[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.14-1-5-gd46ae92
Charles Plessy
plessy at debian.org
Mon Jul 11 12:21:59 UTC 2011
The following commit has been merged in the meta branch:
commit 14dd842e8223ef33866bbb3b1e17731d23fc3bc7
Author: Charles Plessy <plessy at debian.org>
Date: Mon Jul 11 21:13:41 2011 +0900
Collected build logs for version 0.1.16-1.
diff --git a/armel.log b/armel.log
index ece10e6..b339e87 100644
--- a/armel.log
+++ b/armel.log
@@ -1,68 +1,75 @@
-From buildd at antheil.debian.org Tue Apr 12 12:14:05 2011
-Return-path: <buildd at antheil.debian.org>
+From buildd at ancina.debian.org Thu May 19 04:48:22 2011
+Return-path: <buildd at ancina.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at antheil.debian.org>)
- id 1Q9cTt-0005mO-0T
- for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:05 +0000
-Received: from antheil.islands.arm.com ([217.140.96.60]
- helo=antheil.debian.org)
+ (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
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+ for logs at buildd.debian.org; Thu, 19 May 2011 04:48:22 +0000
+Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
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- CN=antheil.debian.org, EMAIL=hostmaster at antheil.debian.org (verified)
+ CN=ancina.debian.org, EMAIL=hostmaster at ancina.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
- id 1Q9cTm-0007Ul-0Z
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-From: buildd on antheil <buildd at antheil.debian.org>
-To: buildd-porters at antheil.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.15-1 on armel (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q9cTk-0004Tf-HY at antheil.debian.org>
-Date: Tue, 12 Apr 2011 12:13:56 +0000
+ (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
+ id 1QMv9p-0003WD-85
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:48:21 +0000
+Received: from buildd by ancina.debian.org with local (Exim 4.69)
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+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
+Date: Thu, 19 May 2011 04:48:14 +0000
+From: Build Daemon <buildd at ancina.debian.org>
+To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.16-1 on armel (dist=sid)
+Key-Id: A1EAA0BB
+Message-Id: <E1QMv9j-0005ww-02 at ancina.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on antheil.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (armel) 12 Apr 2011 12:05 ║
+║ samtools 0.1.16-1 (armel) 19 May 2011 04:42 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: armel
-Get:1 http://ftp.uk.debian.org unstable InRelease [151 kB]
-Get:2 http://incoming.debian.org unstable InRelease [151 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5265 kB]
+Get:1 http://ftp.de.debian.org sid InRelease [146 kB]
+Get:2 http://incoming.debian.org sid InRelease [146 kB]
+Get:3 http://ftp.de.debian.org sid/main Sources/DiffIndex [2038 B]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [48.2 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [97.4 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armel Packages [6998 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
-Get:11 http://incoming.debian.org unstable/main armel Packages [6998 kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [52.2 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2264 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib armel Packages [52.2 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [49.7 kB]
-Get:18 http://incoming.debian.org Packages [772 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
+Get:4 http://ftp.de.debian.org sid/main armel Packages/DiffIndex [2038 B]
+Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
+Ign http://ftp.de.debian.org sid/contrib TranslationIndex
+Get:5 http://ftp.de.debian.org sid/main TranslationIndex [2264 B]
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://ftp.de.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:8 http://ftp.de.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
+Get:9 http://ftp.de.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:10 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:11 http://incoming.debian.org sid/main armel Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Get:12 http://incoming.debian.org sid/main TranslationIndex [2264 B]
+Get:13 http://ftp.de.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
+Ign http://ftp.de.debian.org sid/contrib Translation-en
+Get:14 http://incoming.debian.org Release [1604 B]
+Get:15 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:16 http://incoming.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
+Get:17 http://incoming.debian.org Sources [26.8 kB]
+Get:18 http://incoming.debian.org Packages [270 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.1 MB in 57s (450 kB/s)
+Get:19 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:20 http://incoming.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
+Fetched 635 kB in 21s (29.5 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +90,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 1s (373 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (378 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +114,18 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+The following packages were automatically installed and are no longer required:
+ groff-base libpipeline1 libssl0.9.8 man-db
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+The following packages were automatically installed and are no longer required:
+ groff-base libpipeline1 libssl0.9.8 man-db
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -121,37 +134,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0)
+dpkg: already installed (1.16.0.2)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-19)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-13)
-gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-2)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -160,131 +173,85 @@ Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following package was automatically installed and is no longer required:
+ libssl0.9.8
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1
- libunistring0 libxml2 man-db ncurses-bin po-debconf
+ file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
+ libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
+ devscripts dh-make gettext-doc ncurses-doc libmail-box-perl
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 20 newly installed, 0 to remove and 14 not upgraded.
-Need to get 11.3 MB of archives.
-After this operation, 29.7 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main ncurses-bin armel 5.9-1 [328 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 armel 5.9-1 [357 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.2 [205 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-5 [1077 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-1 [33.8 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.1-1 [983 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5 [237 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-3 [129 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-3 [258 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-2 [816 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.4-1 [1531 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian armel 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf armel 1.0.16+nmu1 [223 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main debhelper armel 8.1.3 [554 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main cdbs armel 0.4.92 [1268 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-1 [474 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
+ cdbs debhelper file gettext gettext-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2 po-debconf
+ zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.3 MB in 3s (2987 kB/s)
-(Reading database ... 10102 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_armel.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 10102 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_armel.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10102 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_1.21-5_armel.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_armel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_armel.deb) ...
+0 upgraded, 15 newly installed, 0 to remove and 20 not upgraded.
+Need to get 0 B/6919 kB of archives.
+After this operation, 21.2 MB of additional disk space will be used.
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_armel.deb) ...
+(Reading database ... 11632 files and directories currently installed.)
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_armel.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_armel.deb) ...
+Unpacking file (from .../file_5.04-5+b1_armel.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-3_armel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_armel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_armel.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_armel.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_armel.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_armel.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_armel.deb) ...
+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_armel.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.3_armel.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_armel.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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 (8.2.2) ...
-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 (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
-Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Processing triggers for man-db ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+The following package was automatically installed and is no longer required:
+ libssl0.9.8
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-1
-Package versions: apt_0.8.13.1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0 dpkg-dev_1.16.0 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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_2.11.2-13 libc6-dev_2.11.2-13 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-8 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-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
+Kernel: Linux 2.6.31-rc9 armel (armv5tel)
+Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-3
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-5 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.7_4.7.25-18 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.4 libldap-2.4-2_2.4.25-1+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libsasl2-2_2.1.23.dfsg1-8 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libssl0.9.8_0.9.8o-7 libssl1.0.0_1.0.0d-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libudev0_168-2 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 nullmailer_1:1.05-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 wget_1.12-3.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -296,12 +263,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -317,8 +284,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -328,18 +295,18 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/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_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/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_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
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
@@ -351,134 +318,193 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/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_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15/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_0.1.15-1-armel-QMGIbq/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-armel-QMGIbq/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
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_0.1.15-1-armel-QMGIbq/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/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_0.1.15-1-armel-QMGIbq/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1213
+Build finished at 20110519-0448
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-677e6a3f-1a1c-435d-b1ac-727b84d7df3a/build/buildd-samtools_0.1.15-1-armel-QMGIbq
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-armel-sbuild-07f266a1-570b-4ca5-950b-e0c54b32a6a0/build/buildd-samtools_0.1.16-1-armel-pTW4iV
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following package was automatically installed and is no longer required:
+ libssl0.9.8
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages were automatically installed and are no longer required:
+ groff-base libpipeline1 libssl0.9.8 man-db
+Use 'apt-get autoremove' to remove them.
+The following packages will be REMOVED:
+ cdbs* debhelper* file* gettext* gettext-base* html2text* intltool-debian*
+ libcroco3* libglib2.0-0* libmagic1* libncurses5-dev* libunistring0* libxml2*
+ po-debconf* zlib1g-dev*
+0 upgraded, 0 newly installed, 15 to remove and 20 not upgraded.
+After this operation, 21.2 MB disk space will be freed.
+(Reading database ... 12552 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 6084
-Build-Time: 295
+Build-Space: 6220
+Build-Time: 252
Distribution: sid
Fail-Stage: build
-Install-Time: 92
-Job: samtools_0.1.15-1
+Install-Time: 32
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 479
-Source-Version: 0.1.15-1
-Space: 6084
+Package-Time: 330
+Source-Version: 0.1.16-1
+Space: 6220
Status: attempted
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1213
-Build needed 00:07:59, 6084k disc space
-
+Finished at 20110519-0448
+Build needed 00:05:30, 6220k disc space
diff --git a/hurd-i386.log b/hurd-i386.log
index 6e4ba54..a0339f9 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,64 +1,67 @@
-From buildd at rossini.debian.net Tue Apr 12 11:41:20 2011
-Return-path: <buildd at rossini.debian.net>
-Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
+From buildd at mozart.debian.net Thu May 19 05:32:44 2011
+Return-path: <buildd at mozart.debian.net>
+Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at rossini.debian.net>)
- id 1Q9byB-000802-AY
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:41:20 +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 1Q9by3-0005pr-9Z; Tue, 12 Apr 2011 13:41:11 +0200
-Received: from buildd by rossini.debian.net with local (Exim 4.72)
- (envelope-from <buildd at rossini.debian.net>)
- id 1Q9by1-0006BB-88; Tue, 12 Apr 2011 11:41:09 +0000
-Date: Tue, 12 Apr 2011 11:41:09 +0000
-Message-Id: <E1Q9by1-0006BB-88 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,
+ (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
+ id 1QMvql-0007PI-EM
+ for logs at buildd.debian.org; Thu, 19 May 2011 05:32:44 +0000
+Received: from mozart.debian.net ([10.1.0.1])
+ by callisto.debian.net with esmtp (Exim 4.69)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1QMvqj-0005St-SU; Thu, 19 May 2011 06:32:41 +0100
+Received: from buildd by mozart.debian.net with local (Exim 4.72)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1QMvr8-0002YF-Jh; Thu, 19 May 2011 05:33:06 +0000
+Date: Thu, 19 May 2011 05:33:06 +0000
+Message-Id: <E1QMvr8-0002YF-Jh at mozart.debian.net>
+From: Build Daemon <buildd at mozart.debian.net>
+To: samuel.thibault at labri.fr, mbanck at gmx.net, logs at buildd.debian-ports.org,
logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.15-1 on hurd-i386 (dist=sid)
+Subject: Log for successful build of samtools_0.1.16-1 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
+sbuild (Debian sbuild) 0.59.1 (31 Jan 2010) on mozart.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (hurd-i386) 12 Apr 2011 11:30 ║
+║ samtools 0.1.16-1 (hurd-i386) 19 mai 2011 05:26 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
+Version: 0.1.16-1
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe
-Start Time: 20110412-1130
+Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759
+Start Time: 20110519-0526
Ign file: ./ InRelease
Ign file: ./ Release.gpg
Ign file: ./ Release
Ign file: ./ Translation-en
+Hit http://ftp.uk.debian.org sid InRelease
+Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
Ign http://ftp.debian-ports.org unreleased InRelease
-Hit http://ftp.uk.debian.org unstable InRelease
-Hit http://ftp.uk.debian.org experimental InRelease
-Hit http://ftp.debian-ports.org unreleased Release.gpg
Ign http://incoming.debian.org InRelease
+Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
+Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
+Hit http://ftp.uk.debian.org sid/main TranslationIndex
+Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
+Hit http://ftp.debian-ports.org unreleased Release.gpg
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Ign http://ftp.uk.debian.org sid/contrib Translation-en
+Ign http://ftp.uk.debian.org sid/non-free Translation-en
+Get:2 http://incoming.debian.org Release [1604 B]
Hit http://ftp.debian-ports.org unreleased Release
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org Release
-Hit http://ftp.uk.debian.org unstable/main Sources/DiffIndex
-Hit http://ftp.uk.debian.org unstable/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org unstable/non-free Sources/DiffIndex
-Hit http://ftp.uk.debian.org unstable/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org unstable/main TranslationIndex
-Hit http://ftp.uk.debian.org experimental/main Sources/DiffIndex
-Hit http://ftp.uk.debian.org experimental/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org experimental/non-free Sources/DiffIndex
+Get:3 http://incoming.debian.org Sources [26.4 kB]
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
+Get:4 http://incoming.debian.org Packages [244 kB]
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
+Fetched 273 kB in 60s (4539 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -79,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 2s (166 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (234 kB/s)
Download complete and in download only mode
Check arch
@@ -97,113 +100,43 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.1.3
+debhelper: already installed (8.1.3 >= 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 packages were automatically installed and are no longer required:
- libboost-iostreams1.42.0 libssl1.0.0
+ libboost-iostreams1.46.1 libsysfs2
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 libncurses5 libunistring0 libxml2 ncurses-bin
- po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc ncurses-doc libmail-box-perl
+ devscripts ncurses-doc
Recommended packages:
- autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- cdbs debhelper file gettext gettext-base html2text intltool-debian libcroco3
- libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2
- po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 16 newly installed, 0 to remove and 40 not upgraded.
-Need to get 1151 kB/9042 kB of archives.
-After this operation, 23.5 MB of additional disk space will be used.
+ cdbs libncurses5-dev
+0 upgraded, 2 newly installed, 0 to remove and 72 not upgraded.
+Need to get 0 B/541 kB of archives.
+After this operation, 1712 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- ncurses-bin libncurses5 libmagic1 file gettext-base libxml2 html2text
- libglib2.0-0 libcroco3 libexpat1 libunistring0 gettext intltool-debian
- po-debconf debhelper cdbs libncurses5-dev zlib1g-dev
+ cdbs libncurses5-dev
Authentication warning overridden.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main ncurses-bin hurd-i386 5.9-1 [326 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 hurd-i386 5.9-1 [359 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev hurd-i386 5.9-1 [466 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 1151 kB in 1s (592 kB/s)
-(Reading database ... 11575 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_hurd-i386.deb) ...
-Unpacking replacement ncurses-bin ...
-Processing triggers for man-db ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 11575 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_hurd-i386.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
-Selecting previously deselected package libmagic1.
-(Reading database ... 11575 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_2.28.4-1_hurd-i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
-Selecting previously deselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_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_8.1.3_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+(Reading database ... 16660 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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 ...
-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 (2.28.4-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libexpat1 (2.0.1-7) ...
-Setting up libunistring0 (0.9.3-3) ...
-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 (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
-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_2.11.2-13 dpkg-dev_1.16.0.1 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_2.21.0.20110327-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
-Package versions: adduser_3.112+nmu2 apt_0.8.13.2 base-files_6.1 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.0.20110327-2 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_4:4.4.5-7 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.6-2 debhelper_8.1.3 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_1.16.0.1 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_4:4.4.5-4 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 gfortran_4:4.4.5-4 gfortran-4.4_4.4.5-10 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_1.21-5 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15+b1 hurd_20110319-2 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 libboost-iostreams1.42.0_1.42.0-4 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_7.21.4-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 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 libgfortran3_4.4.5-10 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-1 libgmpxx4ldbl_2:5.0.1+dfsg-7 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_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 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_1.2.0-1 libpng12-0_1.2.44-2 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsasl2-modules_2.1.23.dfsg1-8 libslang2_2.2.3-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libssl1.0.0_1.0.0d-1 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_5.9-1 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_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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
+Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.16.0.2 hurd-dev_20110303-1~1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.6_4.6.0-7 g++-4.6_4.6.0-7 binutils_2.21.51.20110419-2 libstdc++6-4.6-dev_4.6.0-7 libstdc++6_4.6.0-7
+Package versions: adduser_3.112+nmu1 apt_0.8.11.5+b1 apt-utils_0.8.11.5+b1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.51.20110419-2 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.4_4.4.5-10 cpp-4.5_4.5.3-1 cpp-4.6_4.6.0-7 cron_3.0pl1-115 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 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_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.2 fontconfig-config_2.8.0-2.2 g++_4:4.4.4-2 g++-4.4_4.4.5-10 g++-4.5_4.5.3-1 g++-4.6_4.6.0-7 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-5 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5_4.5.3-1 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran-4.4_4.4.5-10 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gobjc-4.4_4.4.5-10 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15+b1 hurd_20110319-2 hurd-dev_20110303-1~1 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libapt-pkg-dev_0.8.11.5+b1 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libboost-iostreams1.46.1_1.46.1-5 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 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcloog-ppl0_0.15.9-2 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.8_4.8.30-5 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libelfg0_0.8.13-1 libept-dev_1.0.3+b2 libept1_1.0.3+b2 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.2 libfreetype6_2.4.4-1 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgfortran3_4.6.0-7 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.0-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-1+b1 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.4-2 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libidn11_1.20-1 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.03-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libobjc2_4.4.5-10 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.2-3 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpng12-0_1.2.44-2 libpopt0_1.16-1 libppl-c2_0.10.2-9 libppl7_0.10.2-9 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libquadmath0_4.6.0-7 libreadline6_6.2-1 libsasl2-2_2.1.23.dfsg1-8 libsasl2-modules_2.1.23.dfsg1-8 libslang2_2.2.4-2 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libssl1.0.0_1.0.0d-2 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.5-10 libstdc++6-4.5-dev_4.5.3-1 libstdc++6-4.6-dev_4.6.0-7 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.11-1.1 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libuuid1_2.16.2-0 libwibble-dev_0.1.26-1 libwrap0_7.6.dbs-14+hurd.2 libxapian-dev_1.2.3-2 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2+b1 lsb-base_3.2-25 lynx-cur_2.8.8dev.8-1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.9-1 netbase_4.42 netcat-traditional_1.10-38 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 pkg-config_0.25-1.1 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-freefont_20100919-1 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -215,12 +148,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -232,28 +165,28 @@ 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-source --before-build samtools-0.1.15
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 0.1.15-1
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
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 -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/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_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/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_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
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
@@ -261,113 +194,132 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
/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 -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/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_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/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_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
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
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
[sam_header_read2] 2 sequences loaded.
-make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/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
+[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.
-[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
-[bam_rmdup_core] processing reference seq1...
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
+[bam_rmdup_core] processing reference seq1...
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
@@ -377,15 +329,15 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/sa
[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-file depth to 8000
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+<mpileup> Set max per-file 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'
+ /usr/bin/fakeroot debian/rules binary-arch
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -410,6 +362,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -417,7 +370,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -431,6 +384,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -442,7 +396,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -457,68 +411,68 @@ 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_0.1.15-1_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_hurd-i386.deb'.
- dpkg-genchanges -B -mhurd-i386 Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../samtools_0.1.15-1_hurd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1139
+Build finished at 20110519-0532
-samtools_0.1.15-1_hurd-i386.changes:
+samtools_0.1.16-1_hurd-i386.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
-Maintainer: hurd-i386 Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- 5a2b52e1a743e81dcdf4cd57a54b802246159028 588956 samtools_0.1.15-1_hurd-i386.deb
- 709fc2c806a278672e608331c77b37c89afb6225 168354 libbam-dev_0.1.15-1_hurd-i386.deb
+ d729804464743d8cdb2b2f29b09e24eec96af24d 612866 samtools_0.1.16-1_hurd-i386.deb
+ c6ce3ca18986ece8279e1e17d6ac950c871b89ab 179160 libbam-dev_0.1.16-1_hurd-i386.deb
Checksums-Sha256:
- d2eb106cfa417c51a00d174e2e800511a8b27efa0c8ff919c58ea5bea452f047 588956 samtools_0.1.15-1_hurd-i386.deb
- 9b8f8cf412601848d6cccebd1e48c5599fd05b7619ad96f52072427f452b455e 168354 libbam-dev_0.1.15-1_hurd-i386.deb
+ 8e1af7bdf6f972f75f95f7c97d1761f3121257e755c9d74a771d491864e61dd1 612866 samtools_0.1.16-1_hurd-i386.deb
+ 2b03cc8eb4670590d70c6df8868dd576e725db8ef7cc10905126e1886441f960 179160 libbam-dev_0.1.16-1_hurd-i386.deb
Files:
- a131d11416146fe7efd8037643dd3420 588956 science optional samtools_0.1.15-1_hurd-i386.deb
- cd846f388ba98037cd47cf6e3027df8a 168354 libdevel optional libbam-dev_0.1.15-1_hurd-i386.deb
+ 833087a78b1a0426fbd9275c72f435ed 612866 science optional samtools_0.1.16-1_hurd-i386.deb
+ b5db8957d16153bcb45cc9478cbff162 179160 libdevel optional libbam-dev_0.1.16-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_hurd-i386.deb
+samtools_0.1.16-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 588956 bytes: control archive= 1797 bytes.
+ size 612866 bytes: control archive= 1793 bytes.
793 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1068
+ Installed-Size: 1140
Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -531,32 +485,32 @@ samtools_0.1.15-1_hurd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 11:37 ./
-drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-04-12 11:37 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-05-19 05:30 ./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 2011-04-12 11:38 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-04-12 11:37 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-12 11:37 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-04-12 11:37 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-05-19 05:31 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-05-19 05:31 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 05:31 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2101 2011-05-19 05:31 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-05-19 05:32 ./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
@@ -569,33 +523,33 @@ drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 11:38 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/bin/
--rwxr-xr-x root/root 104676 2011-04-12 11:38 ./usr/bin/bcftools
--rwxr-xr-x root/root 23788 2011-04-12 11:38 ./usr/bin/razip
--rwxr-xr-x root/root 366060 2011-04-12 11:38 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-04-12 11:37 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/lib/samtools/
--rwxr-xr-x root/root 17488 2011-04-12 11:38 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6336 2011-04-12 11:38 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6320 2011-04-12 11:38 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10084 2011-04-12 11:38 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6920 2011-04-12 11:38 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.15-1_hurd-i386.deb
+-rwxr-xr-x root/root 5778 2011-05-19 05:32 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/bin/
+-rwxr-xr-x root/root 129252 2011-05-19 05:31 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25836 2011-05-19 05:31 ./usr/bin/razip
+-rwxr-xr-x root/root 412296 2011-05-19 05:31 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18208 2011-05-19 05:31 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6696 2011-05-19 05:31 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6696 2011-05-19 05:31 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10556 2011-05-19 05:31 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7384 2011-05-19 05:31 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.16-1_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 168354 bytes: control archive= 903 bytes.
+ size 179160 bytes: control archive= 934 bytes.
678 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 408
+ Installed-Size: 456
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -606,23 +560,25 @@ libbam-dev_0.1.15-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 05:32 ./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 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/lib/
--rw-r--r-- root/root 257596 2011-04-12 11:38 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/include/
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./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
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 05:32 ./usr/lib/
+-rw-r--r-- root/root 296362 2011-05-19 05:32 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -631,35 +587,12 @@ drwxr-xr-x root/root 0 2011-04-12 11:38 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.15-1-hurd-i386-HHZabe
-(Reading database ... 12510 files and directories currently installed.)
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759
+(Reading database ... 16760 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 20110412-1139
-Build needed 00:08:59, 9120k disc space
+Finished at 20110519-0532
+Build needed 00:06:51, 10420k disc space
diff --git a/i386.log b/i386.log
index e1ce44d..15f18a7 100644
--- a/i386.log
+++ b/i386.log
@@ -1,68 +1,68 @@
-From buildd at biber.debian.org Tue Apr 12 11:32:31 2011
+From buildd at biber.debian.org Thu May 19 04:45:52 2011
Return-path: <buildd at biber.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at biber.debian.org>)
- id 1Q9bpf-0006Vp-DV
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:32:31 +0000
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1QMv7Q-0007TP-DC
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:45:52 +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 1Q9bpb-0004tm-2l; Tue, 12 Apr 2011 11:32:27 +0000
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1QMv7P-0003OT-8l; Thu, 19 May 2011 04:45:51 +0000
Received: from buildd by biber.debian.org with local (Exim 4.72)
(envelope-from <buildd at biber.debian.org>)
- id 1Q9bpY-0002y6-7W; Tue, 12 Apr 2011 11:32:24 +0000
-Message-Id: <E1Q9bpY-0002y6-7W at biber.debian.org>
+ id 1QMv7N-0003bK-Cn; Thu, 19 May 2011 04:45:49 +0000
+Message-Id: <E1QMv7N-0003bK-Cn at biber.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Tue, 12 Apr 2011 11:32:24 +0000
+Date: Thu, 19 May 2011 04:45:49 +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_0.1.15-1 on i386 (dist=sid)
+Subject: Log for successful build of samtools_0.1.16-1 on i386 (dist=sid)
Key-Id: 44C3EAC7
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (i386) 12 Apr 2011 11:30 ║
+║ samtools 0.1.16-1 (i386) 19 May 2011 04:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: i386
-Get:1 http://ftp.gr.debian.org unstable InRelease [151 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5265 kB]
-Get:3 http://incoming.debian.org unstable InRelease [151 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [48.2 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [97.4 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7149 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [62.6 kB]
+Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [5221 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:4 http://ftp.gr.debian.org unstable/contrib Sources [49.8 kB]
+Get:5 http://ftp.gr.debian.org unstable/non-free Sources [91.7 kB]
+Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7295 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [64.8 kB]
Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2264 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 [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5265 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7149 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [62.6 kB]
+Get:10 http://incoming.debian.org unstable/main Sources [5221 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [7295 kB]
+Get:14 http://incoming.debian.org unstable/contrib i386 Packages [64.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [49.7 kB]
-Get:18 http://incoming.debian.org Packages [772 kB]
+Get:17 http://incoming.debian.org Sources [26.8 kB]
+Get:18 http://incoming.debian.org Packages [270 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.4 MB in 14s (1771 kB/s)
+Fetched 26.0 MB in 13s (1870 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 1s (240 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (260 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +107,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -121,37 +121,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.2)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.1)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-19)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-2)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -162,82 +162,70 @@ 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 libpipeline1
- 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 ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc 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
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 20 newly installed, 0 to remove and 6 not upgraded.
-Need to get 11.4 MB of archives.
-After this operation, 29.9 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main ncurses-bin i386 5.9-1 [326 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main libncurses5 i386 5.9-1 [361 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.2 [200 kB]
-Get:4 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-5 [1125 kB]
-Get:5 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-1 [35.6 kB]
-Get:6 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.1-1 [991 kB]
-Get:7 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
-Get:8 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
-Get:10 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2 [827 kB]
-Get:12 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:13 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.4-1 [1498 kB]
-Get:14 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.1.3 [554 kB]
-Get:20 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:21 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-1 [467 kB]
-Get:22 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+0 upgraded, 20 newly installed, 0 to remove and 12 not upgraded.
+Need to get 9515 kB of archives.
+After this operation, 28.5 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 1.21-5 [1125 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-1 [35.6 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.2-1 [991 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5+b1 [233 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5+b1 [49.4 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2+b1 [831 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.6-1 [1503 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-4 [431 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-1 [467 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 0s (12.2 MB/s)
-(Reading database ... 10201 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_i386.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 10201 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_i386.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
+Fetched 9515 kB in 1s (5827 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10201 files and directories currently installed.)
+(Reading database ... 10641 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_1.21-5_i386.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_i386.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_i386.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_i386.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_i386.deb) ...
+Unpacking file (from .../file_5.04-5+b1_i386.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_i386.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_i386.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package intltool-debian.
@@ -245,9 +233,9 @@ 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_8.1.3_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_i386.deb) ...
Selecting previously deselected package zlib1g-dev.
@@ -257,34 +245,34 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-2
-Package versions: apt_0.8.13.2 base-files_6.2 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-2 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 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_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-5
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-7 libreadline6_6.2-1 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -295,12 +283,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -315,25 +303,25 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/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_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/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_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
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
@@ -341,100 +329,119 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
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_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/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_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/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_0.1.15-1-i386-_MkcrA/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
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_0.1.15-1-i386-_MkcrA/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -463,7 +470,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -490,6 +497,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -497,7 +505,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -511,6 +519,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -522,7 +531,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-i386-_MkcrA/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -537,27 +546,27 @@ 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_0.1.15-1_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.15-1_i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1132
+Build finished at 20110519-0445
-samtools_0.1.15-1_i386.changes:
+samtools_0.1.16-1_i386.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
@@ -565,40 +574,40 @@ 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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- f6769201eee133381979e4bcb1f36f497d0f5e3c 587560 samtools_0.1.15-1_i386.deb
- 30e5a53f00ba8532c3a8156f51e4c5d13375ed82 168190 libbam-dev_0.1.15-1_i386.deb
+ d30726d6d0eab2144afe1c486ac9574cde4b27c1 604418 samtools_0.1.16-1_i386.deb
+ 07c2bc69c52e74960291daf88718d81f6f4a2bf5 178562 libbam-dev_0.1.16-1_i386.deb
Checksums-Sha256:
- 8f39c955763b94089f37feec52bbd36da7a40a73d70c470ac8763aa8dec5d9e4 587560 samtools_0.1.15-1_i386.deb
- 6316b914212af74d376eaa0f4c1e61e19e1a7f1eae34334797e027938256507f 168190 libbam-dev_0.1.15-1_i386.deb
+ d408cd2b3f00081e83594e3e491575243cd0fee75bd38f2b1d5323f61bb429b7 604418 samtools_0.1.16-1_i386.deb
+ 798f80d407f0a9f598896e0a5a232ef4ae1bfb4c51fa8b0b7a65a479e14fe07b 178562 libbam-dev_0.1.16-1_i386.deb
Files:
- 716ed3a43095468adaa5898a181a14b4 587560 science optional samtools_0.1.15-1_i386.deb
- c06abfed92ff1b516614c5eda25f719c 168190 libdevel optional libbam-dev_0.1.15-1_i386.deb
+ e5847dc9e0609f4a1ccd20d7fe89d931 604418 science optional samtools_0.1.16-1_i386.deb
+ cc391c4fcbb8c92cb7cd9aec540fcdec 178562 libdevel optional libbam-dev_0.1.16-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_i386.deb
+samtools_0.1.16-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 587560 bytes: control archive= 1786 bytes.
+ size 604418 bytes: control archive= 1785 bytes.
785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1072
+ Installed-Size: 1140
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -611,50 +620,50 @@ samtools_0.1.15-1_i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/samtools/
--rwxr-xr-x root/root 6664 2011-04-12 11:32 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6144 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6112 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10116 2011-04-12 11:32 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17384 2011-04-12 11:32 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/bin/
--rwxr-xr-x root/root 104676 2011-04-12 11:32 ./usr/bin/bcftools
--rwxr-xr-x root/root 22584 2011-04-12 11:32 ./usr/bin/razip
--rwxr-xr-x root/root 370284 2011-04-12 11:32 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7144 2011-05-19 04:45 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6536 2011-05-19 04:45 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6536 2011-05-19 04:45 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10380 2011-05-19 04:45 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17680 2011-05-19 04:45 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/bin/
+-rwxr-xr-x root/root 129252 2011-05-19 04:45 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24748 2011-05-19 04:45 ./usr/bin/razip
+-rwxr-xr-x root/root 411368 2011-05-19 04:45 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./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 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2011-04-12 11:32 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-05-19 04:45 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2011-04-12 11:32 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-04-12 11:32 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8393 2011-04-12 11:32 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-04-12 11:32 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-05-19 04:45 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/man/man1/
+-rw-r--r-- root/root 2101 2011-05-19 04:45 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 04:45 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-05-19 04:45 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 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 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 11:32 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-05-19 04:45 ./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
@@ -663,19 +672,19 @@ drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-libbam-dev_0.1.15-1_i386.deb
+libbam-dev_0.1.16-1_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 168190 bytes: control archive= 895 bytes.
+ size 178562 bytes: control archive= 926 bytes.
673 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 412
+ Installed-Size: 456
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -686,23 +695,25 @@ libbam-dev_0.1.15-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
--rw-r--r-- root/root 260232 2011-04-12 11:32 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/lib/
+-rw-r--r-- root/root 295422 2011-05-19 04:45 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/include/
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/include/samtools/
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -716,7 +727,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-04b94330-7968-42e2-8364-991a65659f4b/build/buildd-samtools_0.1.15-1-i386-_MkcrA
+Purging /var/lib/schroot/mount/sid-i386-sbuild-a8a9eaac-dae5-4b1a-9d7b-aa07cd3b0949/build/buildd-samtools_0.1.16-1-i386-q2Ku0q
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -724,18 +735,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 9880
-Build-Time: 46
+Build-Space: 10396
+Build-Time: 48
Distribution: sid
-Install-Time: 39
-Job: samtools_0.1.15-1
+Install-Time: 38
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 113
-Source-Version: 0.1.15-1
-Space: 9880
+Package-Time: 112
+Source-Version: 0.1.16-1
+Space: 10396
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1132
-Build needed 00:01:53, 9880k disc space
+Finished at 20110519-0445
+Build needed 00:01:52, 10396k disc space
Signature with key '44C3EAC7' requested:
diff --git a/ia64.log b/ia64.log
index 40cf09d..09aedea 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,67 +1,65 @@
-From buildd at mundy.debian.org Tue Apr 12 11:34:44 2011
-Return-path: <buildd at mundy.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at caballero.debian.org Thu May 19 11:26:08 2011
+Return-path: <buildd at caballero.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at mundy.debian.org>)
- id 1Q9bro-00076Q-GX
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:34:44 +0000
-Received: from mundy.debian.org ([192.25.206.62])
+ (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
+ id 1QN1Ml-00054I-LN
+ for logs at buildd.debian.org; Thu, 19 May 2011 11:26:08 +0000
+Received: from caballero.debian.org ([193.201.200.200])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mundy.debian.org, EMAIL=hostmaster at mundy.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at mundy.debian.org>)
- id 1Q9brj-0004xW-OG
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:34:40 +0000
-Received: from buildd by mundy.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mundy.debian.org>)
- id 1Q9brf-00081G-Kx; Tue, 12 Apr 2011 11:34:35 +0000
-From: buildd on mundy <buildd at mundy.debian.org>
-To: buildd-porters at mundy.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.15-1 on ia64 (dist=sid)
+ CN=caballero.debian.org,
+ EMAIL=hostmaster at caballero.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
+ id 1QN1Mk-0005lq-Cf; Thu, 19 May 2011 11:26:06 +0000
+Received: from buildd by caballero.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at caballero.debian.org>) id 1QN1Mj-0006JC-J2
+ for buildd-porters at caballero.debian.org; Thu, 19 May 2011 11:26:05 +0000
+From: buildd on caballero <buildd at caballero.debian.org>
+To: buildd-porters at caballero.debian.org
+Subject: Log for successful build of samtools_0.1.16-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q9brf-00081G-Kx at mundy.debian.org>
-Date: Tue, 12 Apr 2011 11:34:35 +0000
+Message-Id: <E1QN1Mj-0006JC-J2 at caballero.debian.org>
+Date: Thu, 19 May 2011 11:26:05 +0000
+Delivered-To: buildd-porters at caballero.debian.org
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mundy.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on caballero.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (ia64) 12 Apr 2011 11:30 ║
+║ samtools 0.1.16-1 (ia64) 19 May 2011 11:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: ia64
-Get:1 http://incoming.debian.org unstable InRelease [151 kB]
+Hit http://mirror.positive-internet.com sid InRelease
+Hit http://mirror.positive-internet.com sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://spohr.debian.org unstable InRelease [151 kB]
-Get:4 http://incoming.debian.org Release [1604 B]
-Get:5 http://spohr.debian.org unstable/main Sources [5265 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [5265 kB]
-Get:7 http://spohr.debian.org unstable/contrib Sources [48.2 kB]
-Get:8 http://spohr.debian.org unstable/non-free Sources [97.4 kB]
-Get:9 http://spohr.debian.org unstable/main ia64 Packages [6981 kB]
-Get:10 http://spohr.debian.org unstable/contrib ia64 Packages [52.9 kB]
-Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:11 http://spohr.debian.org unstable/main TranslationIndex [2264 B]
-Ign http://spohr.debian.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
-Get:14 http://incoming.debian.org unstable/main ia64 Packages [6981 kB]
-Get:15 http://incoming.debian.org unstable/contrib ia64 Packages [52.9 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
-Get:17 http://incoming.debian.org Sources [49.7 kB]
-Get:18 http://incoming.debian.org Packages [772 kB]
+Hit http://mirror.positive-internet.com sid/contrib Sources/DiffIndex
+Hit http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex
+Hit http://mirror.positive-internet.com sid/contrib ia64 Packages/DiffIndex
+Ign http://mirror.positive-internet.com sid/contrib TranslationIndex
+Hit http://mirror.positive-internet.com sid/main TranslationIndex
+Hit http://incoming.debian.org Release.gpg
+Ign http://mirror.positive-internet.com sid/contrib 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/main ia64 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Hit http://incoming.debian.org Release
+Hit http://incoming.debian.org Sources
+Hit http://incoming.debian.org Packages
+Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 26.0 MB in 18s (1412 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +80,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 0s (479 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://mirror.positive-internet.com/debian/ sid/main samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://mirror.positive-internet.com/debian/ sid/main samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://mirror.positive-internet.com/debian/ sid/main samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 0s (1261 kB/s)
Download complete and in download only mode
Check arch
@@ -106,12 +104,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -120,37 +118,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.2)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.1)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-19)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6.1-dev: already installed (2.11.2-13)
-gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
+libc6.1-dev: already installed (2.13-2)
+gcc: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -164,8 +162,8 @@ The following extra packages will be installed:
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 ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc 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
@@ -173,58 +171,37 @@ 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
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 6 not upgraded.
-Need to get 12.9 MB of archives.
-After this operation, 43.8 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 1.21-5 [1440 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-1 [47.2 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.1-1 [1122 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 2.28.4-1 [1972 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 8.1.3 [554 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 5.8+20110307-1 [614 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
-Fetched 12.9 MB in 0s (14.3 MB/s)
+0 upgraded, 20 newly installed, 0 to remove and 10 not upgraded.
+Need to get 0 B/11.7 MB of archives.
+After this operation, 41.4 MB of additional disk space will be used.
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10045 files and directories currently installed.)
+(Reading database ... 10484 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_ia64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_ia64.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_ia64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_ia64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_ia64.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_ia64.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_ia64.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_ia64.deb) ...
+Unpacking file (from .../file_5.04-5+b1_ia64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_ia64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_ia64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_ia64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_ia64.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_ia64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package intltool-debian.
@@ -232,11 +209,11 @@ 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_8.1.3_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_ia64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_ia64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
Setting up bsdmainutils (8.2.2) ...
@@ -244,34 +221,34 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6.1-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
-Package versions: apt_0.8.13.2 base-files_6.2 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-7 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-2 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 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 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_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-3 gcc-4.4_4.4.6-3 libc6.1-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 linux-libc-dev_2.6.38-5
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-9 g++-4.4_4.4.6-3 gcc_4:4.4.5-9 gcc-4.4_4.4.6-3 gcc-4.4-base_4.4.6-3 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6.1_2.13-2 libc6.1-dev_2.13-2 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.2-1 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -283,12 +260,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -304,8 +281,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -315,18 +292,18 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/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_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/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_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
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
@@ -338,100 +315,101 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/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_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/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_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
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_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -460,7 +438,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -491,6 +469,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -498,7 +477,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -512,6 +491,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -523,7 +503,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-ia64-SpdKwR/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -538,68 +518,68 @@ 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_0.1.15-1_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../samtools_0.1.15-1_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1134
+Build finished at 20110519-1125
-samtools_0.1.15-1_ia64.changes:
+samtools_0.1.16-1_ia64.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
+Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero 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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- be1bd3c93aaaadf03288167ba6bb1655ee5c62ec 734940 samtools_0.1.15-1_ia64.deb
- 6670e1538467c88c1d41dcf459b4814d1f6a0fe9 220220 libbam-dev_0.1.15-1_ia64.deb
+ 2d814117eb6228b4f746ad9580f9b2855d93ccf6 763130 samtools_0.1.16-1_ia64.deb
+ a3ae4eda51357142e0bbb2c3d570c477165df47a 225830 libbam-dev_0.1.16-1_ia64.deb
Checksums-Sha256:
- 64a80169be82c10e90f4b6579e294c09be3ce210d51e47062618c7afbc57eb91 734940 samtools_0.1.15-1_ia64.deb
- f314a6ef5b167cf6b024c02a84263a238dd5831ed0f081b34cfd90ce0026e5de 220220 libbam-dev_0.1.15-1_ia64.deb
+ 24fda0427420cd875626e586841c679a89da1ff764e7b3682b8a75380f4c54e4 763130 samtools_0.1.16-1_ia64.deb
+ 2f2e39507ac6e18c60b376c746c873084b20be7f37b116370c3e30c01f01142b 225830 libbam-dev_0.1.16-1_ia64.deb
Files:
- a584db0e6fc201f8480ebe449f12d63d 734940 science optional samtools_0.1.15-1_ia64.deb
- ad4f05972f350b79c73746e2d010959b 220220 libdevel optional libbam-dev_0.1.15-1_ia64.deb
+ 5a9924fdc7c72111c1a693608f34e91b 763130 science optional samtools_0.1.16-1_ia64.deb
+ fd54a55ad6e186dca773abdd40c5fb29 225830 libdevel optional libbam-dev_0.1.16-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_ia64.deb
+samtools_0.1.16-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 734940 bytes: control archive= 1785 bytes.
+ size 763130 bytes: control archive= 1782 bytes.
787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1748
+ Installed-Size: 1784
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -612,71 +592,71 @@ samtools_0.1.15-1_ia64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2011-04-12 11:34 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./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 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 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-04-12 11:34 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-04-12 11:34 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-05-19 11:25 ./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 2011-05-19 11:25 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-05-19 11:25 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 11:25 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2101 2011-05-19 11:25 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./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 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 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 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 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 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 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
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/man/man1/
--rw-r--r-- root/root 8393 2011-04-12 11:34 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-04-12 11:34 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 2005 2011-04-12 11:34 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/bin/
--rwxr-xr-x root/root 821792 2011-04-12 11:34 ./usr/bin/samtools
--rwxr-xr-x root/root 52520 2011-04-12 11:34 ./usr/bin/razip
--rwxr-xr-x root/root 263216 2011-04-12 11:34 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/lib/samtools/
--rwxr-xr-x root/root 13296 2011-04-12 11:34 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13360 2011-04-12 11:34 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 14944 2011-04-12 11:34 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 30712 2011-04-12 11:34 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 22384 2011-04-12 11:34 ./usr/lib/samtools/md5fa
-
-
-libbam-dev_0.1.15-1_ia64.deb
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2011-05-19 11:25 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/bin/
+-rwxr-xr-x root/root 287712 2011-05-19 11:25 ./usr/bin/bcftools
+-rwxr-xr-x root/root 52520 2011-05-19 11:25 ./usr/bin/razip
+-rwxr-xr-x root/root 832184 2011-05-19 11:25 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30712 2011-05-19 11:25 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13360 2011-05-19 11:25 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13296 2011-05-19 11:25 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 22384 2011-05-19 11:25 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2011-05-19 11:25 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.16-1_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 220220 bytes: control archive= 893 bytes.
+ size 225830 bytes: control archive= 926 bytes.
673 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 692
+ Installed-Size: 716
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -687,23 +667,25 @@ libbam-dev_0.1.15-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./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 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./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 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./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 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
-drwxr-xr-x root/root 0 2011-04-12 11:34 ./usr/lib/
--rw-r--r-- root/root 548572 2011-04-12 11:34 ./usr/lib/libbam.a
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/lib/
+-rw-r--r-- root/root 565154 2011-05-19 11:25 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -717,26 +699,71 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-7be68e6b-7380-4d4e-9038-b157c91941a9/build/buildd-samtools_0.1.15-1-ia64-SpdKwR
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-6a35d064-ee4f-4030-a03e-85b48da87405/build/buildd-samtools_0.1.16-1-ia64-WI6whj
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ 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, 0 newly installed, 20 to remove and 10 not upgraded.
+After this operation, 41.4 MB disk space will be freed.
+(Reading database ... 11917 files and directories currently installed.)
+Removing cdbs ...
+Removing debhelper ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 13888
-Build-Time: 110
+Build-Space: 14204
+Build-Time: 111
Distribution: sid
-Install-Time: 62
-Job: samtools_0.1.15-1
+Install-Time: 21
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 220
-Source-Version: 0.1.15-1
-Space: 13888
+Package-Time: 142
+Source-Version: 0.1.16-1
+Space: 14204
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1134
-Build needed 00:03:40, 13888k disc space
+Finished at 20110519-1125
+Build needed 00:02:22, 14204k disc space
diff --git a/info b/info
index 48db04e..ed09071 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-i386~1302607952~sid~successful
-kfreebsd-amd64~1302607962~sid~successful
-s390~1302607983~sid~successful
-kfreebsd-i386~1302608031~sid~successful
-ia64~1302608085~sid~successful
-powerpc~1302608148~sid~successful
-sparc~1302608174~sid~failed
-hurd-i386~1302608480~sid~successful
-armel~1302610453~sid~failed
-mips~1302610493~sid~successful
-mipsel~1302632104~sid~successful
+powerpc~1305780308~sid~successful
+i386~1305780353~sid~successful
+armel~1305780503~sid~failed
+s390~1305780519~sid~successful
+sparc~1305780540~sid~failed
+kfreebsd-amd64~1305780549~sid~successful
+kfreebsd-i386~1305780607~sid~successful
+mips~1305780671~sid~successful
+mipsel~1305780676~sid~successful
+hurd-i386~1305783164~sid~successful
+ia64~1305804368~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index a5cd1c7..aeeb745 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,75 +1,85 @@
-From buildd at fasch.debian.org Tue Apr 12 11:32:42 2011
-Return-path: <buildd at fasch.debian.org>
+From buildd at fano.debian.org Thu May 19 04:49:08 2011
+Return-path: <buildd at fano.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at fasch.debian.org>)
- id 1Q9bpp-0006Zs-Im
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:32:42 +0000
-Received: from fasch.debian.org ([194.177.211.201])
+ (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
+ id 1QMvAa-0007sT-EP
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:49:08 +0000
+Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
+ CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
- id 1Q9bpi-0006Aq-F6; Tue, 12 Apr 2011 11:32:35 +0000
-Received: from buildd by fasch.debian.org with local (Exim 4.72)
- (envelope-from <buildd at fasch.debian.org>)
- id 1Q9bph-000E5g-8K; Tue, 12 Apr 2011 11:32:33 +0000
-Date: Tue, 12 Apr 2011 11:32:33 +0000
-Message-Id: <E1Q9bph-000E5g-8K at fasch.debian.org>
-From: buildd on fasch <buildd at fasch.debian.org>
-To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
-Subject: Log for successful build of samtools_0.1.15-1 on kfreebsd-amd64
+ (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
+ id 1QMvAY-0003Xp-FX; Thu, 19 May 2011 04:49:07 +0000
+Received: from buildd by fano.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fano.debian.org>)
+ id 1QMvAV-000B4m-PJ; Thu, 19 May 2011 04:49:03 +0000
+Message-Id: <E1QMvAV-000B4m-PJ at fano.debian.org>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Thu, 19 May 2011 04:49:03 +0000
+From: buildd on fano <buildd at fano.debian.org>
+To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
+Subject: Log for successful build of samtools_0.1.16-1 on kfreebsd-amd64
(dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+Key-Id: 91116966
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (kfreebsd-amd64) 12 Apr 2011 11:29 ║
+║ samtools 0.1.16-1 (kfreebsd-amd64) 19 May 2011 04:46 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: kfreebsd-amd64
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Get:2 http://mirror-ubc.debian.org sid InRelease [146 kB]
+Get:3 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.gr.debian.org sid/main TranslationIndex
-Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
-Ign http://ftp.gr.debian.org sid/contrib Translation-en
-Ign http://ftp.gr.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
+Get:4 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
+Get:5 http://mirror-ubc.debian.org sid/main TranslationIndex [2264 B]
+Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://mirror-ubc.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:8 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
+Get:9 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [81.2 kB]
+Get:10 http://mirror-ubc.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Ign http://mirror-ubc.debian.org sid/contrib Translation-en
+Ign http://mirror-ubc.debian.org sid/non-free Translation-en
+Get:11 http://incoming.debian.org Release [1604 B]
+Get:12 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Get:13 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
+Get:14 http://incoming.debian.org sid/main TranslationIndex [2264 B]
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Get:3 http://incoming.debian.org Sources [49.7 kB]
-Get:4 http://incoming.debian.org Packages [772 kB]
+Get:15 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
+Get:16 http://incoming.debian.org Sources [26.8 kB]
+Get:17 http://incoming.debian.org Packages [270 kB]
+Get:18 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:19 http://incoming.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
+Get:20 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [81.2 kB]
+Get:21 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Ign http://incoming.debian.org Translation-en
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 825 kB in 5s (155 kB/s)
+Get:22 http://incoming.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
+Fetched 796 kB in 13s (57.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,11 +100,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 2s (163 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (291 kB/s)
Download complete and in download only mode
Check arch
@@ -114,17 +124,11 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpipeline1 libpcre3 groff-base libssl0.9.8 man-db
-Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpipeline1 libpcre3 groff-base libssl0.9.8 man-db
-Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
@@ -139,32 +143,32 @@ base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (3.4.5)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.1)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.1-4+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
+ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.10.1-19)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -173,42 +177,49 @@ Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libssl0.9.8
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
- libmagic1 libunistring0 libxml2 po-debconf
+ 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 ncurses-doc libmail-box-perl
+ devscripts dh-make gettext-doc groff ncurses-doc 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 file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2 po-debconf
- zlib1g-dev
+ 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, 15 newly installed, 0 to remove and 7 not upgraded.
-Need to get 0 B/8460 kB of archives.
-After this operation, 22.9 MB of additional disk space will be used.
+0 upgraded, 19 newly installed, 0 to remove and 7 not upgraded.
+Need to get 0 B/9714 kB of archives.
+After this operation, 27.5 MB of additional disk space will be used.
+Selecting previously deselected package groff-base.
+(Reading database ... 12278 files and directories currently installed.)
+Unpacking groff-base (from .../groff-base_1.21-5_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libpipeline1.
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-amd64.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libmagic1.
-(Reading database ... 13818 files and directories currently installed.)
-Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-amd64.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_kfreebsd-amd64.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5_kfreebsd-amd64.deb) ...
+Unpacking file (from .../file_5.04-5+b1_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_kfreebsd-amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_kfreebsd-amd64.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package intltool-debian.
@@ -216,42 +227,43 @@ 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_8.1.3_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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) ...
-Processing triggers for man-db ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
+Setting up man-db (2.6.0.2-1) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libssl0.9.8
-Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8
-Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-2 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.3-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-7 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 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_3.81-8.1 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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 type-handling_0.2.23 tzdata_2011e-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 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: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.13-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.5 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-4 libc-dev-bin_2.13-4 libc0.1_2.13-4 libc0.1-dev_2.13-4 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-7 libreadline6_6.2-2 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 type-handling_0.2.23 tzdata_2011g-1 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 │
@@ -262,12 +274,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -282,25 +294,25 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/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_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/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_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
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
@@ -308,100 +320,113 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
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_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/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_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/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_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
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_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -430,7 +455,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -457,6 +482,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -464,7 +490,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -478,6 +504,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -489,7 +516,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -504,68 +531,68 @@ 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_0.1.15-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../samtools_0.1.15-1_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1132
+Build finished at 20110519-0448
-samtools_0.1.15-1_kfreebsd-amd64.changes:
+samtools_0.1.16-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
+Closes: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- bdecb3f4156ed114cb5b0c9a2b8c677b5cac97a6 602150 samtools_0.1.15-1_kfreebsd-amd64.deb
- cc2e151f4d8a5ae113f8b588e336f91ad8055a1c 168960 libbam-dev_0.1.15-1_kfreebsd-amd64.deb
+ dc4d27fdb1baf8a28e0158f1c06acc5492b10687 606552 samtools_0.1.16-1_kfreebsd-amd64.deb
+ 5c0dff2ccbc0b725d6c34168482700e25f7b4b54 171268 libbam-dev_0.1.16-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 3f9819ebccb1d379cd218f9d12a8cfdea4477815966f6715244ddebf599e0bdd 602150 samtools_0.1.15-1_kfreebsd-amd64.deb
- 6a54d9faa6a3398fada63982828d5cf5c7865efaf13abc66204ed34fc30af8e7 168960 libbam-dev_0.1.15-1_kfreebsd-amd64.deb
+ 981670e02108f5079d5b5ca5ef0d07a2d7312cf7f4ce3a0535e7d35cc2006c9c 606552 samtools_0.1.16-1_kfreebsd-amd64.deb
+ 3e898dca30f23b4b26f5411f3f3a8644165aa19c92d99b19389f23921afea56d 171268 libbam-dev_0.1.16-1_kfreebsd-amd64.deb
Files:
- 21fdc857a1eac4755bb32006758e06f2 602150 science optional samtools_0.1.15-1_kfreebsd-amd64.deb
- fd26e727e8483ea35b476ecf053a86f3 168960 libdevel optional libbam-dev_0.1.15-1_kfreebsd-amd64.deb
+ 7f2c8c1b5d563906c3e7c00057383137 606552 science optional samtools_0.1.16-1_kfreebsd-amd64.deb
+ c0bbfd9d86e432571ce304d66a8e9f63 171268 libdevel optional libbam-dev_0.1.16-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_kfreebsd-amd64.deb
+samtools_0.1.16-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 602150 bytes: control archive= 1793 bytes.
+ size 606552 bytes: control archive= 1789 bytes.
797 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1042
+ Installed-Size: 1052
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -578,32 +605,32 @@ samtools_0.1.15-1_kfreebsd-amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./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 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./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 2011-04-12 11:31 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-05-19 04:48 ./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 2011-04-12 11:31 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-04-12 11:31 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-12 11:31 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-04-12 11:31 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-05-19 04:48 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-05-19 04:48 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 04:48 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2101 2011-05-19 04:48 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./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
@@ -616,33 +643,33 @@ drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 11:31 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/bin/
--rwxr-xr-x root/root 114088 2011-04-12 11:31 ./usr/bin/bcftools
--rwxr-xr-x root/root 24800 2011-04-12 11:31 ./usr/bin/razip
--rwxr-xr-x root/root 384272 2011-04-12 11:31 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/lib/samtools/
--rwxr-xr-x root/root 19248 2011-04-12 11:31 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8288 2011-04-12 11:31 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8192 2011-04-12 11:31 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11912 2011-04-12 11:31 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8608 2011-04-12 11:31 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.15-1_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2011-05-19 04:48 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/bin/
+-rwxr-xr-x root/root 126376 2011-05-19 04:48 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24544 2011-05-19 04:48 ./usr/bin/razip
+-rwxr-xr-x root/root 384280 2011-05-19 04:48 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19272 2011-05-19 04:48 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8160 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8096 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11952 2011-05-19 04:48 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8696 2011-05-19 04:48 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.16-1_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 168960 bytes: control archive= 901 bytes.
+ size 171268 bytes: control archive= 932 bytes.
683 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 458
+ Installed-Size: 480
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -653,23 +680,25 @@ libbam-dev_0.1.15-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./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 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/lib/
--rw-r--r-- root/root 323908 2011-04-12 11:31 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 11:31 ./usr/include/
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./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
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
+-rw-r--r-- root/root 328218 2011-05-19 04:48 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -683,27 +712,22 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1302607781-51888/build/buildd-samtools_0.1.15-1-kfreebsd-amd64-TsMKt4
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1305780415-40848/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libssl0.9.8
-Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpipeline1 libpcre3 groff-base libssl0.9.8 man-db
-Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* debhelper* file* gettext* gettext-base* html2text* intltool-debian*
- libcroco3* libglib2.0-0* libmagic1* libncurses5-dev* libunistring0* libxml2*
- po-debconf* zlib1g-dev*
-0 upgraded, 0 newly installed, 15 to remove and 7 not upgraded.
-After this operation, 22.9 MB disk space will be freed.
-(Reading database ... 14739 files and directories currently installed.)
+ 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, 0 newly installed, 19 to remove and 7 not upgraded.
+After this operation, 27.5 MB disk space will be freed.
+(Reading database ... 13603 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing file ...
@@ -711,6 +735,10 @@ Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
@@ -720,31 +748,33 @@ Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
Removing libncurses5-dev ...
+Removing libpcre3 ...
+Purging configuration files for libpcre3 ...
+Removing libpipeline1 ...
+Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
Purging configuration files for libunistring0 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
Removing zlib1g-dev ...
-Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 11688
-Build-Time: 52
+Build-Space: 12066
+Build-Time: 50
Distribution: sid
-Install-Time: 65
-Job: samtools_0.1.15-1
+Install-Time: 36
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 139
-Source-Version: 0.1.15-1
-Space: 11688
+Package-Time: 110
+Source-Version: 0.1.16-1
+Space: 12066
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1132
-Build needed 00:02:19, 11688k disc space
-Signature with key '516A3A7B' requested:
-
+Finished at 20110519-0448
+Build needed 00:01:50, 12066k disc space
+Signature with key '91116966' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index ecc37cd..9b98db1 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,55 +1,59 @@
-From buildd at field.debian.org Tue Apr 12 11:33:51 2011
+From buildd at field.debian.org Thu May 19 04:50:07 2011
Return-path: <buildd at field.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at field.debian.org>)
- id 1Q9bqx-0006sv-2f
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:33:51 +0000
+ (Exim 4.72) (envelope-from <buildd at field.debian.org>)
+ id 1QMvBW-0008EJ-Pl
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:50:06 +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 1Q9bqs-0004ud-Ic; Tue, 12 Apr 2011 11:33:46 +0000
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at field.debian.org>)
+ id 1QMvBV-0003Y2-Hx; Thu, 19 May 2011 04:50:05 +0000
Received: from buildd by field.debian.org with local (Exim 4.72)
(envelope-from <buildd at field.debian.org>)
- id 1Q9bqp-0003sn-G3; Tue, 12 Apr 2011 11:33:43 +0000
-Date: Tue, 12 Apr 2011 11:33:43 +0000
-Message-Id: <E1Q9bqp-0003sn-G3 at field.debian.org>
+ id 1QMvBU-000DTE-9K; Thu, 19 May 2011 04:50:04 +0000
+Message-Id: <E1QMvBU-000DTE-9K at field.debian.org>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Thu, 19 May 2011 04:50:04 +0000
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_0.1.15-1 on kfreebsd-i386
+To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
+Subject: Log for successful build of samtools_0.1.16-1 on kfreebsd-i386
(dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+Key-Id: 22C61858
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (kfreebsd-i386) 12 Apr 2011 11:30 ║
+║ samtools 0.1.16-1 (kfreebsd-i386) 19 May 2011 04:46 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: kfreebsd-i386
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Get:1 http://ftp.gr.debian.org sid InRelease [146 kB]
+Get:2 http://ftp.gr.debian.org sid/main Sources/DiffIndex [2038 B]
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
+Get:3 http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages [6663 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
Hit http://ftp.gr.debian.org sid/main TranslationIndex
Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://ftp.gr.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:6 http://ftp.gr.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 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
@@ -61,13 +65,13 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
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 [49.7 kB]
-Get:4 http://incoming.debian.org Packages [772 kB]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://incoming.debian.org Sources [26.8 kB]
+Get:9 http://incoming.debian.org Packages [270 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 825 kB in 6s (136 kB/s)
+Fetched 7116 kB in 5s (1388 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -88,11 +92,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 2s (180 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (205 kB/s)
Download complete and in download only mode
Check arch
@@ -112,12 +116,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -131,32 +135,32 @@ base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (3.4.5)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.1)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.1-4)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
+ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.10.1-19)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-5 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -170,7 +174,7 @@ The following extra packages will be installed:
libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
+ devscripts dh-make gettext-doc groff ncurses-doc less www-browser
libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
@@ -180,34 +184,34 @@ The following NEW packages will be installed:
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, 19 newly installed, 0 to remove and 5 not upgraded.
-Need to get 0 B/10.4 MB of archives.
-After this operation, 27.2 MB of additional disk space will be used.
+0 upgraded, 19 newly installed, 0 to remove and 7 not upgraded.
+Need to get 0 B/9244 kB of archives.
+After this operation, 25.9 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 11815 files and directories currently installed.)
+(Reading database ... 12220 files and directories currently installed.)
Unpacking groff-base (from .../groff-base_1.21-5_kfreebsd-i386.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_kfreebsd-i386.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_kfreebsd-i386.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_kfreebsd-i386.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5_kfreebsd-i386.deb) ...
+Unpacking file (from .../file_5.04-5+b1_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_kfreebsd-i386.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-i386.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package intltool-debian.
@@ -215,43 +219,43 @@ 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_8.1.3_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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 (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8
-Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-2 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 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_2.6.0.1-1 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-1 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
+Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.13-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.5 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-4 libc-dev-bin_2.13-4 libc0.1_2.13-4 libc0.1-dev_2.13-4 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-7 libreadline6_6.2-2 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 type-handling_0.2.23 tzdata_2011g-1 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 │
@@ -262,12 +266,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -282,25 +286,25 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/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_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/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_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
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
@@ -308,100 +312,119 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
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_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/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_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/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_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
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_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -430,7 +453,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -457,6 +480,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -464,7 +488,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -478,6 +502,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -489,7 +514,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -504,27 +529,27 @@ 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_0.1.15-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.15-1_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1133
+Build finished at 20110519-0449
-samtools_0.1.15-1_kfreebsd-i386.changes:
+samtools_0.1.16-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
@@ -532,40 +557,40 @@ 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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- db4b84316a10ef99e527d0cf28e8f3e69be87a3a 588572 samtools_0.1.15-1_kfreebsd-i386.deb
- 955ef5a1f33ac243d2d03197e80dd3ffbfa53484 168586 libbam-dev_0.1.15-1_kfreebsd-i386.deb
+ 59c2ca026bef8ab1fe5a5b04614331f80be21dee 612828 samtools_0.1.16-1_kfreebsd-i386.deb
+ f093e93bf617d98712f11167a439aa884d24b18b 179098 libbam-dev_0.1.16-1_kfreebsd-i386.deb
Checksums-Sha256:
- 7ce964a460d5c951b11fdbd6f6768bcbd73e81d8774bd52fa98d876b93a843fd 588572 samtools_0.1.15-1_kfreebsd-i386.deb
- 5163f38d291e1c4eeb8b4338925df64a7529eec4f642f50740e97d719f7f0276 168586 libbam-dev_0.1.15-1_kfreebsd-i386.deb
+ eb40119fa981b7a38f1616cb2b671c24fce1ac10db6acb5882d9543787335e05 612828 samtools_0.1.16-1_kfreebsd-i386.deb
+ 4fb2209112d595e22cf283c8dfaffc2bcb68b44ceaad90f34efcdb8ad4e3e318 179098 libbam-dev_0.1.16-1_kfreebsd-i386.deb
Files:
- 5469df2a1f7e3283d08b5a4a2de35666 588572 science optional samtools_0.1.15-1_kfreebsd-i386.deb
- 1287f3c54405cefaea50e66aae19e9ea 168586 libdevel optional libbam-dev_0.1.15-1_kfreebsd-i386.deb
+ 4425dad329f2c01c745fc168a85d9bf0 612828 science optional samtools_0.1.16-1_kfreebsd-i386.deb
+ 1e17c04130d252b8895b62095249a0c6 179098 libdevel optional libbam-dev_0.1.16-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_kfreebsd-i386.deb
+samtools_0.1.16-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 588572 bytes: control archive= 1787 bytes.
+ size 612828 bytes: control archive= 1792 bytes.
796 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1004
+ Installed-Size: 1086
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -578,32 +603,32 @@ samtools_0.1.15-1_kfreebsd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-04-12 11:32 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-05-19 04:49 ./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 2011-04-12 11:32 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-04-12 11:32 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-12 11:32 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-04-12 11:32 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-05-19 04:49 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-05-19 04:49 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 04:49 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2101 2011-05-19 04:49 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./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
@@ -616,33 +641,33 @@ drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 11:32 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/bin/
--rwxr-xr-x root/root 104676 2011-04-12 11:32 ./usr/bin/bcftools
--rwxr-xr-x root/root 23352 2011-04-12 11:32 ./usr/bin/razip
--rwxr-xr-x root/root 371020 2011-04-12 11:32 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/samtools/
--rwxr-xr-x root/root 17424 2011-04-12 11:32 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6128 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6096 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10084 2011-04-12 11:32 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6616 2011-04-12 11:32 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.15-1_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2011-05-19 04:49 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/bin/
+-rwxr-xr-x root/root 129252 2011-05-19 04:49 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25676 2011-05-19 04:49 ./usr/bin/razip
+-rwxr-xr-x root/root 412264 2011-05-19 04:49 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18184 2011-05-19 04:49 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6520 2011-05-19 04:49 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6520 2011-05-19 04:49 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10348 2011-05-19 04:49 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7096 2011-05-19 04:49 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.16-1_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 168586 bytes: control archive= 899 bytes.
+ size 179098 bytes: control archive= 934 bytes.
682 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 394
+ Installed-Size: 448
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -653,23 +678,25 @@ libbam-dev_0.1.15-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./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 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
--rw-r--r-- root/root 261096 2011-04-12 11:32 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/include/
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./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
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/lib/
+-rw-r--r-- root/root 296410 2011-05-19 04:49 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -683,11 +710,11 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1302607836-13199/build/buildd-samtools_0.1.15-1-kfreebsd-i386-XdT2ma
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1305780418-49932/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -696,9 +723,9 @@ The following packages will be REMOVED:
intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf*
zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 5 not upgraded.
-After this operation, 27.2 MB disk space will be freed.
-(Reading database ... 13143 files and directories currently installed.)
+0 upgraded, 0 newly installed, 19 to remove and 7 not upgraded.
+After this operation, 25.9 MB disk space will be freed.
+(Reading database ... 13545 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing file ...
@@ -734,19 +761,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 9576
-Build-Time: 53
+Build-Space: 10124
+Build-Time: 54
Distribution: sid
-Install-Time: 77
-Job: samtools_0.1.15-1
+Install-Time: 73
+Job: samtools_0.1.16-1
Package: samtools
Package-Time: 148
-Source-Version: 0.1.15-1
-Space: 9576
+Source-Version: 0.1.16-1
+Space: 10124
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1133
-Build needed 00:02:28, 9576k disc space
+Finished at 20110519-0449
+Build needed 00:02:28, 10124k disc space
Signature with key '22C61858' requested:
-
diff --git a/mips.log b/mips.log
index bbfd28b..71be0d9 100644
--- a/mips.log
+++ b/mips.log
@@ -1,68 +1,67 @@
-From buildd at lucatelli.debian.org Tue Apr 12 12:14:47 2011
-Return-path: <buildd at lucatelli.debian.org>
+From buildd at ball.debian.org Thu May 19 04:51:06 2011
+Return-path: <buildd at ball.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 lucatelli.debian.org>)
- id 1Q9cUY-0005t7-He
- for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:46 +0000
-Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1QMvCT-00007D-Ul
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:51:06 +0000
+Received: from ball.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d09])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lucatelli.debian.org,
- EMAIL=hostmaster at lucatelli.debian.org (verified)
+ CN=ball.debian.org, EMAIL=hostmaster at ball.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at lucatelli.debian.org>)
- id 1Q9cUT-00060G-GL
- for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:42 +0000
-Received: from buildd by lucatelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd at lucatelli.debian.org>) id 1Q9cUK-0005Yt-9Y
- for logs at buildd.debian.org; Tue, 12 Apr 2011 12:14:32 +0000
-From: buildd on lucatelli <buildd at lucatelli.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.15-1 on mips (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
+ id 1QMvCT-0008RL-1c
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:51:05 +0000
+Received: from buildd by ball.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at ball.debian.org>)
+ id 1QMvCS-0007R9-2b; Thu, 19 May 2011 04:51:04 +0000
+Date: Thu, 19 May 2011 04:51:04 +0000
+Message-Id: <E1QMvCS-0007R9-2b at ball.debian.org>
+From: buildd on ball <buildd at ball.debian.org>
+To: logs at buildd.debian.org,buildd-porters at ball.debian.org
+Subject: Log for successful build of samtools_0.1.16-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q9cUK-0005Yt-9Y at lucatelli.debian.org>
-Date: Tue, 12 Apr 2011 12:14:32 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ball.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (mips) 12 Apr 2011 11:30 ║
+║ samtools 0.1.16-1 (mips) 19 May 2011 04:42 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [151 kB]
-Get:2 http://incoming.debian.org unstable InRelease [151 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5265 kB]
+Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5221 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [48.2 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [97.4 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [6928 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [52.7 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2264 B]
-Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [6928 kB]
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [52.7 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5221 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [49.8 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [91.7 kB]
+Get:8 http://ftp.de.debian.org unstable/main mips Packages [7091 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib mips Packages [54.4 kB]
+Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2264 B]
+Ign http://ftp.de.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7091 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [54.4 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [49.7 kB]
-Get:18 http://incoming.debian.org Packages [772 kB]
+Get:17 http://incoming.debian.org Sources [26.8 kB]
+Get:18 http://incoming.debian.org Packages [270 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.9 MB in 59s (439 kB/s)
+Fetched 25.6 MB in 1min 7s (382 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 1s (337 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 0s (417 kB/s)
Download complete and in download only mode
Check arch
@@ -107,12 +106,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -128,30 +127,30 @@ coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.1)
+dpkg: already installed (1.16.0.2)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-19)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-2)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -162,82 +161,70 @@ 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 libpipeline1
- 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 ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc 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
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 20 newly installed, 0 to remove and 2 not upgraded.
-Need to get 11.6 MB of archives.
-After this operation, 32.7 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin mips 5.9-1 [328 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 mips 5.9-1 [361 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.2 [210 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-5 [1203 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-1 [35.7 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.1-1 [996 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5 [239 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5 [49.7 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2 [837 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.4-1 [1505 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-3 [415 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.1.3 [554 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-1 [509 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+0 upgraded, 20 newly installed, 0 to remove and 37 not upgraded.
+Need to get 9755 kB of archives.
+After this operation, 31.3 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips 8.2.2 [210 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base mips 1.21-5 [1203 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-1 [35.7 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db mips 2.6.0.2-1 [1005 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 mips 5.04-5+b1 [239 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main file mips 5.04-5+b1 [49.9 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2+b1 [837 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.6-1 [1509 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-4 [415 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 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 8.1.6 [557 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-1 [509 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.6 MB in 2s (5350 kB/s)
-(Reading database ... 10115 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_mips.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 10115 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_mips.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
+Fetched 9755 kB in 1s (6702 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10115 files and directories currently installed.)
+(Reading database ... 11381 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mips.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-5_mips.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mips.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_mips.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_mips.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_mips.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mips.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_mips.deb) ...
+Unpacking file (from .../file_5.04-5+b1_mips.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_mips.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_mips.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mips.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mips.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mips.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package intltool-debian.
@@ -245,9 +232,9 @@ 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_8.1.3_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mips.deb) ...
Selecting previously deselected package zlib1g-dev.
@@ -257,34 +244,34 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.0.20110327-3 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-3
-Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-3 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_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-7 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-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
+Kernel: Linux 2.6.32-5-sb1-bcm91250a mips (mips64)
+Toolchain package versions: binutils_2.21.51.20110421-3 dpkg-dev_1.16.0.2 g++-4.4_4.4.6-2 g++-4.6_4.6.0-6 gcc-4.4_4.4.6-2 gcc-4.6_4.6.0-6 libc6-dev_2.13-2 libstdc++6_4.6.0-6 libstdc++6-4.4-dev_4.4.6-2 libstdc++6-4.6-dev_4.6.0-6 linux-libc-dev_2.6.38-4
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.4_4.4.6-2 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.4_4.4.6-2 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4_4.4.6-2 gcc-4.4-base_4.4.6-2 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-18 libdb4.8_4.8.30-7 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-1 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.4-dev_4.4.6-2 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -294,14 +281,13 @@ Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -310,141 +296,151 @@ Check disc space
dpkg-buildpackage
─────────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
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 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
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_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/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_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/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_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
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
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
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_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/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_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/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_0.1.15-1-mips-zd9hwI/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
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_0.1.15-1-mips-zd9hwI/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -473,13 +469,9 @@ 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_0.1.15-1-mips-zd9hwI/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -504,6 +496,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -511,7 +504,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -525,6 +518,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -536,7 +530,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-mips-zd9hwI/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -551,68 +545,68 @@ 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_0.1.15-1_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.15-1_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_mips.deb'.
+ dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1214
+Build finished at 20110519-0450
-samtools_0.1.15-1_mips.changes:
+samtools_0.1.16-1_mips.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
+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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- 8c4fcceda767e27396a4fc8a52ca7c20fa147ba9 604934 samtools_0.1.15-1_mips.deb
- 8c85a8e7669a5141d911c467f27c5103b04b46e1 184540 libbam-dev_0.1.15-1_mips.deb
+ 55c1a23a0d88c2ecad20124d60bf46afd7975690 642396 samtools_0.1.16-1_mips.deb
+ 89378ff7eb087f4ca816d964dd9c9bdd9cf49391 200826 libbam-dev_0.1.16-1_mips.deb
Checksums-Sha256:
- 7f527d67d4e178dc4b2d2b398c9aa81795915b03cf70b1d005157c7f6eb41882 604934 samtools_0.1.15-1_mips.deb
- e0af6490110eee0a6e0dd497a66d1f7213a78540f60849fb130009e584d33323 184540 libbam-dev_0.1.15-1_mips.deb
+ c9195e03fed7f253826074241ba79c18df53479cdf95c88484dce05513f032a7 642396 samtools_0.1.16-1_mips.deb
+ 2baa61a4103179779b184b4ec70712ac736d928cff3b40879a7b2d0125f4a5bf 200826 libbam-dev_0.1.16-1_mips.deb
Files:
- e03565577e980ba81420ebdf38b615d0 604934 science optional samtools_0.1.15-1_mips.deb
- 82c52cecb4aa8227ef12c93c5e1871ae 184540 libdevel optional libbam-dev_0.1.15-1_mips.deb
+ 7748d6133eb54120fabe64918ef733cc 642396 science optional samtools_0.1.16-1_mips.deb
+ 14b030bb99223024b49cf8b9fbfcd7d1 200826 libdevel optional libbam-dev_0.1.16-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_mips.deb
+samtools_0.1.16-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 604934 bytes: control archive= 1794 bytes.
+ size 642396 bytes: control archive= 1783 bytes.
785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1228
+ Installed-Size: 1216
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -625,71 +619,71 @@ samtools_0.1.15-1_mips.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/lib/samtools/
--rwxr-xr-x root/root 7764 2011-04-12 12:13 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9768 2011-04-12 12:13 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 13268 2011-04-12 12:13 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2011-04-12 12:13 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 19944 2011-04-12 12:13 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/bin/
--rwxr-xr-x root/root 142088 2011-04-12 12:13 ./usr/bin/bcftools
--rwxr-xr-x root/root 477880 2011-04-12 12:13 ./usr/bin/samtools
--rwxr-xr-x root/root 30712 2011-04-12 12:13 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 2011-05-19 04:50 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./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 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 126609 2011-05-19 04:49 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 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 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/man1/
+-rw-r--r-- root/root 2101 2011-05-19 04:50 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 04:50 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-05-19 04:50 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/samtools/
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 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 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 5778 2011-05-19 04:50 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 12:13 ./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 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.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 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2011-04-12 11:39 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 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 1362 2011-04-12 10:45 ./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 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2011-04-12 12:13 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-04-12 12:13 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-04-12 12:13 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-12 12:13 ./usr/share/man/man1/samtools.1.gz
-
-
-libbam-dev_0.1.15-1_mips.deb
+-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 2011-05-19 04:50 ./usr/bin/
+-rwxr-xr-x root/root 29264 2011-05-19 04:50 ./usr/bin/razip
+-rwxr-xr-x root/root 462772 2011-05-19 04:50 ./usr/bin/samtools
+-rwxr-xr-x root/root 146724 2011-05-19 04:50 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18676 2011-05-19 04:50 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9252 2011-05-19 04:50 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 12512 2011-05-19 04:50 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-short
+
+
+libbam-dev_0.1.16-1_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 184540 bytes: control archive= 900 bytes.
+ size 200826 bytes: control archive= 931 bytes.
673 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 472
+ Installed-Size: 500
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -700,23 +694,25 @@ libbam-dev_0.1.15-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/lib/
--rw-r--r-- root/root 319948 2011-04-12 12:13 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/include/
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.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
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 12:13 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/samtools/
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
+-rw-r--r-- root/root 340398 2011-05-19 04:50 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -730,7 +726,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-1b551950-178e-4287-b8db-1140f6befd10/build/buildd-samtools_0.1.15-1-mips-zd9hwI
+Purging /var/lib/schroot/mount/sid-mips-sbuild-3aef4ba4-a3b8-4919-a5ff-30ef7e006e4f/build/buildd-samtools_0.1.16-1-mips-2pLxAp
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -738,84 +734,84 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 10108
-Build-Time: 2475
+Build-Space: 10976
+Build-Time: 284
Distribution: sid
-Install-Time: 72
-Job: samtools_0.1.15-1
+Install-Time: 115
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 2647
-Source-Version: 0.1.15-1
-Space: 10108
+Package-Time: 522
+Source-Version: 0.1.16-1
+Space: 10976
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1214
-Build needed 00:44:07, 10108k disc space
-Signature with key 'F4C69470' requested:
+Finished at 20110519-0450
+Build needed 00:08:42, 10976k disc space
+Signature with key '40E097C5' requested:
-From buildd at mayer.debian.org Tue Apr 12 18:15:03 2011
+From buildd at mayer.debian.org Thu May 19 04:51:16 2011
Return-path: <buildd at mayer.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
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CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
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- (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
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+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
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+ for logs at buildd.debian.org; Thu, 19 May 2011 04:51:14 +0000
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+ (envelope-from <buildd at mayer.debian.org>) id 1QMvCY-00052Y-48
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:51:10 +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_0.1.15-1 on mipsel (dist=sid)
+To: logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.16-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q9i73-00020h-1Z at mayer.debian.org>
-Date: Tue, 12 Apr 2011 18:14:53 +0000
+Message-Id: <E1QMvCY-00052Y-48 at mayer.debian.org>
+Date: Thu, 19 May 2011 04:51:10 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (mipsel) 12 Apr 2011 18:09 ║
+║ samtools 0.1.16-1 (mipsel) 19 May 2011 04:44 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: mipsel
-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
+Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
+Get:2 http://incoming.debian.org sid InRelease [146 kB]
+Get:3 http://debian.oregonstate.edu sid/main Sources [5221 kB]
+Ign http://incoming.debian.org InRelease
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org sid/main Sources [5221 kB]
+Get:6 http://debian.oregonstate.edu sid/contrib Sources [49.8 kB]
+Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [7108 kB]
+Get:8 http://debian.oregonstate.edu sid/contrib mipsel Packages [54.7 kB]
Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Get:9 http://debian.oregonstate.edu sid/main TranslationIndex [2264 B]
Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://incoming.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
+Get:10 http://incoming.debian.org sid/contrib Sources [49.8 kB]
+Get:11 http://incoming.debian.org sid/main mipsel Packages [7108 kB]
+Get:12 http://incoming.debian.org sid/contrib mipsel Packages [54.7 kB]
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 [44.6 kB]
-Get:4 http://incoming.debian.org Packages [720 kB]
+Get:13 http://incoming.debian.org sid/main TranslationIndex [2264 B]
+Get:14 http://incoming.debian.org Release [1604 B]
+Get:15 http://incoming.debian.org Sources [26.8 kB]
+Get:16 http://incoming.debian.org Packages [270 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 767 kB in 3s (206 kB/s)
+Fetched 25.5 MB in 55s (457 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -836,11 +832,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 0s (5078 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 0s (426 kB/s)
Download complete and in download only mode
Check arch
@@ -860,12 +856,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -874,146 +870,74 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.2)
+e2fsprogs: already installed (1.41.12-3)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-19)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 8.1.3
+libc6-dev: already installed (2.13-2)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
+debhelper: already installed (8.1.6 >= 8 is satisfied)
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following extra packages will be installed:
- file gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1 libunistring0
- libxml2 man-db ncurses-bin po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl
+ devscripts ncurses-doc
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- 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
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 12 not upgraded.
-Need to get 1193 kB/11.3 MB of archives.
-After this operation, 31.9 MB of additional disk space will be used.
-Get:1 http://debian.oregonstate.edu/debian/ sid/main ncurses-bin mipsel 5.9-1 [329 kB]
-Get:2 http://debian.oregonstate.edu/debian/ sid/main libncurses5 mipsel 5.9-1 [359 kB]
-Get:3 http://debian.oregonstate.edu/debian/ sid/main libncurses5-dev mipsel 5.9-1 [506 kB]
+ cdbs libncurses5-dev zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 1193 kB in 0s (7682 kB/s)
-(Reading database ... 10374 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_mipsel.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 10374 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_mipsel.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
-Selecting previously deselected package groff-base.
-(Reading database ... 10374 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-5_mipsel.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_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_8.12-3_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_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_2.28.4-1_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_8.1.3_all.deb) ...
+0 upgraded, 3 newly installed, 0 to remove and 20 not upgraded.
+Need to get 0 B/774 kB of archives.
+After this operation, 2384 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+(Reading database ... 12237 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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 groff-base (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
-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 (2.28.4-1) ...
-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 (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Processing triggers for man-db ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
-Package versions: apt_0.8.13.2 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.15.8.10 dpkg-dev_1.16.0 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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_2:1.02.63-3 libdpkg-perl_1.16.0 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_167-1 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_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-4
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-3 e2fsprogs_1.41.12-3 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtimedate-perl_1.2000-1 libudev0_168-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 module-init-tools_3.12-1 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 udev_168-1 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 │
@@ -1025,12 +949,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -1046,8 +970,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -1057,18 +981,18 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
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
@@ -1080,100 +1004,119 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1202,7 +1145,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -1233,6 +1176,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -1240,7 +1184,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1254,6 +1198,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -1265,7 +1210,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -1280,27 +1225,27 @@ 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_0.1.15-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.15-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1814
+Build finished at 20110519-0450
-samtools_0.1.15-1_mipsel.changes:
+samtools_0.1.16-1_mipsel.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -1308,40 +1253,40 @@ 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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- e8a2a36bd95a0cace6b5fb0668887ea0a57ad039 630590 samtools_0.1.15-1_mipsel.deb
- a4ef0498879bab0e622fd6ff0b2734c2ea9d2c78 185178 libbam-dev_0.1.15-1_mipsel.deb
+ b2148541e752f5aaccabada3bb2717e861d896cc 642924 samtools_0.1.16-1_mipsel.deb
+ fb651f8517cf3a151030cdfd03283bdf040f419c 200948 libbam-dev_0.1.16-1_mipsel.deb
Checksums-Sha256:
- 39dba8e0ce67feb495e581be4f491fe0bb43c5e7ba10400d57f447f3f5b8e8bc 630590 samtools_0.1.15-1_mipsel.deb
- be1db8a82299c4b8ac98d381c27aa983166bd5521bf8b16e8a5abbad848a2ee3 185178 libbam-dev_0.1.15-1_mipsel.deb
+ d14e7b7580a68da2f14a393e715ca8d3bab81830265b4052d3a59616be5843af 642924 samtools_0.1.16-1_mipsel.deb
+ 15428af9658f7601a743250beddf9012b150ade02b2339dbb53c6404dd51cae9 200948 libbam-dev_0.1.16-1_mipsel.deb
Files:
- a99f620ad1d711deed10c0ecd08e5179 630590 science optional samtools_0.1.15-1_mipsel.deb
- 0dfecb73c451d8002b5cf5d9201a842e 185178 libdevel optional libbam-dev_0.1.15-1_mipsel.deb
+ e7c7374c687aefca57d1ffdfc3e81f04 642924 science optional samtools_0.1.16-1_mipsel.deb
+ 2d7fe9dff0e0dc49ae911564a9a5a9cf 200948 libdevel optional libbam-dev_0.1.16-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_mipsel.deb
+samtools_0.1.16-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 630590 bytes: control archive= 1789 bytes.
+ size 642924 bytes: control archive= 1786 bytes.
787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1228
+ Installed-Size: 1216
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -1354,32 +1299,32 @@ samtools_0.1.15-1_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 18:13 ./
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./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 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./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 2011-04-12 18:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-05-19 04:49 ./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 2011-04-12 18:14 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-04-12 18:13 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-12 18:13 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-04-12 18:13 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-05-19 04:50 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-05-19 04:50 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 04:50 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2101 2011-05-19 04:50 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./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
@@ -1392,33 +1337,33 @@ drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 18:14 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/bin/
--rwxr-xr-x root/root 142088 2011-04-12 18:14 ./usr/bin/bcftools
--rwxr-xr-x root/root 30584 2011-04-12 18:14 ./usr/bin/razip
--rwxr-xr-x root/root 477880 2011-04-12 18:14 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/samtools/
--rwxr-xr-x root/root 19960 2011-04-12 18:14 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13268 2011-04-12 18:14 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9768 2011-04-12 18:14 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.15-1_mipsel.deb
+-rwxr-xr-x root/root 5778 2011-05-19 04:50 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/bin/
+-rwxr-xr-x root/root 146724 2011-05-19 04:50 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29136 2011-05-19 04:50 ./usr/bin/razip
+-rwxr-xr-x root/root 462692 2011-05-19 04:50 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18676 2011-05-19 04:50 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12512 2011-05-19 04:50 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9252 2011-05-19 04:50 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.16-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 185178 bytes: control archive= 894 bytes.
+ size 200948 bytes: control archive= 927 bytes.
675 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 472
+ Installed-Size: 500
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -1429,23 +1374,25 @@ libbam-dev_0.1.15-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
--rw-r--r-- root/root 320036 2011-04-12 18:14 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/include/
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./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
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
+-rw-r--r-- root/root 340310 2011-05-19 04:50 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1459,70 +1406,42 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ef7274bc-3984-429a-b457-5c8f9ccc646c/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-6a84821d-880a-40fd-b190-007198c56346/build/buildd-samtools_0.1.16-1-mipsel-fZSyln
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- 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, 0 newly installed, 19 to remove and 12 not upgraded.
-After this operation, 31.9 MB disk space will be freed.
-(Reading database ... 11702 files and directories currently installed.)
+ cdbs* libncurses5-dev* zlib1g-dev*
+0 upgraded, 0 newly installed, 3 to remove and 20 not upgraded.
+After this operation, 2384 kB disk space will be freed.
+(Reading database ... 12361 files and directories currently installed.)
Removing cdbs ...
-Removing debhelper ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10128
-Build-Time: 241
+Build-Space: 10972
+Build-Time: 283
Distribution: sid
-Install-Time: 53
-Job: samtools_0.1.15-1
+Install-Time: 34
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 326
-Source-Version: 0.1.15-1
-Space: 10128
+Package-Time: 409
+Source-Version: 0.1.16-1
+Space: 10972
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1814
-Build needed 00:05:26, 10128k disc space
+Finished at 20110519-0450
+Build needed 00:06:49, 10972k disc space
Signature with key '68D1B022' requested:
diff --git a/mipsel.log b/mipsel.log
index 3ed34d6..1db7756 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,65 +1,65 @@
-From buildd at mayer.debian.org Tue Apr 12 18:15:03 2011
+From buildd at mayer.debian.org Thu May 19 04:51:16 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 1Q9i7D-0002Va-BU
- for logs at buildd.debian.org; Tue, 12 Apr 2011 18:15:03 +0000
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1QMvCd-00009N-CD
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:51:16 +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 1Q9i78-000858-1k
- for logs at buildd.debian.org; Tue, 12 Apr 2011 18:14:59 +0000
+ (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
+ id 1QMvCb-0008RR-Qe
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:51:14 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>)
- id 1Q9i73-00020h-1Z; Tue, 12 Apr 2011 18:14:53 +0000
+ (envelope-from <buildd at mayer.debian.org>) id 1QMvCY-00052Y-48
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:51:10 +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_0.1.15-1 on mipsel (dist=sid)
+To: logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.16-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Q9i73-00020h-1Z at mayer.debian.org>
-Date: Tue, 12 Apr 2011 18:14:53 +0000
+Message-Id: <E1QMvCY-00052Y-48 at mayer.debian.org>
+Date: Thu, 19 May 2011 04:51:10 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (mipsel) 12 Apr 2011 18:09 ║
+║ samtools 0.1.16-1 (mipsel) 19 May 2011 04:44 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: mipsel
-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
+Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
+Get:2 http://incoming.debian.org sid InRelease [146 kB]
+Get:3 http://debian.oregonstate.edu sid/main Sources [5221 kB]
+Ign http://incoming.debian.org InRelease
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org sid/main Sources [5221 kB]
+Get:6 http://debian.oregonstate.edu sid/contrib Sources [49.8 kB]
+Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [7108 kB]
+Get:8 http://debian.oregonstate.edu sid/contrib mipsel Packages [54.7 kB]
Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
+Get:9 http://debian.oregonstate.edu sid/main TranslationIndex [2264 B]
Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://incoming.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
+Get:10 http://incoming.debian.org sid/contrib Sources [49.8 kB]
+Get:11 http://incoming.debian.org sid/main mipsel Packages [7108 kB]
+Get:12 http://incoming.debian.org sid/contrib mipsel Packages [54.7 kB]
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 [44.6 kB]
-Get:4 http://incoming.debian.org Packages [720 kB]
+Get:13 http://incoming.debian.org sid/main TranslationIndex [2264 B]
+Get:14 http://incoming.debian.org Release [1604 B]
+Get:15 http://incoming.debian.org Sources [26.8 kB]
+Get:16 http://incoming.debian.org Packages [270 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 767 kB in 3s (206 kB/s)
+Fetched 25.5 MB in 55s (457 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,11 +80,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://debian.oregonstate.edu/debian/ sid/main samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 0s (5078 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 0s (426 kB/s)
Download complete and in download only mode
Check arch
@@ -104,12 +104,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -118,146 +118,74 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.2)
+e2fsprogs: already installed (1.41.12-3)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-19)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 8.1.3
+libc6-dev: already installed (2.13-2)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
+debhelper: already installed (8.1.6 >= 8 is satisfied)
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following extra packages will be installed:
- file gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libncurses5 libpcre3 libpipeline1 libunistring0
- libxml2 man-db ncurses-bin po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl
+ devscripts ncurses-doc
Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ autotools-dev
The following NEW packages will be installed:
- 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
-The following packages will be upgraded:
- libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 12 not upgraded.
-Need to get 1193 kB/11.3 MB of archives.
-After this operation, 31.9 MB of additional disk space will be used.
-Get:1 http://debian.oregonstate.edu/debian/ sid/main ncurses-bin mipsel 5.9-1 [329 kB]
-Get:2 http://debian.oregonstate.edu/debian/ sid/main libncurses5 mipsel 5.9-1 [359 kB]
-Get:3 http://debian.oregonstate.edu/debian/ sid/main libncurses5-dev mipsel 5.9-1 [506 kB]
+ cdbs libncurses5-dev zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 1193 kB in 0s (7682 kB/s)
-(Reading database ... 10374 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_mipsel.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 10374 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_mipsel.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
-Selecting previously deselected package groff-base.
-(Reading database ... 10374 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-5_mipsel.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_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_8.12-3_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_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_2.28.4-1_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_8.1.3_all.deb) ...
+0 upgraded, 3 newly installed, 0 to remove and 20 not upgraded.
+Need to get 0 B/774 kB of archives.
+After this operation, 2384 kB of additional disk space will be used.
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+(Reading database ... 12237 files and directories currently installed.)
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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 groff-base (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
-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 (2.28.4-1) ...
-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 (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Processing triggers for man-db ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
-Package versions: apt_0.8.13.2 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.4.5-7 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.15.8.10 dpkg-dev_1.16.0 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-7 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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_2:1.02.63-3 libdpkg-perl_1.16.0 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_167-1 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_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-4
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-3 e2fsprogs_1.41.12-3 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtimedate-perl_1.2000-1 libudev0_168-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 module-init-tools_3.12-1 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 udev_168-1 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 │
@@ -269,12 +197,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -290,8 +218,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -301,18 +229,18 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
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
@@ -324,100 +252,119 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
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_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -446,7 +393,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -477,6 +424,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -484,7 +432,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -498,6 +446,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -509,7 +458,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-mipsel-3CHu3o/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -524,27 +473,27 @@ 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_0.1.15-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.15-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1814
+Build finished at 20110519-0450
-samtools_0.1.15-1_mipsel.changes:
+samtools_0.1.16-1_mipsel.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -552,40 +501,40 @@ 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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- e8a2a36bd95a0cace6b5fb0668887ea0a57ad039 630590 samtools_0.1.15-1_mipsel.deb
- a4ef0498879bab0e622fd6ff0b2734c2ea9d2c78 185178 libbam-dev_0.1.15-1_mipsel.deb
+ b2148541e752f5aaccabada3bb2717e861d896cc 642924 samtools_0.1.16-1_mipsel.deb
+ fb651f8517cf3a151030cdfd03283bdf040f419c 200948 libbam-dev_0.1.16-1_mipsel.deb
Checksums-Sha256:
- 39dba8e0ce67feb495e581be4f491fe0bb43c5e7ba10400d57f447f3f5b8e8bc 630590 samtools_0.1.15-1_mipsel.deb
- be1db8a82299c4b8ac98d381c27aa983166bd5521bf8b16e8a5abbad848a2ee3 185178 libbam-dev_0.1.15-1_mipsel.deb
+ d14e7b7580a68da2f14a393e715ca8d3bab81830265b4052d3a59616be5843af 642924 samtools_0.1.16-1_mipsel.deb
+ 15428af9658f7601a743250beddf9012b150ade02b2339dbb53c6404dd51cae9 200948 libbam-dev_0.1.16-1_mipsel.deb
Files:
- a99f620ad1d711deed10c0ecd08e5179 630590 science optional samtools_0.1.15-1_mipsel.deb
- 0dfecb73c451d8002b5cf5d9201a842e 185178 libdevel optional libbam-dev_0.1.15-1_mipsel.deb
+ e7c7374c687aefca57d1ffdfc3e81f04 642924 science optional samtools_0.1.16-1_mipsel.deb
+ 2d7fe9dff0e0dc49ae911564a9a5a9cf 200948 libdevel optional libbam-dev_0.1.16-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_mipsel.deb
+samtools_0.1.16-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 630590 bytes: control archive= 1789 bytes.
+ size 642924 bytes: control archive= 1786 bytes.
787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1228
+ Installed-Size: 1216
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -598,32 +547,32 @@ samtools_0.1.15-1_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 18:13 ./
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./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 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./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 2011-04-12 18:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-05-19 04:49 ./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 2011-04-12 18:14 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 18:13 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-04-12 18:13 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-12 18:13 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2005 2011-04-12 18:13 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-05-19 04:50 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-05-19 04:50 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 04:50 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2101 2011-05-19 04:50 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./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
@@ -636,33 +585,33 @@ drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 18:14 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/bin/
--rwxr-xr-x root/root 142088 2011-04-12 18:14 ./usr/bin/bcftools
--rwxr-xr-x root/root 30584 2011-04-12 18:14 ./usr/bin/razip
--rwxr-xr-x root/root 477880 2011-04-12 18:14 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/samtools/
--rwxr-xr-x root/root 19960 2011-04-12 18:14 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7764 2011-04-12 18:14 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13268 2011-04-12 18:14 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9768 2011-04-12 18:14 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.15-1_mipsel.deb
+-rwxr-xr-x root/root 5778 2011-05-19 04:50 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/bin/
+-rwxr-xr-x root/root 146724 2011-05-19 04:50 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29136 2011-05-19 04:50 ./usr/bin/razip
+-rwxr-xr-x root/root 462692 2011-05-19 04:50 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18676 2011-05-19 04:50 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12512 2011-05-19 04:50 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9252 2011-05-19 04:50 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.16-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 185178 bytes: control archive= 894 bytes.
+ size 200948 bytes: control archive= 927 bytes.
675 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 472
+ Installed-Size: 500
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -673,23 +622,25 @@ libbam-dev_0.1.15-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./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 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/lib/
--rw-r--r-- root/root 320036 2011-04-12 18:14 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 18:14 ./usr/include/
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./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
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
+-rw-r--r-- root/root 340310 2011-05-19 04:50 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -703,70 +654,42 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ef7274bc-3984-429a-b457-5c8f9ccc646c/build/buildd-samtools_0.1.15-1-mipsel-3CHu3o
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-6a84821d-880a-40fd-b190-007198c56346/build/buildd-samtools_0.1.16-1-mipsel-fZSyln
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- 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, 0 newly installed, 19 to remove and 12 not upgraded.
-After this operation, 31.9 MB disk space will be freed.
-(Reading database ... 11702 files and directories currently installed.)
+ cdbs* libncurses5-dev* zlib1g-dev*
+0 upgraded, 0 newly installed, 3 to remove and 20 not upgraded.
+After this operation, 2384 kB disk space will be freed.
+(Reading database ... 12361 files and directories currently installed.)
Removing cdbs ...
-Removing debhelper ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10128
-Build-Time: 241
+Build-Space: 10972
+Build-Time: 283
Distribution: sid
-Install-Time: 53
-Job: samtools_0.1.15-1
+Install-Time: 34
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 326
-Source-Version: 0.1.15-1
-Space: 10128
+Package-Time: 409
+Source-Version: 0.1.16-1
+Space: 10972
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1814
-Build needed 00:05:26, 10128k disc space
+Finished at 20110519-0450
+Build needed 00:06:49, 10972k disc space
Signature with key '68D1B022' requested:
diff --git a/powerpc.log b/powerpc.log
index 4b022d4..07ad9a4 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,69 @@
-From buildd at porpora.debian.org Tue Apr 12 11:35:48 2011
+From buildd at porpora.debian.org Thu May 19 04:45:08 2011
Return-path: <buildd at porpora.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at porpora.debian.org>)
- id 1Q9bsq-0007J9-85
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:35:48 +0000
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1QMv6i-0007Ia-2K
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:45:08 +0000
Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
helo=porpora.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at porpora.debian.org>)
- id 1Q9bsm-00050s-08; Tue, 12 Apr 2011 11:35:44 +0000
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1QMv6g-0003Gx-T0; Thu, 19 May 2011 04:45:07 +0000
Received: from buildd by porpora.debian.org with local (Exim 4.69)
(envelope-from <buildd at porpora.debian.org>)
- id 1Q9bsi-0003YH-RH; Tue, 12 Apr 2011 11:35:40 +0000
+ id 1QMv6f-00031W-QB; Thu, 19 May 2011 04:45:05 +0000
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Tue, 12 Apr 2011 11:35:40 +0000
+Date: Thu, 19 May 2011 04:45:05 +0000
From: buildd on porpora <buildd at porpora.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.15-1 on powerpc (dist=sid)
+Subject: Log for successful build of samtools_0.1.16-1 on powerpc (dist=sid)
Key-Id: CDFA0A89
-Message-Id: <E1Q9bsi-0003YH-RH at porpora.debian.org>
+Message-Id: <E1QMv6f-00031W-QB at porpora.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (powerpc) 12 Apr 2011 11:32 ║
+║ samtools 0.1.16-1 (powerpc) 19 May 2011 04:41 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [151 kB]
-Get:2 http://incoming.debian.org unstable InRelease [151 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5265 kB]
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://ftp.uk.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5221 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [48.2 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [97.4 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7058 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
-Get:11 http://incoming.debian.org unstable/main powerpc Packages [7058 kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [52.4 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5221 kB]
+Get:6 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
+Get:7 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
+Get:8 http://incoming.debian.org unstable/main powerpc Packages [7196 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib Sources [49.8 kB]
+Get:10 http://ftp.uk.debian.org unstable/non-free Sources [91.7 kB]
+Get:11 http://ftp.uk.debian.org unstable/main powerpc Packages [7196 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [54.0 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2264 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [52.4 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [54.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [49.7 kB]
-Get:18 http://incoming.debian.org Packages [772 kB]
+Get:17 http://incoming.debian.org Sources [26.8 kB]
+Get:18 http://incoming.debian.org Packages [270 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.2 MB in 28s (923 kB/s)
+Fetched 25.8 MB in 30s (836 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 1s (350 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (254 kB/s)
Download complete and in download only mode
Check arch
@@ -108,18 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl7 libppl-c2
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl7 libppl-c2
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -128,37 +122,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
+dpkg: already installed (1.16.0.2)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8-1)
-ncurses-bin: already installed (5.8-1)
-perl-base: already installed (5.10.1-18)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.5.2-4 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.5.2-4 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-2)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -167,95 +161,84 @@ Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl7 libppl-c2
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- bsdmainutils dpkg-dev file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdpkg-perl libglib2.0-0 libmagic1 libpcre3
- libpipeline1 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:
- wamerican wordlist whois vacation devscripts doc-base dh-make debian-keyring
- gettext-doc groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev libalgorithm-merge-perl curl wget lynx-cur autopoint
- libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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
-The following packages will be upgraded:
- dpkg-dev libdpkg-perl
-2 upgraded, 20 newly installed, 0 to remove and 15 not upgraded.
-Need to get 12.7 MB of archives.
-After this operation, 31.8 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 30 not upgraded.
+Need to get 9874 kB of archives.
+After this operation, 30.2 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 1.21-5 [1189 kB]
Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-1 [37.2 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.1-1 [1018 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:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-1 [1020 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5+b1 [240 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5+b1 [49.9 kB]
Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141 kB]
Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-3 [258 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-2 [849 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main dpkg-dev powerpc 1.16.0.1 [871 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libdpkg-perl powerpc 1.16.0.1 [748 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.4-1 [1601 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-3 [422 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian powerpc 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf powerpc 1.0.16+nmu1 [223 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main debhelper powerpc 8.1.3 [554 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main cdbs powerpc 0.4.92 [1268 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.8-1 [500 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-2+b1 [853 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.6-1 [1611 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-4 [422 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
+Get: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 8.1.6 [557 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-1 [489 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 12.7 MB in 8s (1421 kB/s)
+Fetched 9874 kB in 4s (2236 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10241 files and directories currently installed.)
+(Reading database ... 10599 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_1.21-5_powerpc.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_powerpc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_powerpc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_powerpc.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_powerpc.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_powerpc.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5_powerpc.deb) ...
+Unpacking file (from .../file_5.04-5+b1_powerpc.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_powerpc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_powerpc.deb) ...
-Preparing to replace dpkg-dev 1.15.8.10 (using .../dpkg-dev_1.16.0.1_powerpc.deb) ...
-Unpacking replacement dpkg-dev ...
-Preparing to replace libdpkg-perl 1.15.8.10 (using .../libdpkg-perl_1.16.0.1_powerpc.deb) ...
-Unpacking replacement libdpkg-perl ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_powerpc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_powerpc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_powerpc.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_powerpc.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_powerpc.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_powerpc.deb) ...
+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_powerpc.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.3_powerpc.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../cdbs_0.4.92_powerpc.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8-1_powerpc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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 (8.2.2) ...
@@ -263,39 +246,34 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up libdpkg-perl (1.16.0.1) ...
-Setting up dpkg-dev (1.16.0.1) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8-1) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
+Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl7 libppl-c2
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-2
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.5.2-4 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-4 g++-4.5_4.5.2-8 gcc_4:4.5.2-4 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8-1 libncurses5-dev_5.8-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c2_0.10.2-9 libppl-c4_0.11.2-3 libppl7_0.10.2-9 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 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_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8-1 ncurses-bin_5.8-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 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_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.51.20110421-3 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-6 gcc-4.6_4.6.0-6 libc6-dev_2.13-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 linux-libc-dev_2.6.38-4
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-2 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-2 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 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-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -307,12 +285,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -328,8 +306,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -339,18 +317,18 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
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
@@ -362,100 +340,119 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -468,8 +465,8 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samt
[samopen] SAM header is present: 2 sequences.
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq1...
+../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
@@ -484,9 +481,9 @@ 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_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/examples'
- fakeroot debian/rules binary-arch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
+ fakeroot debian/rules binary-arch
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -515,6 +512,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -522,7 +520,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -536,6 +534,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -547,7 +546,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-powerpc-cEIz0k/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -562,27 +561,27 @@ 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_0.1.15-1_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.15-1_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1135
+Build finished at 20110519-0445
-samtools_0.1.15-1_powerpc.changes:
+samtools_0.1.16-1_powerpc.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
@@ -590,40 +589,40 @@ 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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- a131f3d15c4a55537e1a1b782d31412a85f03ebc 609838 samtools_0.1.15-1_powerpc.deb
- b4c70804d95b277476351ef26cf1d6c83eceaec5 173522 libbam-dev_0.1.15-1_powerpc.deb
+ 1c7d432fb60c24c6443c3718c2b0e6d77b4ad398 613252 samtools_0.1.16-1_powerpc.deb
+ aacbba612655c0b569ddb33742ddbb8d3a5f2e38 177132 libbam-dev_0.1.16-1_powerpc.deb
Checksums-Sha256:
- fb1f28cd6f680e385afaa707b535ec6023013f3717f84d841af215ad859bd6c8 609838 samtools_0.1.15-1_powerpc.deb
- d8fae678d0ca71b94adaa13baf7bf17f05efe02ee348eb41c5b49d06f0792ff5 173522 libbam-dev_0.1.15-1_powerpc.deb
+ c16194d78bcd8e296cd82d9832c8b4ffdeaba33b977084aaf078be1ba8d4b6e9 613252 samtools_0.1.16-1_powerpc.deb
+ a91c00bca09d0d6d8ea3be5887fa73c8ca684305b9efa54d5a8394b1642f9492 177132 libbam-dev_0.1.16-1_powerpc.deb
Files:
- a5c5027cf691b194c741fdce56a9d158 609838 science optional samtools_0.1.15-1_powerpc.deb
- cb4fb89242d0277f45b11cf192e27c3e 173522 libdevel optional libbam-dev_0.1.15-1_powerpc.deb
+ f25d0ed9745876880cca6f83ac5cea13 613252 science optional samtools_0.1.16-1_powerpc.deb
+ 9e59cee60d51ce7c7dd8482c76164734 177132 libdevel optional libbam-dev_0.1.16-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_powerpc.deb
+samtools_0.1.16-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 609838 bytes: control archive= 1785 bytes.
+ size 613252 bytes: control archive= 1786 bytes.
788 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1120
+ Installed-Size: 1116
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -636,14 +635,14 @@ samtools_0.1.15-1_powerpc.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/bin/
--rwxr-xr-x root/root 116632 2011-04-12 11:35 ./usr/bin/bcftools
--rwxr-xr-x root/root 402604 2011-04-12 11:35 ./usr/bin/samtools
--rwxr-xr-x root/root 26824 2011-04-12 11:35 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/bin/
+-rwxr-xr-x root/root 123916 2011-05-19 04:44 ./usr/bin/bcftools
+-rwxr-xr-x root/root 392588 2011-05-19 04:44 ./usr/bin/samtools
+-rwxr-xr-x root/root 25280 2011-05-19 04:44 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/samtools/
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
@@ -651,56 +650,56 @@ drwxr-xr-x root/root 0 2011-04-12 11:35 ./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 5778 2011-04-12 11:35 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-05-19 04:44 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-04-12 11:35 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8393 2011-04-12 11:35 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-04-12 11:35 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/man/man1/
+-rw-r--r-- root/root 2101 2011-05-19 04:44 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8438 2011-05-19 04:44 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-05-19 04:44 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/samtools/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-04-12 11:35 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126609 2011-05-19 04:44 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2011-04-12 11:35 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/lib/samtools/
--rwxr-xr-x root/root 19668 2011-04-12 11:35 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7992 2011-04-12 11:35 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7384 2011-04-12 11:35 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7368 2011-04-12 11:35 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11148 2011-04-12 11:35 ./usr/lib/samtools/md5fa
-
-
-libbam-dev_0.1.15-1_powerpc.deb
+-rw-r--r-- root/root 1966 2011-05-19 04:44 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18908 2011-05-19 04:44 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7832 2011-05-19 04:44 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7112 2011-05-19 04:44 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7128 2011-05-19 04:44 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10956 2011-05-19 04:44 ./usr/lib/samtools/md5fa
+
+
+libbam-dev_0.1.16-1_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 173522 bytes: control archive= 896 bytes.
+ size 177132 bytes: control archive= 928 bytes.
676 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 428
+ Installed-Size: 436
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -711,23 +710,25 @@ libbam-dev_0.1.15-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./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 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/include/
--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
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-04-12 11:35 ./usr/lib/
--rw-r--r-- root/root 278472 2011-04-12 11:35 ./usr/lib/libbam.a
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/include/samtools/
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/lib/
+-rw-r--r-- root/root 278090 2011-05-19 04:44 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -741,7 +742,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-210a4603-30fd-4fa4-a922-fee45f8bbba1/build/buildd-samtools_0.1.15-1-powerpc-cEIz0k
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-a9ae3202-a878-453f-a305-b429f5998cfe/build/buildd-samtools_0.1.16-1-powerpc-stuaIj
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -749,18 +750,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 10328
-Build-Time: 88
+Build-Space: 10464
+Build-Time: 91
Distribution: sid
-Install-Time: 79
-Job: samtools_0.1.15-1
+Install-Time: 65
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 214
-Source-Version: 0.1.15-1
-Space: 10328
+Package-Time: 204
+Source-Version: 0.1.16-1
+Space: 10464
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1135
-Build needed 00:03:34, 10328k disc space
+Finished at 20110519-0445
+Build needed 00:03:24, 10464k disc space
Signature with key 'CDFA0A89' requested:
diff --git a/s390.log b/s390.log
index 0cc9798..781b402 100644
--- a/s390.log
+++ b/s390.log
@@ -1,69 +1,69 @@
-From buildd at zandonai.debian.org Tue Apr 12 11:33:03 2011
+From buildd at zandonai.debian.org Thu May 19 04:48:39 2011
Return-path: <buildd at zandonai.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
- id 1Q9bqB-0006gE-7j
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:33:03 +0000
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1QMvA7-0007lC-Cc
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:48:39 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1Q9bq4-0006BE-MW; Tue, 12 Apr 2011 11:32:56 +0000
+ id 1QMvA6-0008L4-F6; Thu, 19 May 2011 04:48:38 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.69)
(envelope-from <buildd at zandonai.debian.org>)
- id 1Q9bq4-0006MU-8O; Tue, 12 Apr 2011 11:32:56 +0000
+ id 1QMvA6-0000cf-1Z; Thu, 19 May 2011 04:48:38 +0000
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Tue, 12 Apr 2011 11:32:56 +0000
+Date: Thu, 19 May 2011 04:48:38 +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_0.1.15-1 on s390 (dist=sid)
+Subject: Log for successful build of samtools_0.1.16-1 on s390 (dist=sid)
Key-Id: 9BD94C88
-Message-Id: <E1Q9bq4-0006MU-8O at zandonai.debian.org>
+Message-Id: <E1QMvA6-0000cf-1Z at zandonai.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (s390) 12 Apr 2011 11:31 ║
+║ samtools 0.1.16-1 (s390) 19 May 2011 04:46 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: s390
-Get:1 http://ftp.de.debian.org unstable InRelease [151 kB]
-Get:2 http://incoming.debian.org unstable InRelease [151 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [5265 kB]
+Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5221 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [5265 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [48.2 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [97.4 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [6985 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [51.4 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5221 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [49.8 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [91.7 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7104 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [53.0 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2264 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [6985 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [51.4 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7104 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [53.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [49.7 kB]
-Get:18 http://incoming.debian.org Packages [772 kB]
+Get:17 http://incoming.debian.org Sources [26.8 kB]
+Get:18 http://incoming.debian.org Packages [270 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.0 MB in 26s (995 kB/s)
+Fetched 25.6 MB in 28s (894 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 1s (291 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (309 kB/s)
Download complete and in download only mode
Check arch
@@ -108,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 31 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 19 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 31 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,37 +122,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
+dpkg: already installed (1.16.0.2)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-18)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-2)
+gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -162,99 +162,81 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils dpkg-dev file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdpkg-perl libglib2.0-0 libmagic1 libncurses5
- libpcre3 libpipeline1 libunistring0 libxml2 man-db ncurses-bin 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:
- wamerican wordlist whois vacation devscripts doc-base dh-make debian-keyring
- gettext-doc groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev libalgorithm-merge-perl curl wget lynx-cur autopoint
- libglib2.0-data shared-mime-info libgpm2 xml-core libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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
-The following packages will be upgraded:
- dpkg-dev libdpkg-perl libncurses5 ncurses-bin
-4 upgraded, 20 newly installed, 0 to remove and 15 not upgraded.
-Need to get 13.5 MB of archives.
-After this operation, 31.3 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main ncurses-bin s390 5.9-1 [335 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main libncurses5 s390 5.9-1 [384 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.2 [208 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-5 [1158 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-1 [38.7 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.1-1 [1017 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main dpkg-dev s390 1.16.0.1 [871 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main libdpkg-perl s390 1.16.0.1 [748 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.4-1 [1635 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main intltool-debian s390 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main po-debconf s390 1.0.16+nmu1 [223 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main debhelper s390 8.1.3 [554 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main cdbs s390 0.4.92 [1268 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-1 [504 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+0 upgraded, 20 newly installed, 0 to remove and 31 not upgraded.
+Need to get 9943 kB of archives.
+After this operation, 29.8 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 1.21-5 [1158 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-1 [38.7 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-1 [1017 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5+b1 [243 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5+b1 [50.1 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2+b1 [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 2.28.6-1 [1639 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-4 [431 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
+Get: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 8.1.6 [557 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-1 [504 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 13.5 MB in 4s (3284 kB/s)
-(Reading database ... 10051 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_s390.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 10051 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_s390.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
+Fetched 9943 kB in 2s (3408 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10051 files and directories currently installed.)
+(Reading database ... 10521 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_1.21-5_s390.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_s390.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_s390.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_s390.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_s390.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_s390.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_s390.deb) ...
+Unpacking file (from .../file_5.04-5+b1_s390.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_s390.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_s390.deb) ...
-Preparing to replace dpkg-dev 1.15.8.10 (using .../dpkg-dev_1.16.0.1_s390.deb) ...
-Unpacking replacement dpkg-dev ...
-Preparing to replace libdpkg-perl 1.15.8.10 (using .../libdpkg-perl_1.16.0.1_s390.deb) ...
-Unpacking replacement libdpkg-perl ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_s390.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_s390.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_s390.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_s390.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_s390.deb) ...
+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_s390.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.3_s390.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_s390.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_s390.deb) ...
Selecting previously deselected package zlib1g-dev.
@@ -264,36 +246,34 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up libdpkg-perl (1.16.0.1) ...
-Setting up dpkg-dev (1.16.0.1) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 31 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.4.5-6 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-6 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 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_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 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_2011d-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.51.20110421-3 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-6 gcc-4.6_4.6.0-6 libc6-dev_2.13-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 linux-libc-dev_2.6.38-4
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-2 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-1 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -305,12 +285,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -326,8 +306,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -337,18 +317,18 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/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_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/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_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
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
@@ -360,100 +340,113 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/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_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/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_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
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_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -482,7 +475,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -513,6 +506,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
+dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -520,7 +514,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -534,6 +528,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -545,7 +540,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.15-1-s390-z4ZdUX/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -560,27 +555,27 @@ 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_0.1.15-1_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.15-1_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.16-1_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-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1132
+Build finished at 20110519-0448
-samtools_0.1.15-1_s390.changes:
+samtools_0.1.16-1_s390.changes:
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -588,40 +583,40 @@ 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: 625622 626044
Changes:
- samtools (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- 4569cbfe059200bc82c27c26ab2adb8a81d20a42 605506 samtools_0.1.15-1_s390.deb
- c43a525cb31adc080f47e21846a73e1fdf444913 175010 libbam-dev_0.1.15-1_s390.deb
+ df8a424feb4767c8f8be139a5ef1cf45f6ecf9f1 613906 samtools_0.1.16-1_s390.deb
+ a4e7768ad9256a7411bcd8bf108f157cf1f89e76 182110 libbam-dev_0.1.16-1_s390.deb
Checksums-Sha256:
- 5bf1d2d1648531dba4e5e6843cb03f9e596822572112b635d1ffebd51b61b970 605506 samtools_0.1.15-1_s390.deb
- 6cb6fad8ac76a1db1a9d1daabe53e8a8dadf97c0c403b3c9698db672bd39fb05 175010 libbam-dev_0.1.15-1_s390.deb
+ 8f30d44d923f05f8fa429c2487c66f3be1534c438d8bd5a47c6b14d7dc70f4ed 613906 samtools_0.1.16-1_s390.deb
+ 5f41a98c70792210f9f7dec900f912bbccf76b07285c6a0d950fe0689daf17f8 182110 libbam-dev_0.1.16-1_s390.deb
Files:
- bb385611e298b1af3c85f80a9c088053 605506 science optional samtools_0.1.15-1_s390.deb
- be0ace00cd33e2aee25ed5813333a3a9 175010 libdevel optional libbam-dev_0.1.15-1_s390.deb
+ 1b88ee56dd430f4819a74461705c3d0d 613906 science optional samtools_0.1.16-1_s390.deb
+ 69fba3e4b57503aa5674e8421bf43bbb 182110 libdevel optional libbam-dev_0.1.16-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_s390.deb
+samtools_0.1.16-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 605506 bytes: control archive= 1782 bytes.
+ size 613906 bytes: control archive= 1785 bytes.
785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1136
+ Installed-Size: 1176
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -634,26 +629,26 @@ samtools_0.1.15-1_s390.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/bin/
--rwxr-xr-x root/root 120940 2011-04-12 11:32 ./usr/bin/bcftools
--rwxr-xr-x root/root 415020 2011-04-12 11:32 ./usr/bin/samtools
--rwxr-xr-x root/root 27380 2011-04-12 11:32 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/samtools/
--rwxr-xr-x root/root 11324 2011-04-12 11:32 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7188 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7188 2011-04-12 11:32 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7932 2011-04-12 11:32 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 18564 2011-04-12 11:32 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/man/man1/
--rw-r--r-- root/root 8393 2011-04-12 11:32 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-04-12 11:32 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 2005 2011-04-12 11:32 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/bin/
+-rwxr-xr-x root/root 133484 2011-05-19 04:48 ./usr/bin/bcftools
+-rwxr-xr-x root/root 439612 2011-05-19 04:48 ./usr/bin/samtools
+-rwxr-xr-x root/root 27484 2011-05-19 04:48 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11548 2011-05-19 04:48 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7428 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7428 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8288 2011-05-19 04:48 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18748 2011-05-19 04:48 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/man1/
+-rw-r--r-- root/root 8438 2011-05-19 04:48 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-05-19 04:48 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 2101 2011-05-19 04:48 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/samtools/
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
@@ -663,42 +658,42 @@ drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/samtools/
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 11:32 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-05-19 04:48 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2011-04-12 10:33 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-04-12 10:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2011-04-12 11:32 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2011-05-19 04:48 ./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 1362 2011-04-12 10:45 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-04-12 11:32 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-05-19 04:48 ./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
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-libbam-dev_0.1.15-1_s390.deb
+libbam-dev_0.1.16-1_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 175010 bytes: control archive= 893 bytes.
+ size 182110 bytes: control archive= 926 bytes.
673 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 424
+ Installed-Size: 452
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -709,23 +704,25 @@ libbam-dev_0.1.15-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/include/
--rw-r--r-- root/root 24338 2011-04-10 22:33 ./usr/include/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/bgzf.h
--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
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/lib/
--rw-r--r-- root/root 271780 2011-04-12 11:32 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 11:32 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 9003 2011-04-10 22:33 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
+-rw-r--r-- root/root 292566 2011-05-19 04:48 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 1362 2011-04-12 10:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5287 2011-04-12 10:43 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -739,7 +736,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-7d8a126e-7575-4dc2-96d3-db399ee093db/build/buildd-samtools_0.1.15-1-s390-z4ZdUX
+Purging /var/lib/schroot/mount/sid-s390-sbuild-5b08dd2a-81c8-46b3-a4d9-7dab745e15f5/build/buildd-samtools_0.1.16-1-s390-i66oQB
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -747,18 +744,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 10024
-Build-Time: 44
+Build-Space: 11204
+Build-Time: 51
Distribution: sid
-Install-Time: 22
-Job: samtools_0.1.15-1
+Install-Time: 21
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 100
-Source-Version: 0.1.15-1
-Space: 10024
+Package-Time: 114
+Source-Version: 0.1.16-1
+Space: 11204
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1132
-Build needed 00:01:40, 10024k disc space
+Finished at 20110519-0448
+Build needed 00:01:54, 11204k disc space
Signature with key '9BD94C88' requested:
diff --git a/sparc.log b/sparc.log
index 4b42d8b..e719067 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,69 @@
-From buildd at schroeder.debian.org Tue Apr 12 11:36:14 2011
-Return-path: <buildd at schroeder.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at lebrun.debian.org Thu May 19 04:48:59 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=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
+ CN=kokkonen.debian.org,
+ EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at schroeder.debian.org>)
- id 1Q9btF-0007O4-Un
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:36:14 +0000
-Received: from schroeder.debian.org ([193.198.184.11])
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1QMvAR-0007oc-QR
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:48:59 +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=schroeder.debian.org,
- EMAIL=hostmaster at schroeder.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1Q9bt9-0006IP-CR
- for logs at buildd.debian.org; Tue, 12 Apr 2011 11:36:07 +0000
-Received: from buildd by schroeder.debian.org with local (Exim 4.69)
- (envelope-from <buildd at schroeder.debian.org>)
- id 1Q9bt9-00073q-29; Tue, 12 Apr 2011 11:36:07 +0000
+ CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1QMvAR-0008LP-0U
+ for logs at buildd.debian.org; Thu, 19 May 2011 04:48:59 +0000
+Received: from buildd by lebrun.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1QMvAQ-0007uq-78; Thu, 19 May 2011 04:48:58 +0000
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Tue, 12 Apr 2011 11:36:06 +0000
-From: buildd on schroeder <buildd at schroeder.debian.org>
-To: logs at buildd.debian.org,buildd-admin at schroeder.debian.org
-Subject: Log for attempted build of samtools_0.1.15-1 on sparc (dist=sid)
-Key-Id: 9BBB678A
-Message-Id: <E1Q9bt9-00073q-29 at schroeder.debian.org>
+Date: Thu, 19 May 2011 04:48:58 +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_0.1.16-1 on sparc (dist=sid)
+Key-Id: 81587D01
+Message-Id: <E1QMvAQ-0007uq-78 at lebrun.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (sparc) 12 Apr 2011 11:32 ║
+║ samtools 0.1.16-1 (sparc) 19 May 2011 04:45 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Architecture: sparc
-Get:1 http://ftp.carnet.hr unstable InRelease [151 kB]
-Get:2 http://incoming.debian.org unstable InRelease [151 kB]
-Get:3 http://ftp.carnet.hr unstable/main Sources [5265 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [5221 kB]
+Get:4 http://debian.carnet.hr unstable/contrib Sources [49.8 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://ftp.carnet.hr unstable/contrib Sources [48.2 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [5265 kB]
-Get:7 http://ftp.carnet.hr unstable/non-free Sources [97.4 kB]
-Get:8 http://ftp.carnet.hr unstable/main sparc Packages [7009 kB]
-Get:9 http://ftp.carnet.hr unstable/contrib sparc Packages [52.5 kB]
-Ign http://ftp.carnet.hr unstable/contrib TranslationIndex
-Get:10 http://ftp.carnet.hr unstable/main TranslationIndex [2264 B]
-Get:11 http://incoming.debian.org unstable/contrib Sources [48.2 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [97.4 kB]
-Get:13 http://incoming.debian.org unstable/main sparc Packages [7009 kB]
-Ign http://ftp.carnet.hr unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib sparc Packages [52.5 kB]
+Get:5 http://incoming.debian.org Release.gpg [836 B]
+Get:6 http://incoming.debian.org unstable/main Sources [5221 kB]
+Get:7 http://debian.carnet.hr unstable/non-free Sources [91.7 kB]
+Get:8 http://debian.carnet.hr unstable/main sparc Packages [7131 kB]
+Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [54.0 kB]
+Ign http://debian.carnet.hr unstable/contrib TranslationIndex
+Get:10 http://debian.carnet.hr unstable/main TranslationIndex [2264 B]
+Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
+Get:13 http://incoming.debian.org unstable/main sparc Packages [7131 kB]
+Ign http://debian.carnet.hr unstable/contrib Translation-en
+Get:14 http://incoming.debian.org unstable/contrib sparc Packages [54.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [49.7 kB]
-Get:18 http://incoming.debian.org Packages [772 kB]
+Get:17 http://incoming.debian.org Sources [26.8 kB]
+Get:18 http://incoming.debian.org Packages [270 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.1 MB in 27s (963 kB/s)
+Fetched 25.7 MB in 27s (923 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 383 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (tar) [374 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.15-1 (diff) [7005 B]
-Fetched 383 kB in 1s (279 kB/s)
+Need to get 389 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
+Fetched 389 kB in 1s (282 kB/s)
Download complete and in download only mode
Check arch
@@ -109,12 +108,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,38 +122,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.1)
+base-files: already installed (6.3)
base-passwd: already installed (3.5.22+b1)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
debianutils: already installed (3.4.4)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.10)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1+b2)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
-ncurses-base: already installed (5.8+20110307-1)
-ncurses-bin: already installed (5.8+20110307-1)
-perl-base: already installed (5.10.1-19)
+ncurses-base: already installed (5.9-1)
+ncurses-bin: already installed (5.9-1)
+perl-base: already installed (5.12.3-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.1)
-sysvinit: already installed (2.88dsf-13.1)
+sysvinit-utils: already installed (2.88dsf-13.2)
+sysvinit: already installed (2.88dsf-13.2)
tar: already installed (1.25-3)
bsdutils: already installed (1:2.17.2-9.1)
mount: already installed (2.17.2-9.1)
util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.11.2-11)
-libc6-dev-sparc64: already installed (2.11.2-11)
-gcc: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-6 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.10 >= 1.13.5 is satisfied)
+libc6-dev: already installed (2.13-4)
+libc6-dev-sparc64: already installed (2.13-4)
+gcc: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.1)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.3
+Using default version 8.1.6
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
@@ -164,99 +163,81 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils dpkg-dev file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libdpkg-perl libglib2.0-0 libmagic1 libncurses5
- libpcre3 libpipeline1 libunistring0 libxml2 man-db ncurses-bin 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:
- wamerican wordlist whois vacation devscripts doc-base dh-make debian-keyring
- gettext-doc groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev libalgorithm-merge-perl curl wget lynx-cur autopoint
- libglib2.0-data shared-mime-info libgpm2 xml-core libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
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
-The following packages will be upgraded:
- dpkg-dev libdpkg-perl libncurses5 ncurses-bin
-4 upgraded, 20 newly installed, 0 to remove and 10 not upgraded.
-Need to get 13.2 MB of archives.
-After this operation, 31.1 MB of additional disk space will be used.
-Get:1 http://ftp.carnet.hr/debian/ unstable/main ncurses-bin sparc 5.9-1 [333 kB]
-Get:2 http://ftp.carnet.hr/debian/ unstable/main libncurses5 sparc 5.9-1 [361 kB]
-Get:3 http://ftp.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.2 [205 kB]
-Get:4 http://ftp.carnet.hr/debian/ unstable/main groff-base sparc 1.21-5 [1152 kB]
-Get:5 http://ftp.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-1 [35.8 kB]
-Get:6 http://ftp.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.1-1 [1013 kB]
-Get:7 http://ftp.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5 [239 kB]
-Get:8 http://ftp.carnet.hr/debian/ unstable/main file sparc 5.04-5 [49.5 kB]
-Get:9 http://ftp.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
-Get:10 http://ftp.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
-Get:11 http://ftp.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-2 [840 kB]
-Get:12 http://ftp.carnet.hr/debian/ unstable/main dpkg-dev sparc 1.16.0.1 [871 kB]
-Get:13 http://ftp.carnet.hr/debian/ unstable/main libdpkg-perl sparc 1.16.0.1 [748 kB]
-Get:14 http://ftp.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:15 http://ftp.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.4-1 [1553 kB]
-Get:16 http://ftp.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:17 http://ftp.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-3 [424 kB]
-Get:18 http://ftp.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
-Get:19 http://ftp.carnet.hr/debian/ unstable/main intltool-debian sparc 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.carnet.hr/debian/ unstable/main po-debconf sparc 1.0.16+nmu1 [223 kB]
-Get:21 http://ftp.carnet.hr/debian/ unstable/main debhelper sparc 8.1.3 [554 kB]
-Get:22 http://ftp.carnet.hr/debian/ unstable/main cdbs sparc 0.4.92 [1268 kB]
-Get:23 http://ftp.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 kB]
-Get:24 http://ftp.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+0 upgraded, 20 newly installed, 0 to remove and 8 not upgraded.
+Need to get 9701 kB of archives.
+After this operation, 29.6 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 1.21-5 [1152 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-1 [35.8 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-1 [1013 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5+b1 [239 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main file sparc 5.04-5+b1 [49.6 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+b1 [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 2.28.6-1 [1556 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 0.9.3-4 [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 8.1.6 [557 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 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 13.2 MB in 9s (1387 kB/s)
-(Reading database ... 10348 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.8+20110307-1 (using .../ncurses-bin_5.9-1_sparc.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-1) ...
-(Reading database ... 10348 files and directories currently installed.)
-Preparing to replace libncurses5 5.8+20110307-1 (using .../libncurses5_5.9-1_sparc.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.9-1) ...
+Fetched 9701 kB in 7s (1231 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10348 files and directories currently installed.)
+(Reading database ... 10783 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_1.21-5_sparc.deb) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_sparc.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_sparc.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_sparc.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_sparc.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_sparc.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_sparc.deb) ...
+Unpacking file (from .../file_5.04-5+b1_sparc.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_sparc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_sparc.deb) ...
-Preparing to replace dpkg-dev 1.15.8.10 (using .../dpkg-dev_1.16.0.1_sparc.deb) ...
-Unpacking replacement dpkg-dev ...
-Preparing to replace libdpkg-perl 1.15.8.10 (using .../libdpkg-perl_1.16.0.1_sparc.deb) ...
-Unpacking replacement libdpkg-perl ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_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_2.28.4-1_sparc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_sparc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_sparc.deb) ...
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_sparc.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_sparc.deb) ...
+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_sparc.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.3_sparc.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_sparc.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_sparc.deb) ...
Selecting previously deselected package zlib1g-dev.
@@ -266,36 +247,34 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.21-5) ...
Setting up libpipeline1 (1.2.0-1) ...
-Setting up man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up libdpkg-perl (1.16.0.1) ...
-Setting up dpkg-dev (1.16.0.1) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-3) ...
+Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.16.0.1 g++-4.4_4.4.5-15 gcc-4.4_4.4.5-15 libc6-dev_2.11.2-11 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 linux-libc-dev_2.6.38-2
-Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.0.20110327-2 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_4:4.4.5-6 cpp-4.4_4.4.5-15 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b2 g++_4:4.4.5-6 g++-4.4_4.4.5-15 gcc_4:4.4.5-6 gcc-4.4_4.4.5-15 gcc-4.4-base_4.4.5-15 gcc-4.6-base_4.6.0-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2.1 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_1.16.0.1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.4-dev_4.4.5-15 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_2.6.38-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.6.0.1-1 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 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_2011e-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-3 gcc-4.4_4.4.6-3 libc6-dev_2.13-4 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 linux-libc-dev_2.6.38-5
+Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b2 g++_4:4.4.5-9 g++-4.4_4.4.6-3 gcc_4:4.4.5-9 gcc-4.4_4.4.6-3 gcc-4.4-base_4.4.6-3 gcc-4.6-base_4.6.0-7 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_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 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_2.13-4 libc-dev-bin_2.13-4 libc6_2.13-4 libc6-dev_2.13-4 libc6-dev-sparc64_2.13-4 libc6-sparc64_2.13-4 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.2-1 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -307,12 +286,12 @@ Unpack source
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:56:49 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Thu May 19 04:26:30 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_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.16-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.16
+dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
Check disc space
────────────────
@@ -328,8 +307,8 @@ dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.15-1
- dpkg-source --before-build samtools-0.1.15
+dpkg-buildpackage: source version 0.1.16-1
+ dpkg-source --before-build samtools-0.1.16
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
@@ -339,18 +318,18 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/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_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/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_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
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
@@ -362,113 +341,120 @@ Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/s
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_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-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. bedidx.c -o bedidx.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
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_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 -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -Wall -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 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -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 bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/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_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
+ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/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 -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/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 ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15/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_0.1.15-1-sparc-UFtlab/samtools-0.1.15/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[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+gcc -g -O2 -g -O2 -Wall -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 bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
+make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.15-1-sparc-UFtlab/samtools-0.1.15'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
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_0.1.15-1-sparc-UFtlab/samtools-0.1.15/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/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_0.1.15-1-sparc-UFtlab/samtools-0.1.15/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1136
+Build finished at 20110519-0448
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-739c441c-242d-42f5-ba20-68c6841adc6d/build/buildd-samtools_0.1.15-1-sparc-UFtlab
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-94375e8b-7bbf-4396-aa26-31919c6c5d18/build/buildd-samtools_0.1.16-1-sparc-psy34J
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -476,18 +462,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 5772
-Build-Time: 98
+Build-Space: 5924
+Build-Time: 102
Distribution: sid
Fail-Stage: build
-Install-Time: 80
-Job: samtools_0.1.15-1
+Install-Time: 66
+Job: samtools_0.1.16-1
Package: samtools
-Package-Time: 229
-Source-Version: 0.1.15-1
-Space: 5772
+Package-Time: 219
+Source-Version: 0.1.16-1
+Space: 5924
Status: attempted
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1136
-Build needed 00:03:49, 5772k disc space
+Finished at 20110519-0448
+Build needed 00:03:39, 5924k disc space
--
Processing of sequence alignments in SAM and BAM formats.
More information about the debian-med-commit
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