49 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-12-04 07:49 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/samtools/
+-rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/man/man1/
+-rw-r--r-- root/root 1229 2011-03-02 08:30 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 08:30 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-02 08:30 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/samtools/
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
@@ -557,40 +590,38 @@ drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2010-12-04 07:49 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-03-02 08:30 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/bin/
--rwxr-xr-x root/root 30712 2010-12-04 07:49 ./usr/bin/razip
--rwxr-xr-x root/root 410760 2010-12-04 07:49 ./usr/bin/samtools
--rwxr-xr-x root/root 108704 2010-12-04 07:49 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/samtools/
--rwxr-xr-x root/root 19928 2010-12-04 07:49 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9768 2010-12-04 07:49 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2010-12-04 07:49 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13268 2010-12-04 07:49 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2010-12-04 07:49 ./usr/lib/samtools/maq2sam-short
-lrwxrwxrwx root/root 0 2010-12-04 07:49 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.12a-1_mips.deb
-─────────────────────────────
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/bin/
+-rwxr-xr-x root/root 30712 2011-03-02 08:30 ./usr/bin/razip
+-rwxr-xr-x root/root 460960 2011-03-02 08:30 ./usr/bin/samtools
+-rwxr-xr-x root/root 121204 2011-03-02 08:30 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19928 2011-03-02 08:30 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9768 2011-03-02 08:30 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2011-03-02 08:30 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13268 2011-03-02 08:30 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-03-02 08:30 ./usr/lib/samtools/maq2sam-short
+
+
+libbam-dev_0.1.13-1_mips.deb
+────────────────────────────
new debian package, version 2.0.
- size 172934 bytes: control archive= 900 bytes.
- 674 bytes, 15 lines control
+ size 178466 bytes: control archive= 898 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: mips
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 448
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 452
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -601,23 +632,23 @@ libbam-dev_0.1.12a-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/libbam-dev/
--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
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 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 2010-12-04 07:49 ./usr/include/
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./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 2010-12-04 07:49 ./usr/lib/
--rw-r--r-- root/root 303238 2010-12-04 07:49 ./usr/lib/libbam.a
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/lib/
+-rw-r--r-- root/root 304468 2011-03-02 08:30 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -626,10 +657,581 @@ drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mips-sbuild-f75c9a7d-199d-45ad-ba56-a30973cbabf2/build/buildd-samtools_0.1.12a-1-mips-QwKHhy
+Purging /var/lib/schroot/mount/sid-mips-sbuild-e12386c2-4fa2-477c-a347-07dc3227f8c5/build/buildd-samtools_0.1.13-1-mips-vcsZoS
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101204-0749
-Build needed 00:06:58, 9308k disc space
+Finished at 20110302-0830
+
+From buildd at mayer.debian.org Wed Mar 02 05:46:32 2011
+Return-path: <buildd at mayer.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
+ id 1PuetL-0005cK-M5
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:32 +0000
+Received: from mayer.debian.org ([140.211.166.78])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
+ id 1PuetI-0001iN-RD
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:29 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>)
+ id 1PuetF-0002Hy-Rz; Wed, 02 Mar 2011 05:46:25 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
+To: buildd-porters at mayer.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on mipsel (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PuetF-0002Hy-Rz at mayer.debian.org>
+Date: Wed, 02 Mar 2011 05:46:25 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on mayer.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 0.1.13-1 (mipsel) 02 Mar 2011 05:41 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.13-1
+Architecture: mipsel
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
+Start Time: 20110302-0541
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Get:1 http://incoming.debian.org Release.gpg [835 B]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [19.5 kB]
+Get:4 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 395 kB in 2s (177 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+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 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 0s (410 kB/s)
+Download complete and in download only mode
+
+Check arch
+──────────
+
+** Using build dependencies supplied by package:
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Checking for already installed source dependencies...
+debhelper: already installed (8.1.2 >= 8 is satisfied)
+cdbs: missing
+libncurses5-dev: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+Checking for source dependency conflicts...
+Installing positive dependencies: cdbs libncurses5-dev
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ libpopt0 pkg-config udev zlib1g-dev
+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
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 2 newly installed, 0 to remove and 10 not upgraded.
+Need to get 0 B/2907 kB of archives.
+After this operation, 8671 kB of additional disk space will be used.
+Selecting previously deselected package cdbs.
+(Reading database ... 11889 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Selecting previously deselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_mipsel.deb) ...
+Processing triggers for man-db ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
+Removing negative dependencies:
+Checking correctness of source dependencies...
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.4.5-12
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 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_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.63-1 libdpkg-perl_1.15.8.10 libgcc1_1:4.4.5-12 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-12 liblocale-gettext-perl_1.05-6 liblzma1_4.999.9beta+20091116-1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpopt0_1.16-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-12 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_166-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 pkg-config_0.25-1.1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 udev_166-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+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 Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+
+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 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 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
+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 -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+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:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+touch debian/stamp-makefile-build
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
+../samtools faidx ex1.fa
+../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
+[sam_header_read2] 2 sequences loaded.
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools index ex1.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+[samopen] SAM header is present: 2 sequences.
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+[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...
+[bam_rmdup_core] processing reference seq2...
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
+../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
+../samtools glfview ex1.glf | gzip > ex1.glfview.gz
+../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
+
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
+touch debian/stamp-makefile-check
+ /usr/bin/fakeroot debian/rules binary-arch
+test -x debian/rules
+dh_testroot
+dh_prep
+dh_installdirs -A
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
+Adding cdbs dependencies to debian/samtools.substvars
+dh_installdirs -psamtools
+Adding cdbs dependencies to debian/libbam-dev.substvars
+dh_installdirs -plibbam-dev
+dh_installdocs -psamtools ./NEWS ./AUTHORS
+dh_installexamples -psamtools
+dh_installman -psamtools
+dh_installinfo -psamtools
+dh_installmenu -psamtools
+dh_installcron -psamtools
+dh_installinit -psamtools
+dh_installdebconf -psamtools
+dh_installemacsen -psamtools
+dh_installcatalogs -psamtools
+dh_installpam -psamtools
+dh_installlogrotate -psamtools
+dh_installlogcheck -psamtools
+dh_installchangelogs -psamtools ./ChangeLog
+dh_installudev -psamtools
+dh_lintian -psamtools
+dh_bugfiles -psamtools
+dh_install -psamtools
+dh_link -psamtools
+dh_installmime -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
+dh_installexamples -plibbam-dev
+dh_installman -plibbam-dev
+dh_installinfo -plibbam-dev
+dh_installmenu -plibbam-dev
+dh_installcron -plibbam-dev
+dh_installinit -plibbam-dev
+dh_installdebconf -plibbam-dev
+dh_installemacsen -plibbam-dev
+dh_installcatalogs -plibbam-dev
+dh_installpam -plibbam-dev
+dh_installlogrotate -plibbam-dev
+dh_installlogcheck -plibbam-dev
+dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installudev -plibbam-dev
+dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
+dh_install -plibbam-dev
+dh_link -plibbam-dev
+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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+dh_strip -plibbam-dev
+dh_compress -plibbam-dev
+dh_fixperms -plibbam-dev
+dh_makeshlibs -plibbam-dev
+dh_installdeb -psamtools
+dh_perl -psamtools
+dh_shlibdeps -psamtools
+dh_installdeb -plibbam-dev
+dh_perl -plibbam-dev
+dh_shlibdeps -plibbam-dev
+dh_gencontrol -psamtools
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+dh_md5sums -psamtools
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_mipsel.deb'.
+dh_gencontrol -plibbam-dev
+dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
+dh_md5sums -plibbam-dev
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.13-1_mipsel.changes
+dpkg-genchanges: arch-specific upload - not including arch-independent packages
+dpkg-genchanges: binary-only upload - not including any source code
+ dpkg-source --after-build samtools-0.1.13
+dpkg-buildpackage: binary only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20110302-0546
+
+samtools_0.1.13-1_mipsel.changes:
+Format: 1.8
+Date: Wed, 02 Mar 2011 13:54:34 +0900
+Source: samtools
+Binary: samtools libbam-dev
+Architecture: mipsel
+Version: 0.1.13-1
+Distribution: sid
+Urgency: low
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description:
+ libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
+ samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
+Changes:
+ samtools (0.1.13-1) unstable; urgency=low
+ .
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
+Checksums-Sha1:
+ 5901d8131d2a5ab7f91d6d5ec34a7590df033c49 614580 samtools_0.1.13-1_mipsel.deb
+ c48e2280335b48710f8035593d4058fc84068915 179140 libbam-dev_0.1.13-1_mipsel.deb
+Checksums-Sha256:
+ adc39bd662310f6d06d8dd0ced4d22c62748fc57d19d2307694b0e52acda5058 614580 samtools_0.1.13-1_mipsel.deb
+ 8f66c76baf784bfdff627e21eb06bab4ef5d317e01862615634e1fba3deaa0ce 179140 libbam-dev_0.1.13-1_mipsel.deb
+Files:
+ 9ee93dbf8080e7350d75f35f0e602351 614580 science optional samtools_0.1.13-1_mipsel.deb
+ 2e123c18f5c6ce1e892587f822e885fe 179140 libdevel optional libbam-dev_0.1.13-1_mipsel.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_0.1.13-1_mipsel.deb
+────────────────────────────
+
+ new debian package, version 2.0.
+ size 614580 bytes: control archive= 1788 bytes.
+ 793 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
+ Package: samtools
+ Version: 0.1.13-1
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1180
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Suggests: python
+ Section: science
+ Priority: optional
+ Homepage: http://samtools.sourceforge.net
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./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 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 2011-03-02 05:45 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-02 05:45 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-02 05:45 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 05:45 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1229 2011-03-02 05:45 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2011-03-02 05:45 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/bin/
+-rwxr-xr-x root/root 121204 2011-03-02 05:45 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-03-02 05:45 ./usr/bin/razip
+-rwxr-xr-x root/root 460960 2011-03-02 05:45 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19960 2011-03-02 05:45 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13268 2011-03-02 05:45 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9768 2011-03-02 05:45 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.13-1_mipsel.deb
+──────────────────────────────
+
+ new debian package, version 2.0.
+ size 179140 bytes: control archive= 896 bytes.
+ 675 bytes, 15 lines control
+ 618 bytes, 10 lines md5sums
+ Package: libbam-dev
+ Source: samtools
+ Version: 0.1.13-1
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 452
+ Section: libdevel
+ Priority: optional
+ Homepage: http://samtools.sourceforge.net
+ Description: manipulates nucleotide sequence alignments in BAM or SAM format
+ The BAM library provides I/O and various operations on manipulating nucleotide
+ sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
+ Alignment/Map) format. It now supports importing from or exporting to SAM,
+ sorting, merging, generating pileup, and quickly retrieval of reads overlapped
+ with a specified region.
+
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:46 ./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 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 05:46 ./usr/lib/
+-rw-r--r-- root/root 304188 2011-03-02 05:46 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
+-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Finished │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Built successfully
+────────────────────────────────────────────────────────────────────────────────
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
+(Reading database ... 12996 files and directories currently installed.)
+Removing libncurses5-dev ...
+Removing cdbs ...
+Processing triggers for man-db ...
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110302-0546
+Build needed 00:04:43, 9760k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/mipsel.log b/mipsel.log
index 9a312ca..ffd9775 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,53 +1,66 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+From buildd at mayer.debian.org Wed Mar 02 05:46:32 2011
+Return-path: <buildd at mayer.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
+ id 1PuetL-0005cK-M5
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:32 +0000
+Received: from mayer.debian.org ([140.211.166.78])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
+ id 1PuetI-0001iN-RD
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:29 +0000
+Received: from buildd by mayer.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at mayer.debian.org>)
+ id 1PuetF-0002Hy-Rz; Wed, 02 Mar 2011 05:46:25 +0000
+From: buildd on mayer <buildd at mayer.debian.org>
+To: buildd-porters at mayer.debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on mipsel (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PuetF-0002Hy-Rz at mayer.debian.org>
+Date: Wed, 02 Mar 2011 05:46:25 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (mipsel) 03 Dec 2010 09:24 ║
+║ samtools 0.1.13-1 (mipsel) 02 Mar 2011 05:41 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: mipsel
-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
-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)
+Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
+Start Time: 20110302-0541
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Get:1 http://incoming.debian.org Release.gpg [835 B]
+Hit http://debian.oregonstate.edu sid InRelease
+Hit http://debian.oregonstate.edu sid/main Sources
+Hit http://debian.oregonstate.edu sid/contrib Sources
+Hit http://debian.oregonstate.edu sid/main mipsel Packages
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
+Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Ign http://debian.oregonstate.edu sid/contrib Translation-en
+Hit http://incoming.debian.org sid/main Sources
+Hit http://incoming.debian.org sid/contrib Sources
+Hit http://incoming.debian.org sid/main mipsel Packages
+Hit http://incoming.debian.org sid/contrib mipsel Packages
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [19.5 kB]
+Get:4 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 395 kB in 2s (177 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -66,140 +79,61 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 0s (410 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), 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 (8.1.2 >= 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:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libunistring0 libxml2 man-db
- po-debconf
+The following packages were automatically installed and are no longer required:
+ libpopt0 pkg-config udev zlib1g-dev
+Use 'apt-get autoremove' to remove them.
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 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]
+ cdbs libncurses5-dev
debconf: delaying package configuration, since apt-utils is not installed
-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) ...
+0 upgraded, 2 newly installed, 0 to remove and 10 not upgraded.
+Need to get 0 B/2907 kB of archives.
+After this operation, 8671 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+(Reading database ... 11889 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_mipsel.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Setting up bsdmainutils (8.0.17) ...
-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) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_mipsel.deb) ...
+Processing triggers for man-db ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Removing negative dependencies:
Checking correctness of source dependencies...
-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
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.4.5-12
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 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_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.63-1 libdpkg-perl_1.15.8.10 libgcc1_1:4.4.5-12 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-12 liblocale-gettext-perl_1.05-6 liblzma1_4.999.9beta+20091116-1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpopt0_1.16-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-12 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_166-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 pkg-config_0.25-1.1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 udev_166-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -210,13 +144,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -231,164 +165,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
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_0.1.12a-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
-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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
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_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -410,11 +340,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -431,6 +361,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -438,7 +369,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-mipsel-COPfIN/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -453,69 +384,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_mipsel.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.13-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0930
+Build finished at 20110302-0546
-samtools_0.1.12a-1_mipsel.changes:
+samtools_0.1.13-1_mipsel.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (monteverdi) <buildd_mipsel-monteverdi at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- f29fd836ed041a1f2088c9d36c8a46ad110d0d4f 578292 samtools_0.1.12a-1_mipsel.deb
- cd679f7269405f59939c75dfd77d99bf3d62e704 173498 libbam-dev_0.1.12a-1_mipsel.deb
+ 5901d8131d2a5ab7f91d6d5ec34a7590df033c49 614580 samtools_0.1.13-1_mipsel.deb
+ c48e2280335b48710f8035593d4058fc84068915 179140 libbam-dev_0.1.13-1_mipsel.deb
Checksums-Sha256:
- a875f6bd7b1d39080160048bf0d7711496303b61d528f637c6798bb7725611bf 578292 samtools_0.1.12a-1_mipsel.deb
- 072b4c5f5635ddb791b86e2be2fa5e5bcb16c4fc03581aa0b181720d5671e5cf 173498 libbam-dev_0.1.12a-1_mipsel.deb
+ adc39bd662310f6d06d8dd0ced4d22c62748fc57d19d2307694b0e52acda5058 614580 samtools_0.1.13-1_mipsel.deb
+ 8f66c76baf784bfdff627e21eb06bab4ef5d317e01862615634e1fba3deaa0ce 179140 libbam-dev_0.1.13-1_mipsel.deb
Files:
- 7de915c17da9a27be7c7aaeeae84489e 578292 science optional samtools_0.1.12a-1_mipsel.deb
- 912706773b87a79e5be0c4df0c4003ec 173498 libdevel optional libbam-dev_0.1.12a-1_mipsel.deb
+ 9ee93dbf8080e7350d75f35f0e602351 614580 science optional samtools_0.1.13-1_mipsel.deb
+ 2e123c18f5c6ce1e892587f822e885fe 179140 libdevel optional libbam-dev_0.1.13-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_mipsel.deb
-─────────────────────────────
+samtools_0.1.13-1_mipsel.deb
+────────────────────────────
new debian package, version 2.0.
- size 578292 bytes: control archive= 1796 bytes.
- 794 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 614580 bytes: control archive= 1788 bytes.
+ 793 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1116
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1180
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -527,72 +462,71 @@ samtools_0.1.12a-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 2010-12-03 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 5778 2010-12-03 09:30 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./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 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 2011-03-02 05:45 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-02 05:45 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-02 05:45 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8164 2011-03-02 05:45 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1229 2011-03-02 05:45 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/samtools/
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 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 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 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 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 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 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
-───────────────────────────────
+-rwxr-xr-x root/root 5778 2011-03-02 05:45 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/bin/
+-rwxr-xr-x root/root 121204 2011-03-02 05:45 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-03-02 05:45 ./usr/bin/razip
+-rwxr-xr-x root/root 460960 2011-03-02 05:45 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19960 2011-03-02 05:45 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13268 2011-03-02 05:45 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9768 2011-03-02 05:45 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.13-1_mipsel.deb
+──────────────────────────────
new debian package, version 2.0.
- size 173498 bytes: control archive= 899 bytes.
- 676 bytes, 15 lines control
+ size 179140 bytes: control archive= 896 bytes.
+ 675 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 444
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 452
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -603,23 +537,23 @@ libbam-dev_0.1.12a-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:46 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-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 16522 2010-11-17 04:16 ./usr/include/khash.h
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-02 05:46 ./usr/lib/
+-rw-r--r-- root/root 304188 2011-03-02 05:46 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./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 09:30 ./usr/lib/
--rw-r--r-- root/root 302950 2010-12-03 09:30 ./usr/lib/libbam.a
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -628,10 +562,12 @@ drwxr-xr-x root/root 0 2010-12-03 09:30 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-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
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
+(Reading database ... 12996 files and directories currently installed.)
+Removing libncurses5-dev ...
+Removing cdbs ...
+Processing triggers for man-db ...
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0930
-Build needed 00:06:40, 9296k disc space
+Finished at 20110302-0546
+Build needed 00:04:43, 9760k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/powerpc.log b/powerpc.log
index 0eaa76a..bf0fc85 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,36 +1,68 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+From buildd at poulenc.debian.org Wed Mar 02 05:25:39 2011
+Return-path: <buildd at poulenc.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at poulenc.debian.org>)
+ id 1PueZ8-0002Xg-Tr
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:25:39 +0000
+Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
+ helo=poulenc.debian.org)
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=poulenc.debian.org, EMAIL=hostmaster at poulenc.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at poulenc.debian.org>)
+ id 1PueZ5-0006Af-Dp; Wed, 02 Mar 2011 05:25:35 +0000
+Received: from buildd by poulenc.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at poulenc.debian.org>)
+ id 1PueZ4-0007wN-Uv; Wed, 02 Mar 2011 05:25:34 +0000
+From: buildd on poulenc <buildd at poulenc.debian.org>
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on powerpc (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PueZ4-0007wN-Uv at poulenc.debian.org>
+Date: Wed, 02 Mar 2011 05:25:34 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on poulenc.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (powerpc) 03 Dec 2010 09:19 ║
+║ samtools 0.1.13-1 (powerpc) 02 Mar 2011 05:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: powerpc
-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)
+Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-dc383189-78ef-48ae-9752-00541d455a5a/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY
+Start Time: 20110302-0522
+Get:1 http://ftp.uk.debian.org unstable InRelease [147 kB]
+Get:2 http://incoming.debian.org unstable InRelease [147 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [4155 kB]
+Ign http://incoming.debian.org InRelease
+Get:4 http://incoming.debian.org Release.gpg [835 B]
+Get:5 http://incoming.debian.org unstable/main Sources [4156 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [38.5 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [82.8 kB]
+Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [6906 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [51.2 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2232 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [6908 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [51.2 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [19.2 kB]
+Get:18 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 23.2 MB in 24s (955 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -49,18 +81,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-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)
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (310 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -68,7 +102,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -79,61 +113,52 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 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]
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 20 newly installed, 0 to remove and 5 not upgraded.
+Need to get 12.1 MB of archives.
+After this operation, 37.0 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.2 [209 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-4 [1168 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.1.0-1 [36.9 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.5.9-4 [1001 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5 [241 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5 [49.9 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-3 [258 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-2 [849 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.1-1+b1 [1594 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-3 [422 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.7+20100313-5 [1633 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.5MB in 1s (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) ...
+Fetched 12.1 MB in 4s (2988 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 9867 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_powerpc.deb) ...
+(Reading database ... 10202 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_powerpc.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_powerpc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_powerpc.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_powerpc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_powerpc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_powerpc.deb) ...
Selecting previously deselected package file.
@@ -141,13 +166,13 @@ Unpacking file (from .../file_5.04-5_powerpc.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_powerpc.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_powerpc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_powerpc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_powerpc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_powerpc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
Selecting previously deselected package libunistring0.
@@ -159,40 +184,42 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_powerpc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
+Setting up bsdmainutils (8.2.2) ...
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) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: libc6-dev_2.11.1-3 dpkg-dev_1.15.7.2 linux-libc-dev_2.6.32-15 gcc-4.4_4.4.4-4 g++-4.4_4.4.4-4 binutils_2.20.1-10 libstdc++6-4.4-dev_4.4.4-4 libstdc++6_4.4.4-4
-Package versions: apt_0.7.25.3 base-files_5.7 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-10 bsdmainutils_8.0.17 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
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.5.2-4
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-12 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -203,13 +230,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -218,169 +245,166 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
+dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.12a-1
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
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_0.1.12a-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
-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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
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_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/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
+[sam_header_read2] 2 sequences loaded.
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -402,11 +426,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -423,6 +447,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -430,7 +455,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -445,68 +470,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_powerpc.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_powerpc.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.13-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0922
+Build finished at 20110302-0525
-samtools_0.1.12a-1_powerpc.changes:
+samtools_0.1.13-1_powerpc.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- b8ae505c9c5fa2cdf3754cfbd3432b433940abc1 560870 samtools_0.1.12a-1_powerpc.deb
- fcf051bc2b68143cb4e792f96e74ce4d0f031dd9 162450 libbam-dev_0.1.12a-1_powerpc.deb
+ ec854a8fd08c95b6eef5d027e164e7a424b577ba 596096 samtools_0.1.13-1_powerpc.deb
+ 64e036078167da575fc8f378d5d106cd51485f17 167942 libbam-dev_0.1.13-1_powerpc.deb
Checksums-Sha256:
- 26ccc7ee17384c17b348c7e4327b37c51f32a93035a26fd2eb03b84aad8c7314 560870 samtools_0.1.12a-1_powerpc.deb
- 4671231fe66c2f4a647c8b80c269088e9383d1e50bcc07ca6b912fc483d8f4f5 162450 libbam-dev_0.1.12a-1_powerpc.deb
+ 014deaaeb06a67a27db7d52215604397974d60b5def385b009236c22b605e492 596096 samtools_0.1.13-1_powerpc.deb
+ dd35627bfbf8f9808e7bc43f19e10f8dc046ed24b0d5c8ad76514390f75f9aa5 167942 libbam-dev_0.1.13-1_powerpc.deb
Files:
- 028831887d836951c07eaf52b9b105b2 560870 science optional samtools_0.1.12a-1_powerpc.deb
- ef55d1299cc1be05e27fdf90636ffbe9 162450 libdevel optional libbam-dev_0.1.12a-1_powerpc.deb
+ c0c3acfb780b67494a4284202432cfca 596096 science optional samtools_0.1.13-1_powerpc.deb
+ 439cf6a8cebeea3997943ab032ab689d 167942 libdevel optional libbam-dev_0.1.13-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_powerpc.deb
-──────────────────────────────
+samtools_0.1.13-1_powerpc.deb
+─────────────────────────────
new debian package, version 2.0.
- size 560870 bytes: control archive= 1794 bytes.
- 795 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 596096 bytes: control archive= 1789 bytes.
+ 794 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: powerpc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1020
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1072
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -518,72 +548,71 @@ samtools_0.1.12a-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 2010-12-03 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
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/man/man1/
+-rw-r--r-- root/root 8164 2011-03-02 05:25 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1229 2011-03-02 05:25 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-03-02 05:25 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/samtools/
+-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 5778 2011-03-02 05:25 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 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 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 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
-────────────────────────────────
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1966 2011-03-02 05:25 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./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 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 126609 2011-03-02 05:25 ./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
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7352 2011-03-02 05:25 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11116 2011-03-02 05:25 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8008 2011-03-02 05:25 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7352 2011-03-02 05:25 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 19404 2011-03-02 05:25 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/bin/
+-rwxr-xr-x root/root 384456 2011-03-02 05:25 ./usr/bin/samtools
+-rwxr-xr-x root/root 26828 2011-03-02 05:25 ./usr/bin/razip
+-rwxr-xr-x root/root 101192 2011-03-02 05:25 ./usr/bin/bcftools
+
+
+libbam-dev_0.1.13-1_powerpc.deb
+───────────────────────────────
new debian package, version 2.0.
- size 162450 bytes: control archive= 898 bytes.
- 677 bytes, 15 lines control
+ size 167942 bytes: control archive= 901 bytes.
+ 676 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: powerpc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 404
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 412
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -594,23 +623,23 @@ libbam-dev_0.1.12a-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/include/
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
-rw-r--r-- root/root 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
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/lib/
+-rw-r--r-- root/root 262160 2011-03-02 05:25 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -619,10 +648,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:22 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-f6484d4d-a7cc-4101-9c13-f7b72cf926c7/build/buildd-samtools_0.1.12a-1-powerpc-g9O8gf
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-dc383189-78ef-48ae-9752-00541d455a5a/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0922
-Build needed 00:02:57, 8908k disc space
+Finished at 20110302-0525
+Build needed 00:02:56, 9344k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/s390.log b/s390.log
index 4b20c51..8477c09 100644
--- a/s390.log
+++ b/s390.log
@@ -1,41 +1,68 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+From buildd at zandonai.debian.org Wed Mar 02 05:22:51 2011
+Return-path: <buildd at zandonai.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
+ id 1PueWQ-0001hb-T1
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:22:51 +0000
+Received: from zandonai.debian.org ([80.245.147.46])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=zandonai.debian.org,
+ EMAIL=hostmaster at zandonai.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
+ id 1PueWO-00019m-QS; Wed, 02 Mar 2011 05:22:48 +0000
+Received: from buildd by zandonai.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at zandonai.debian.org>)
+ id 1PueWN-0002FS-EF; Wed, 02 Mar 2011 05:22:47 +0000
+From: buildd on zandonai <buildd at zandonai.debian.org>
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.13-1 on s390 (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PueWN-0002FS-EF at zandonai.debian.org>
+Date: Wed, 02 Mar 2011 05:22:47 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (s390) 03 Dec 2010 09:22 ║
+║ samtools 0.1.13-1 (s390) 02 Mar 2011 05:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: s390
-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
-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)
+Chroot Build Dir: /var/lib/schroot/mount/sid-s390-sbuild-043a721a-9346-4640-90d0-b639032ed477/build/buildd-samtools_0.1.13-1-s390-Msk1pi
+Start Time: 20110302-0521
+Get:1 http://ftp.de.debian.org unstable InRelease [147 kB]
+Get:2 http://incoming.debian.org unstable InRelease [147 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [4156 kB]
+Ign http://incoming.debian.org InRelease
+Get:4 http://incoming.debian.org Release.gpg [835 B]
+Get:5 http://incoming.debian.org unstable/main Sources [4156 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [38.5 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [82.8 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [6828 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [49.9 kB]
+Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2232 B]
+Ign http://ftp.de.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [6828 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [49.9 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [19.2 kB]
+Get:18 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 23.0 MB in 26s (855 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,20 +81,20 @@ 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:
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-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)
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (287 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -75,7 +102,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -86,8 +113,8 @@ 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 libpcre3 libpipeline1 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
@@ -97,38 +124,41 @@ Recommended packages:
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 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]
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
+Need to get 12.2 MB of archives.
+After this operation, 36.5 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.2 [208 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-4 [1158 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.1.0-1 [38.0 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.5.9-4 [1015 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.1-1+b1 [1629 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.7+20100313-5 [1634 kB]
+Get:20 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)
+Fetched 12.2 MB in 3s (3519 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10060 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_s390.deb) ...
+(Reading database ... 10125 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_s390.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_s390.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_s390.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_s390.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_s390.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_s390.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_s390.deb) ...
Selecting previously deselected package file.
@@ -136,13 +166,13 @@ Unpacking file (from .../archives/file_5.04-5_s390.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_s390.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_s390.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_s390.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_s390.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_s390.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_s390.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
Selecting previously deselected package libunistring0.
@@ -154,40 +184,42 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_s390.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
+Setting up bsdmainutils (8.2.2) ...
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) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
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-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_8.0.17 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
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-2 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libstdc++6_4.5.2-4
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,13 +230,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -219,158 +251,160 @@ 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 0.1.12a-1
- dpkg-source --before-build samtools-0.1.12a
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
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_0.1.12a-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
-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
-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
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_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
+../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
[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
+(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...
[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'
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 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
-<mpileup> Set max per-sample depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
+<mpileup> Set max per-sample depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: 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
@@ -392,11 +426,11 @@ dh_installlogcheck -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
+dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -413,6 +447,7 @@ dh_installlogcheck -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
@@ -420,7 +455,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-s390-zpFbOY/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -435,69 +470,73 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_s390.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_s390.deb'.
-dpkg-genchanges -B
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.13-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.12a
+ dpkg-source --after-build samtools-0.1.13
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0924
+Build finished at 20110302-0522
-samtools_0.1.12a-1_s390.changes:
+samtools_0.1.13-1_s390.changes:
Format: 1.8
-Date: Fri, 03 Dec 2010 13:32:21 +0900
+Date: Wed, 02 Mar 2011 13:54:34 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.12a-1
-Distribution: unstable
+Version: 0.1.13-1
+Distribution: sid
Urgency: low
-Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd...>
-Changed-By: Charles Plessy <plessy at debian...>
+Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 606004 616025
Changes:
- samtools (0.1.12a-1) unstable; urgency=low
+ samtools (0.1.13-1) 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).
+ * New upstream release:
+ - backward incompatible with VCF/BCF generated by samtools older
+ than r921 inclusive (0.1.12a is r862);
+ - buildable with with ld --as-needed (Closes: #606004);
+ - the helper tool bcf-fix.pl was removed.
+ * Install the manual page of bcftools (debian/rules,
+ debian/samtools.manpages). Closes: #616025.
Checksums-Sha1:
- 63f318ed9acaa790b238ac22e0ac2d313b09754e 568074 samtools_0.1.12a-1_s390.deb
- 15ccbda0b9f67f67811be5cbcaa6bcbb71bd4611 163484 libbam-dev_0.1.12a-1_s390.deb
+ 46e902da61e714377fe849430ef98c069f158890 592758 samtools_0.1.13-1_s390.deb
+ 6c100382b345290d249c94504122c864636f3e80 169590 libbam-dev_0.1.13-1_s390.deb
Checksums-Sha256:
- 1f8c1fb50700acfdcddf4ae12261b0484d0226ae70a98b3432c0c65d5f36815c 568074 samtools_0.1.12a-1_s390.deb
- fe61bcca670f8c22ad0e3531def8caa07711a97d088a47eb4239af12f204aa46 163484 libbam-dev_0.1.12a-1_s390.deb
+ 2396f980b7c9a6bbe8104b1cffc8918221794b14a2fa4f16fd4416df1eda84d9 592758 samtools_0.1.13-1_s390.deb
+ 13987d40937564a92cb650132863f65cf9d21295b3c748efc6d3069ba1a1ffff 169590 libbam-dev_0.1.13-1_s390.deb
Files:
- 1e960b993581b710a92f6a85a2ea1cf4 568074 science optional samtools_0.1.12a-1_s390.deb
- ccf263db0121acdae17ea2f30ff59265 163484 libdevel optional libbam-dev_0.1.12a-1_s390.deb
+ 7dce94745af66705410759840c4bb6cc 592758 science optional samtools_0.1.13-1_s390.deb
+ ce14ed862c383d2110c6655b4dd2c9e7 169590 libdevel optional libbam-dev_0.1.13-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.12a-1_s390.deb
-───────────────────────────
+samtools_0.1.13-1_s390.deb
+──────────────────────────
new debian package, version 2.0.
- size 568074 bytes: control archive= 1785 bytes.
- 792 bytes, 16 lines control
- 2517 bytes, 38 lines md5sums
+ size 592758 bytes: control archive= 1783 bytes.
+ 791 bytes, 16 lines control
+ 2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: s390
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1032
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1092
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -509,72 +548,71 @@ samtools_0.1.12a-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 2010-12-03 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/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/bin/
+-rwxr-xr-x root/root 104532 2011-03-02 05:22 ./usr/bin/bcftools
+-rwxr-xr-x root/root 399072 2011-03-02 05:22 ./usr/bin/samtools
+-rwxr-xr-x root/root 27380 2011-03-02 05:22 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11324 2011-03-02 05:22 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7188 2011-03-02 05:22 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7188 2011-03-02 05:22 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7932 2011-03-02 05:22 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18564 2011-03-02 05:22 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/man/man1/
+-rw-r--r-- root/root 8164 2011-03-02 05:22 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-02 05:22 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 1229 2011-03-02 05:22 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./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 15437 2011-03-01 19:50 ./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 5778 2011-03-02 05:22 ./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
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2011-03-02 04:30 ./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 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2011-03-02 05:22 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./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 126609 2010-12-03 09:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-02 05:22 ./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 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
-─────────────────────────────
+libbam-dev_0.1.13-1_s390.deb
+────────────────────────────
new debian package, version 2.0.
- size 163484 bytes: control archive= 894 bytes.
- 674 bytes, 15 lines control
+ size 169590 bytes: control archive= 891 bytes.
+ 673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.12a-1
+ Version: 0.1.13-1
Architecture: s390
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 400
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 408
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -585,23 +623,23 @@ libbam-dev_0.1.12a-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-01 19:50 ./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 17815 2011-03-01 19:50 ./usr/include/khash.h
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/lib/
+-rw-r--r-- root/root 258332 2011-03-02 05:22 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 7887 2011-03-01 19:50 ./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
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -610,10 +648,9 @@ drwxr-xr-x root/root 0 2010-12-03 09:24 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390-sbuild-235df352-e04a-4a75-a746-dc247b89ec10/build/buildd-samtools_0.1.12a-1-s390-zpFbOY
+Purging /var/lib/schroot/mount/sid-s390-sbuild-043a721a-9346-4640-90d0-b639032ed477/build/buildd-samtools_0.1.13-1-s390-Msk1pi
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0924
-Build needed 00:01:38, 9204k disc space
+Finished at 20110302-0522
+Build needed 00:01:38, 9672k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
diff --git a/sparc.log b/sparc.log
index e265982..1139afa 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,36 +1,68 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<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
+From buildd at lebrun.debian.org Wed Mar 02 05:26:12 2011
+Return-path: <buildd at lebrun.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at lebrun.debian.org>)
+ id 1PueZg-0002ja-3h
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:26:12 +0000
+Received: from lebrun.debian.org ([193.198.184.10])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at lebrun.debian.org>)
+ id 1PueZd-0001F3-Kw
+ for logs at buildd.debian.org; Wed, 02 Mar 2011 05:26:10 +0000
+Received: from buildd by lebrun.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1PueZb-0005Ep-LC; Wed, 02 Mar 2011 05:26:07 +0000
+From: buildd on lebrun <buildd at lebrun.debian.org>
+To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
+Subject: Log for attempted build of samtools_0.1.13-1 on sparc (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1PueZb-0005Ep-LC at lebrun.debian.org>
+Date: Wed, 02 Mar 2011 05:26:07 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.12a-1 (sparc) 03 Dec 2010 09:22 ║
+║ samtools 0.1.13-1 (sparc) 02 Mar 2011 05:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.12a-1
+Version: 0.1.13-1
Architecture: sparc
-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 [6789kB]
-Get:7 http://incoming.debian.org Release [1604B]
-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 [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 [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)
+Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-30bb6ad2-5de7-4de9-950a-9c1381aa6c71/build/buildd-samtools_0.1.13-1-sparc-0vH7vX
+Start Time: 20110302-0522
+Get:1 http://debian.carnet.hr unstable InRelease [147 kB]
+Get:2 http://incoming.debian.org unstable InRelease [147 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [4156 kB]
+Get:4 http://debian.carnet.hr unstable/contrib Sources [38.5 kB]
+Ign http://incoming.debian.org InRelease
+Get:5 http://incoming.debian.org Release.gpg [835 B]
+Get:6 http://incoming.debian.org unstable/main Sources [4156 kB]
+Get:7 http://debian.carnet.hr unstable/non-free Sources [82.8 kB]
+Get:8 http://debian.carnet.hr unstable/main sparc Packages [6855 kB]
+Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [51.2 kB]
+Ign http://debian.carnet.hr unstable/contrib TranslationIndex
+Get:10 http://debian.carnet.hr unstable/main TranslationIndex [2232 B]
+Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
+Get:13 http://incoming.debian.org unstable/main sparc Packages [6855 kB]
+Get:14 http://incoming.debian.org unstable/contrib sparc Packages [51.2 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Ign http://debian.carnet.hr unstable/contrib Translation-en
+Get:17 http://incoming.debian.org Sources [19.2 kB]
+Get:18 http://incoming.debian.org Packages [373 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 23.1 MB in 24s (929 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -49,18 +81,20 @@ Download source files with APT
Reading package lists...
Building dependency tree...
Reading state information...
-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)
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 374 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
+Fetched 374 kB in 1s (255 kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -68,7 +102,7 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed source dependencies...
debhelper: missing
-Using default version 8.0.0
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -79,61 +113,52 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libunistring0 libxml2
- man-db ncurses-bin po-debconf
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
groff less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 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 8.0.17 [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]
-Get:7 http://mirrors.ece.ubc.ca unstable/main file 5.04-5 [49.5kB]
-Get:8 http://mirrors.ece.ubc.ca unstable/main gettext-base 0.18.1.1-3 [140kB]
-Get:9 http://mirrors.ece.ubc.ca unstable/main libpcre3 8.02-1.1 [237kB]
-Get:10 http://mirrors.ece.ubc.ca unstable/main libxml2 2.7.8.dfsg-1 [840kB]
-Get:11 http://mirrors.ece.ubc.ca unstable/main html2text 1.3.2a-15 [100kB]
-Get:12 http://mirrors.ece.ubc.ca unstable/main libglib2.0-0 2.24.2-1 [1074kB]
-Get:13 http://mirrors.ece.ubc.ca unstable/main libcroco3 0.6.2-1 [119kB]
-Get:14 http://mirrors.ece.ubc.ca unstable/main libunistring0 0.9.3-3 [424kB]
-Get:15 http://mirrors.ece.ubc.ca unstable/main gettext 0.18.1.1-3 [2006kB]
-Get:16 http://mirrors.ece.ubc.ca unstable/main intltool-debian 0.35.0+20060710.1 [30.8kB]
-Get:17 http://mirrors.ece.ubc.ca unstable/main po-debconf 1.0.16+nmu1 [223kB]
-Get:18 http://mirrors.ece.ubc.ca unstable/main debhelper 8.0.0 [454kB]
-Get:19 http://mirrors.ece.ubc.ca unstable/main cdbs 0.4.89 [1240kB]
-Get:20 http://mirrors.ece.ubc.ca unstable/main libncurses5-dev 5.7+20100313-4 [1610kB]
-Get:21 http://mirrors.ece.ubc.ca unstable/main zlib1g-dev 1:1.2.3.4.dfsg-3 [189kB]
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 20 newly installed, 0 to remove and 5 not upgraded.
+Need to get 12.0 MB of archives.
+After this operation, 36.3 MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.2 [205 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-4 [1155 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.1.0-1 [35.0 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.5.9-4 [1007 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5 [239 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main file sparc 5.04-5 [49.5 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-2 [840 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.1-1+b1 [1546 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-3 [424 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.7+20100313-5 [1611 kB]
+Get:20 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 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 ...
-Setting up ncurses-bin (5.7+20100313-4) ...
-(Reading database ... 10166 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-2 (using .../libncurses5_5.7+20100313-4_sparc.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-4) ...
+Fetched 12.0 MB in 7s (1516 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10166 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_sparc.deb) ...
+(Reading database ... 10479 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_sparc.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.20.1-10_sparc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-4_sparc.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_sparc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.5.7-6_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.5.9-4_sparc.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5_sparc.deb) ...
Selecting previously deselected package file.
@@ -141,13 +166,13 @@ Unpacking file (from .../archives/file_5.04-5_sparc.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.02-1.1_sparc.deb) ...
+Unpacking libpcre3 (from .../libpcre3_8.12-3_sparc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.24.2-1_sparc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_sparc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
Selecting previously deselected package libunistring0.
@@ -159,40 +184,42 @@ 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) ...
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.89_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_sparc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_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 (8.0.17) ...
+Setting up bsdmainutils (8.2.2) ...
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) ...
+Setting up groff-base (1.21-4) ...
+Setting up libpipeline1 (1.1.0-1) ...
+Setting up man-db (2.5.9-4) ...
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 libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.24.2-1) ...
+Setting up libglib2.0-0 (2.28.1-1+b1) ...
+No schema files found: doing nothing.
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 debhelper (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.7+20100313-5) ...
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 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_8.0.17 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
+Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-2 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.5.2-4
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b2 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libc6-dev-sparc64_2.11.2-11 libc6-sparc64_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -203,13 +230,13 @@ 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 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_0.1.12a-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
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.13
+dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
Check disc space
────────────────
@@ -218,148 +245,144 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
+dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.12a-1
+dpkg-buildpackage: source version 0.1.13-1
+ dpkg-source --before-build samtools-0.1.13
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_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
-make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/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_0.1.12a-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]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/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_0.1.12a-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'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
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_0.1.12a-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
-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. 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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-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
-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
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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_0.1.12a-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_0.1.12a-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
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-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 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-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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_0.1.12a-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
-gcc -g -O2 -g -Wall -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -Wall -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-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_0.1.12a-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_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+gcc -g -O2 -g -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 cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -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_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
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_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/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_0.1.12a-1-sparc-UAUacU/samtools-0.1.12a/examples'
+make[1]: *** Deleting file `ex1.bam'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101203-0928
+Build finished at 20110302-0526
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-5f94f0dc-8583-4e98-bc68-e5cff85fb5ae/build/buildd-samtools_0.1.12a-1-sparc-UAUacU
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-30bb6ad2-5de7-4de9-950a-9c1381aa6c71/build/buildd-samtools_0.1.13-1-sparc-0vH7vX
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101203-0928
-Build needed 00:06:40, 5208k disc space
+Finished at 20110302-0526
+Build needed 00:03:28, 5524k disc space
-</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
--
Processing of sequence alignments in SAM and BAM formats.
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