[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. meta/0.1.13-1-3-gbb0d984
Charles Plessy
plessy at debian.org
Tue Apr 12 11:02:30 UTC 2011
The following commit has been merged in the meta branch:
commit b1423bf5a410843efce61b31e45e02431b08879c
Author: Charles Plessy <plessy at debian.org>
Date: Tue Apr 12 19:52:05 2011 +0900
Collected build logs for version 0.1.14-1.
diff --git a/alpha.log b/alpha.log
index 4d6e0d9..c953805 100644
--- a/alpha.log
+++ b/alpha.log
@@ -1,63 +1,68 @@
-From buildd at goedel.debian.org Wed Mar 02 06:28:50 2011
-Return-path: <buildd at goedel.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at goetz.debian.org Tue Mar 29 05:05:38 2011
+Return-path: <buildd at goetz.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 goedel.debian.org>)
- id 1PufYI-0001wH-5y
- for logs at buildd.debian.org; Wed, 02 Mar 2011 06:28:50 +0000
-Received: from goedel.cst.com ([213.188.99.214] helo=goedel.debian.org)
+ (Exim 4.69) (envelope-from <buildd at goetz.debian.org>)
+ id 1Q4R7a-0003fE-4c
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:05:38 +0000
+Received: from goetz.debian.org ([193.62.202.26])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
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- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at goedel.debian.org>)
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-Received: from buildd by goedel.debian.org with local (Exim 4.69)
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-From: buildd at goedel.debian.org
+ CN=goetz.debian.org, EMAIL=hostmaster at goetz.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at goetz.debian.org>)
+ id 1Q4R7W-0003Zv-Oi; Tue, 29 Mar 2011 05:05:34 +0000
+Received: from buildd by goetz.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at goetz.debian.org>)
+ id 1Q4R7P-0003oI-FF; Tue, 29 Mar 2011 05:05:27 +0000
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
+Date: Tue, 29 Mar 2011 05:05:27 +0000
+From: buildd on goetz <buildd at goetz.debian.org>
To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on alpha (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1PufYD-0002or-90 at goedel.debian.org>
-Date: Wed, 02 Mar 2011 06:28:45 +0000
+Subject: Log for successful build of samtools_0.1.14-1 on alpha (dist=sid)
+Key-Id: C9E783F4
+Message-Id: <E1Q4R7P-0003oI-FF at goetz.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on goedel.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on goetz.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (alpha) 02 Mar 2011 06:17 ║
+║ samtools 0.1.14-1 (alpha) 29 Mar 2011 04:57 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: alpha
-Chroot Build Dir: /var/lib/schroot/mount/sid-alpha-sbuild-14927942-aadb-44e8-aa29-895355cebfe1/build/buildd-samtools_0.1.13-1-alpha-MDqSxB
-Start Time: 20110302-0617
-Hit http://ftp.de.debian.org sid InRelease
-Hit http://ftp.de.debian.org sid/main alpha Packages/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://ftp.uk.debian.org unstable InRelease [184 kB]
+Get:2 http://incoming.debian.org unstable InRelease [185 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5169 kB]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.de.debian.org sid/contrib alpha Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Hit http://ftp.de.debian.org sid/main TranslationIndex
-Ign http://ftp.de.debian.org sid/contrib Translation-en
-Get:1 http://incoming.debian.org Release.gpg [835 B]
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main alpha Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib alpha Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [19.5 kB]
-Get:4 http://incoming.debian.org Packages [373 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://ftp.uk.debian.org unstable/contrib Sources [47.0 kB]
+Get:6 http://ftp.uk.debian.org unstable/non-free Sources [99.0 kB]
+Get:7 http://incoming.debian.org unstable/main Sources [5142 kB]
+Get:8 http://ftp.uk.debian.org unstable/main alpha Packages [6845 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib alpha Packages [51.2 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2232 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:13 http://incoming.debian.org unstable/main alpha Packages [6854 kB]
+Get:14 http://incoming.debian.org unstable/contrib alpha Packages [51.1 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [30.5 kB]
+Get:18 http://incoming.debian.org Packages [608 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 395 kB in 7s (53.6 kB/s)
+Fetched 25.4 MB in 31s (795 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,30 +83,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 0s (441 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 1s (326 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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 (6.1)
+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)
+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 (5.10.1-17)
+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)
+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 (4:4.4.5-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-4 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -112,7 +166,7 @@ The following extra packages will be installed:
man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ 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
@@ -120,17 +174,38 @@ 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 16 not upgraded.
+Need to get 11.6 MB of archives.
+After this operation, 34.2 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils alpha 8.2.2 [215 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base alpha 1.21-5 [1183 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 alpha 1.2.0-1 [40.5 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db alpha 2.5.9-4 [1070 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 alpha 5.04-5 [243 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main file alpha 5.04-5 [50.2 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base alpha 0.18.1.1-3 [160 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 alpha 8.12-3 [285 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 alpha 2.7.8.dfsg-2 [901 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text alpha 1.3.2a-15 [111 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 alpha 2.28.2-1 [1676 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 alpha 0.6.2-1 [128 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 alpha 0.9.3-3 [447 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext alpha 0.18.1.1-3 [2218 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian alpha 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf alpha 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper alpha 8.1.2 [553 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs alpha 0.4.92 [1268 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev alpha 5.8+20110307-1 [573 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev alpha 1:1.2.3.4.dfsg-3 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/12.7 MB of archives.
-After this operation, 39.5 MB of additional disk space will be used.
+Fetched 11.6 MB in 1s (6632 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10132 files and directories currently installed.)
+(Reading database ... 10145 files and directories currently installed.)
Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_alpha.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-4_alpha.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_alpha.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_alpha.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_alpha.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_alpha.deb) ...
Selecting previously deselected package libmagic1.
@@ -146,7 +221,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_alpha.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_alpha.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_alpha.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_alpha.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_alpha.deb) ...
Selecting previously deselected package libunistring0.
@@ -154,22 +229,22 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_alpha.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_alpha.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_alpha.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_alpha.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_alpha.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_alpha.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_alpha.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_alpha.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_alpha.deb) ...
Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -178,7 +253,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
@@ -187,13 +262,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.26-2-alpha-generic alpha (alpha)
-Toolchain package versions: libc6.1-dev_2.11.2-13 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libstdc++6_4.5.2-4
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6.1_2.11.2-13 libc6.1-dev_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-bpo.5-alpha-generic alpha (alpha)
+Toolchain package versions: binutils_2.21.0.20110302-2 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-14 gcc-4.4_4.4.5-14 libc6.1-dev_2.11.2-13 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 linux-libc-dev_2.6.37-2
+Package versions: apt_0.8.12 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110302-2 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_4:4.4.5-4 cpp-4.4_4.4.5-14 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-4 g++-4.4_4.4.5-14 gcc_4:4.4.5-4 gcc-4.4_4.4.5-14 gcc-4.4-base_4.4.5-14 gcc-4.5-base_4.5.2-6 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-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6.1_2.11.2-13 libc6.1-dev_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-6 libgomp1_4.5.2-6 liblocale-gettext-perl_1.05-6 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_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 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 vim-common_2:7.3.035+hg~8fdc12103333-1 vim-tiny_2:7.3.035+hg~8fdc12103333-1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -203,14 +282,14 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
+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 Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -219,41 +298,50 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture alpha
- /usr/bin/fakeroot debian/rules clean
+ 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_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
rm -f debian/stamp-makefile-check
dh_clean
- debian/rules build
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+ debian/rules build
+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_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
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
@@ -272,9 +360,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/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
@@ -285,10 +374,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/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
@@ -307,24 +396,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/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
@@ -334,14 +423,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -363,16 +452,20 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtoo
[bam_rmdupse_core] 4666 / 6542 = 0.7132 in library 'ex1'
[bam_rmdupse_core] 1395 / 3271 = 0.4265 in library 'ex1b'
../samtools glfview ex1.glf | gzip > ex1.glfview.gz
-[mpileup] 1 samples in 1 input files
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[mpileup] 1 samples in 1 input files
<mpileup> Set max per-sample depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ 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
@@ -404,7 +497,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -429,7 +522,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-alpha-MDqSxB/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-alpha-wRNWnM/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -444,73 +537,66 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_alpha.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_alpha.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_alpha.deb'.
- dpkg-genchanges -B -mDebian Build Daemon <buildd_alpha-goedel at buildd.debian.org> >../samtools_0.1.13-1_alpha.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_alpha.deb'.
+ dpkg-genchanges -B -malpha Build Daemon (goetz) <buildd_alpha-goetz at buildd.debian.org> >../samtools_0.1.14-1_alpha.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0627
+Build finished at 20110329-0505
-samtools_0.1.13-1_alpha.changes:
+samtools_0.1.14-1_alpha.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: alpha
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
-Maintainer: Debian Build Daemon <buildd_alpha-goedel at buildd.debian.org>
+Maintainer: alpha Build Daemon (goetz) <buildd_alpha-goetz at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 8579ee901338d7a0837511a07aed429d848030d6 637112 samtools_0.1.13-1_alpha.deb
- 2ba7369eb96064e1e98b1e3613e5baf294a5fadd 193980 libbam-dev_0.1.13-1_alpha.deb
+ 2fb37a759d9625771e6f84b1abbd78a1d294d7b0 632344 samtools_0.1.14-1_alpha.deb
+ e0b4d734c63ee323ab1e52e305c09f80f068289a 196904 libbam-dev_0.1.14-1_alpha.deb
Checksums-Sha256:
- 53fc211136e32a8ac58788124909b45d9599b05815124343dfefb37642e0e90a 637112 samtools_0.1.13-1_alpha.deb
- f9c2453f5fdce4892c931421e982680885473de62a8d33dad8eb67fc76052704 193980 libbam-dev_0.1.13-1_alpha.deb
+ 34d3c69ddcd76b87aff55e72a9eec57b4dd9d02c6248de911627d9cd3c9d1c7c 632344 samtools_0.1.14-1_alpha.deb
+ 71e5a6a05da867b22d2345e5d1cdf115391a620cb556b036838b342667c5c1c9 196904 libbam-dev_0.1.14-1_alpha.deb
Files:
- 57b848558a0ce24df0daf637cc9aa6c6 637112 science optional samtools_0.1.13-1_alpha.deb
- a4d50dc064ac6b9a9ed244a1744a6ea1 193980 libdevel optional libbam-dev_0.1.13-1_alpha.deb
+ 1674299f87a3c486a866d6beae55fd00 632344 science optional samtools_0.1.14-1_alpha.deb
+ 5dfeffb84ad1be59b007dfd8edad7321 196904 libdevel optional libbam-dev_0.1.14-1_alpha.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_alpha.deb
+samtools_0.1.14-1_alpha.deb
───────────────────────────
new debian package, version 2.0.
- size 637112 bytes: control archive= 1786 bytes.
- 794 bytes, 16 lines control
+ size 632344 bytes: control archive= 1782 bytes.
+ 788 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: alpha
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1200
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1224
+ Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -522,71 +608,71 @@ samtools_0.1.13-1_alpha.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/lib/samtools/
+-rwxr-xr-x root/root 22296 2011-03-29 05:05 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 11136 2011-03-29 05:05 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 15320 2011-03-29 05:05 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9728 2011-03-29 05:05 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9728 2011-03-29 05:05 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/bin/
+-rwxr-xr-x root/root 31568 2011-03-29 05:05 ./usr/bin/razip
+-rwxr-xr-x root/root 466408 2011-03-29 05:05 ./usr/bin/samtools
+-rwxr-xr-x root/root 135704 2011-03-29 05:05 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2011-03-29 05:05 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 126609 2011-03-29 05:00 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-02 06:21 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-02 06:27 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-02 06:27 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-02 06:27 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 1229 2011-03-02 06:27 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-29 05:05 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 05:05 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 05:05 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/samtools/
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2011-03-29 05:05 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 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 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-03-02 06:27 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/bin/
--rwxr-xr-x root/root 127432 2011-03-02 06:27 ./usr/bin/bcftools
--rwxr-xr-x root/root 31568 2011-03-02 06:27 ./usr/bin/razip
--rwxr-xr-x root/root 460768 2011-03-02 06:27 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/lib/samtools/
--rwxr-xr-x root/root 22296 2011-03-02 06:27 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9728 2011-03-02 06:27 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9728 2011-03-02 06:27 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 15320 2011-03-02 06:27 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 11136 2011-03-02 06:27 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.13-1_alpha.deb
+
+
+libbam-dev_0.1.14-1_alpha.deb
─────────────────────────────
new debian package, version 2.0.
- size 193980 bytes: control archive= 895 bytes.
+ size 196904 bytes: control archive= 895 bytes.
674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: alpha
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 620
+ Installed-Size: 636
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -597,23 +683,23 @@ libbam-dev_0.1.13-1_alpha.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/lib/
--rw-r--r-- root/root 478092 2011-03-02 06:27 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/include/
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/lib/
+-rw-r--r-- root/root 488754 2011-03-29 05:05 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:05 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -622,40 +708,31 @@ drwxr-xr-x root/root 0 2011-03-02 06:27 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-alpha-sbuild-14927942-aadb-44e8-aa29-895355cebfe1/build/buildd-samtools_0.1.13-1-alpha-MDqSxB
-(Reading database ... 12577 files and directories currently installed.)
-Removing zlib1g-dev ...
-Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
-Removing libncurses5-dev ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing intltool-debian ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing gettext ...
-Removing file ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0627
-Build needed 00:09:54, 12028k disc space
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-alpha-sbuild-f18f663f-c406-41c6-a710-7390dff00879/build/buildd-samtools_0.1.14-1-alpha-wRNWnM
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: alpha
+Build-Space: 12244
+Build-Time: 366
+Distribution: sid
+Install-Time: 56
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 486
+Source-Version: 0.1.14-1
+Space: 12244
+Status: successful
+Version: 0.1.14-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110329-0505
+Build needed 00:08:06, 12244k disc space
+Signature with key 'C9E783F4' requested:
diff --git a/armel.log b/armel.log
index fde4879..65fc57d 100644
--- a/armel.log
+++ b/armel.log
@@ -1,4 +1,483 @@
-From buildd at arnold.debian.org Wed Mar 02 05:27:42 2011
+From buildd at ancina.debian.org Wed Mar 30 06:50:59 2011
+Return-path: <buildd at ancina.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 ancina.debian.org>)
+ id 1Q4pF4-0002Rl-TO
+ for logs at buildd.debian.org; Wed, 30 Mar 2011 06:50:59 +0000
+Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ 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 ancina.debian.org>)
+ id 1Q4pEz-0002Lq-3t
+ for logs at buildd.debian.org; Wed, 30 Mar 2011 06:50:53 +0000
+Received: from buildd by ancina.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at ancina.debian.org>)
+ id 1Q4pEt-0007o3-00; Wed, 30 Mar 2011 06:50:47 +0000
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
+Date: Wed, 30 Mar 2011 06:50:46 +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_0.1.14-1 on armel (dist=sid)
+Key-Id: A1EAA0BB
+Message-Id: <E1Q4pEt-0007o3-00 at ancina.debian.org>
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ancina.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 0.1.14-1 (armel) 30 Mar 2011 06:45 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.14-1
+Source Version: 0.1.14-1
+Architecture: armel
+Hit http://ftp.de.debian.org sid InRelease
+Hit http://incoming.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org Release.gpg
+Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
+Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
+Ign http://ftp.de.debian.org sid/contrib TranslationIndex
+Hit http://ftp.de.debian.org sid/main TranslationIndex
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/main armel Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
+Ign http://incoming.debian.org sid/contrib TranslationIndex
+Hit http://incoming.debian.org sid/main TranslationIndex
+Hit http://incoming.debian.org Release
+Ign http://ftp.de.debian.org sid/contrib Translation-en
+Get:1 http://incoming.debian.org Sources [47.6 kB]
+Get:2 http://incoming.debian.org Packages [546 kB]
+Ign http://incoming.debian.org sid/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 594 kB in 9s (59.6 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 379 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 0s (1039 kB/s)
+Download complete and in download only mode
+
+Check arch
+──────────
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 8 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.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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)
+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)
+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 (4:4.5.2-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-2 >= 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)
+debhelper: missing
+Using default version 8.1.2
+cdbs: missing
+libncurses5-dev: missing
+zlib1g-dev: missing
+Checking for dependency conflicts...
+Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ file gettext gettext-base groff-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
+Suggested packages:
+ devscripts doc-base 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 groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 18 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/10.2 MB of archives.
+After this operation, 28.4 MB of additional disk space will be used.
+Selecting previously deselected package groff-base.
+(Reading database ... 10908 files and directories currently installed.)
+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_2.5.9-4_armel.deb) ...
+Selecting previously deselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.04-5_armel.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../archives/file_5.04-5_armel.deb) ...
+Selecting previously deselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
+Selecting previously deselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_armel.deb) ...
+Selecting previously deselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
+Selecting previously deselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_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) ...
+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) ...
+Selecting previously deselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_armel.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.1.2_armel.deb) ...
+Selecting previously deselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.92_armel.deb) ...
+Selecting previously deselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_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 groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
+Setting up man-db (2.5.9-4) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up 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 (8.1.2) ...
+Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
+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 8 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.31-rc9 armel (armv5tel)
+Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-6 gcc-4.5_4.5.2-6 libc6-dev_2.11.2-13 libstdc++6_4.5.2-6 libstdc++6-4.5-dev_4.5.2-6 linux-libc-dev_2.6.38-1
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110322-1 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_4:4.5.2-3 cpp-4.5_4.5.2-6 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-2 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-2 g++-4.5_4.5.2-6 gawk_1:3.1.7.dfsg-5 gcc_4:4.5.2-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.5-14 gcc-4.5_4.5.2-6 gcc-4.5-base_4.5.2-6 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-13.1 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 libdevmapper1.02.1_2:1.02.63-2 libdpkg-perl_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgcrypt11_1.4.6-5 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 libgnutls26_2.10.5-1 libgomp1_4.5.2-6 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.3 libldap-2.4-2_2.4.23-7 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+20110307-1 libncurses5-dev_5.8+20110307-1 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 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-6 libstdc++6-4.5-dev_4.5.2-6 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 libudev0_166-1 libunistring0_0.9.3-3 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 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_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 netbase_4.45 nullmailer_1:1.04-1.2 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 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 tzdata_2011d-1 util-linux_2.17.2-9.1 wget_1.12-2.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+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 `~/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Tue Mar 29 04:36:06 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_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
+
+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 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
+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.
+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_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/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_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/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_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+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_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+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
+ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/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_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
+gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
+gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14/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_0.1.14-1-armel-rQGmWd/samtools-0.1.14/misc'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[1]: Nothing to be done for `lib'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-rQGmWd/samtools-0.1.14'
+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_0.1.14-1-armel-rQGmWd/samtools-0.1.14/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_0.1.14-1-armel-rQGmWd/samtools-0.1.14/examples'
+make: *** [debian/stamp-makefile-check] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20110330-0650
+FAILED [dpkg-buildpackage died]
+────────────────────────────────────────────────────────────────────────────────
+Purging /var/lib/schroot/mount/sid-armel-sbuild-dcfb9a37-2d85-45f3-b333-4887e86a90e9/build/buildd-samtools_0.1.14-1-armel-rQGmWd
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 8 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*
+ libpipeline1* libunistring0* libxml2* man-db* po-debconf* zlib1g-dev*
+0 upgraded, 0 newly installed, 18 to remove and 8 not upgraded.
+After this operation, 28.4 MB disk space will be freed.
+(Reading database ... 12222 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 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: armel
+Build-Space: 5972
+Build-Time: 253
+Distribution: sid
+Fail-Stage: build
+Install-Time: 29
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 302
+Source-Version: 0.1.14-1
+Space: 5972
+Status: attempted
+Version: 0.1.14-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110330-0650
+Build needed 00:05:02, 5972k disc space
+Signature with key 'A1EAA0BB' requested:
+From buildd at arnold.debian.org Sat Apr 02 02:07:08 2011
Return-path: <buildd at arnold.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,62 +485,62 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at arnold.debian.org>)
- id 1Pueb8-0002rP-JT
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:27:42 +0000
+ id 1Q5qF2-0001iw-B0
+ for logs at buildd.debian.org; Sat, 02 Apr 2011 02:07:08 +0000
Received: from arnold.islands.arm.com ([217.140.96.57] helo=arnold.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=arnold.debian.org, EMAIL=hostmaster at arnold.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at arnold.debian.org>)
- id 1Pueb6-0001G2-F6
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:27:40 +0000
+ id 1Q5qEt-0003Fn-En
+ for logs at buildd.debian.org; Sat, 02 Apr 2011 02:06:59 +0000
Received: from buildd by arnold.debian.org with local (Exim 4.69)
(envelope-from <buildd at arnold.debian.org>)
- id 1Pueaj-00059Z-Li; Wed, 02 Mar 2011 05:27:17 +0000
+ id 1Q5qEp-0005c1-Pi; Sat, 02 Apr 2011 02:06:55 +0000
From: buildd on arnold <buildd at arnold.debian.org>
To: buildd-porters at arnold.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.13-1 on armel (dist=sid)
+Subject: Log for attempted build of samtools_0.1.14-1 on armel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Pueaj-00059Z-Li at arnold.debian.org>
-Date: Wed, 02 Mar 2011 05:27:17 +0000
+Message-Id: <E1Q5qEp-0005c1-Pi at arnold.debian.org>
+Date: Sat, 02 Apr 2011 02:06:55 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on arnold.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on arnold.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (armel) 02 Mar 2011 05:21 ║
+║ samtools 0.1.14-1 (armel) 02 Apr 2011 01:59 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: armel
-Chroot Build Dir: /var/lib/schroot/mount/sid-armel-sbuild-c25d4e2a-8085-46ea-a3fe-2707dc746f1c/build/buildd-samtools_0.1.13-1-armel-m5S1Vn
-Start Time: 20110302-0521
-Get:1 http://ftp.uk.debian.org unstable Release.gpg [835 B]
-Ign http://ftp.uk.debian.org/debian/ unstable/contrib Translation-en
-Ign http://ftp.uk.debian.org/debian/ unstable/main Translation-en
-Get:2 http://ftp.uk.debian.org unstable Release [146 kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835 B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://incoming.debian.org Release.gpg [835 B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:5 http://incoming.debian.org unstable Release [146 kB]
-Get:6 http://ftp.uk.debian.org unstable/main Sources [4155 kB]
-Get:7 http://incoming.debian.org Release [1604 B]
-Get:8 http://incoming.debian.org unstable/main Sources [4156 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib Sources [38.5 kB]
-Get:10 http://ftp.uk.debian.org unstable/non-free Sources [82.8 kB]
-Get:11 http://ftp.uk.debian.org unstable/main armel Packages [6831 kB]
-Get:12 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
-Get:14 http://incoming.debian.org unstable/main armel Packages [6831 kB]
-Get:15 http://ftp.uk.debian.org unstable/contrib armel Packages [50.7 kB]
-Get:16 http://incoming.debian.org unstable/contrib armel Packages [50.7 kB]
-Get:17 http://incoming.debian.org Sources [19.2 kB]
-Get:18 http://incoming.debian.org Packages [373 kB]
-Fetched 23.0 MB in 51s (446 kB/s)
+Get:1 http://ftp.uk.debian.org unstable InRelease [186 kB]
+Get:2 http://incoming.debian.org unstable InRelease [186 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5195 kB]
+Ign http://incoming.debian.org InRelease
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org Release [1604 B]
+Get:6 http://incoming.debian.org unstable/main Sources [5195 kB]
+Get:7 http://ftp.uk.debian.org unstable/contrib Sources [48.7 kB]
+Get:8 http://ftp.uk.debian.org unstable/non-free Sources [98.4 kB]
+Get:9 http://ftp.uk.debian.org unstable/main armel Packages [6919 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [48.7 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [98.4 kB]
+Get:12 http://incoming.debian.org unstable/main armel Packages [6919 kB]
+Get:13 http://ftp.uk.debian.org unstable/contrib armel Packages [52.4 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:14 http://ftp.uk.debian.org unstable/main TranslationIndex [2232 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:15 http://incoming.debian.org unstable/contrib armel Packages [52.4 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:17 http://incoming.debian.org Sources [36.9 kB]
+Get:18 http://incoming.debian.org Packages [498 kB]
+Ign http://incoming.debian.org Translation-en
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 25.5 MB in 57s (446 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,30 +561,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (336 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 0s (2305 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.15-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 8 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.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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)
+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)
+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 (4:4.5.2-4 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -116,7 +644,7 @@ The following extra packages will be installed:
man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ 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
@@ -124,12 +652,12 @@ 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 35 not upgraded.
-Need to get 11.8 MB of archives.
-After this operation, 35.1 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 8 not upgraded.
+Need to get 10.6 MB of archives.
+After this operation, 29.6 MB of additional disk space will be used.
Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.2 [205 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-4 [1082 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.1.0-1 [33.7 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-5 [1077 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-1 [33.8 kB]
Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.5.9-4 [976 kB]
Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5 [237 kB]
Get:6 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5 [49.4 kB]
@@ -137,25 +665,25 @@ Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1
Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-3 [258 kB]
Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-2 [816 kB]
Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.1-1+b1 [1516 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.4-1 [1531 kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-3 [410 kB]
Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-3 [1981 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.7+20100313-5 [1607 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian armel 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf armel 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper armel 8.1.2 [553 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs armel 0.4.92 [1268 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.8+20110307-1 [473 kB]
Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.8 MB in 6s (1764 kB/s)
+Fetched 10.6 MB in 4s (2184 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10042 files and directories currently installed.)
+(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_1.21-4_armel.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_armel.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_armel.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_armel.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_armel.deb) ...
Selecting previously deselected package libmagic1.
@@ -171,7 +699,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_armel.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_armel.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
Selecting previously deselected package libunistring0.
@@ -179,22 +707,22 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_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_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_armel.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_armel.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_armel.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_armel.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_armel.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_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 (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -203,7 +731,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+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) ...
@@ -212,13 +740,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: apt_0.8.10.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sudo_1.7.4p4-6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011a-1 util-linux_2.17.2-9 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-2 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-6 gcc-4.5_4.5.2-6 libc6-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-6 linux-libc-dev_2.6.38-1
+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_4.5.2-6 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-4 g++-4.5_4.5.2-6 gcc_4:4.5.2-4 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-6 gcc-4.5-base_4.5.2-6 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_1.15.8.10 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_5.8+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 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_4.5.2-6 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 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_2.5.9-4 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_5.10.1-18 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -228,14 +760,14 @@ Package versions: apt_0.8.10.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
+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 Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -244,41 +776,50 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture armel
- /usr/bin/fakeroot debian/rules clean
+ 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_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
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_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
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
@@ -297,9 +838,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/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
@@ -310,10 +852,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/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
@@ -332,24 +874,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/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
@@ -359,30 +901,48 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/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_0.1.13-1-armel-m5S1Vn/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-armel-wkCxdP/samtools-0.1.14/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0527
+Build finished at 20110402-0206
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-c25d4e2a-8085-46ea-a3fe-2707dc746f1c/build/buildd-samtools_0.1.13-1-armel-m5S1Vn
-Not removing build depends: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-armel-sbuild-0e6c2ddd-c764-4d7f-b937-429869013d12/build/buildd-samtools_0.1.14-1-armel-wkCxdP
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: armel
+Build-Space: 5972
+Build-Time: 260
+Distribution: sid
+Fail-Stage: build
+Install-Time: 85
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 437
+Source-Version: 0.1.14-1
+Space: 5972
+Status: attempted
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0527
-Build needed 00:06:14, 5288k disc space
+Finished at 20110402-0206
+Build needed 00:07:17, 5972k disc space
diff --git a/hppa.log b/hppa.log
index 4b4df16..23b184b 100644
--- a/hppa.log
+++ b/hppa.log
@@ -1,71 +1,76 @@
-From buildd at penalosa.debian.org Wed Mar 02 09:37:27 2011
-Return-path: <buildd at penalosa.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at peri.debian.org Tue Mar 29 09:19:05 2011
+Return-path: <buildd at peri.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 penalosa.debian.org>)
- id 1PuiUo-0002eg-DL
- for logs at buildd.debian.org; Wed, 02 Mar 2011 09:37:26 +0000
-Received: from penalosa.debian.org ([192.25.206.68])
+ (Exim 4.69) (envelope-from <buildd at peri.debian.org>)
+ id 1Q4V4r-0001Zl-61
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 09:19:05 +0000
+Received: from peri.debian.org ([192.25.206.15])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=penalosa.debian.org,
- EMAIL=hostmaster at penalosa.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at penalosa.debian.org>)
- id 1PuiUk-0003uT-Di; Wed, 02 Mar 2011 09:37:23 +0000
-Received: from buildd by penalosa.debian.org with local (Exim 4.69)
- (envelope-from <buildd at penalosa.debian.org>)
- id 1PuiUe-0008Pe-Tn; Wed, 02 Mar 2011 09:37:17 +0000
-From: buildd on penalosa <buildd at penalosa.debian.org>
+ CN=peri.debian.org, EMAIL=hostmaster at peri.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.69) (envelope-from <buildd at peri.debian.org>)
+ id 1Q4V4n-0002w2-7c; Tue, 29 Mar 2011 09:19:01 +0000
+Received: from buildd by peri.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at peri.debian.org>)
+ id 1Q4V4j-00049P-54; Tue, 29 Mar 2011 09:18:57 +0000
+From: buildd on peri <buildd at peri.debian.org>
To: dannf+buildd at dannf.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on hppa (dist=sid)
+Subject: Log for successful build of samtools_0.1.14-1 on hppa (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PuiUe-0008Pe-Tn at penalosa.debian.org>
-Date: Wed, 02 Mar 2011 09:37:16 +0000
+Message-Id: <E1Q4V4j-00049P-54 at peri.debian.org>
+Date: Tue, 29 Mar 2011 09:18:57 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on penalosa.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on peri.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (hppa) 02 Mar 2011 09:33 ║
+║ samtools 0.1.14-1 (hppa) 29 Mar 2011 09:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: hppa
-Chroot Build Dir: /var/lib/schroot/mount/sid-hppa-sbuild-e02e2472-e461-4194-b7d0-5bc4f17318db/build/buildd-samtools_0.1.13-1-hppa-xspK0E
-Start Time: 20110302-0933
-Hit http://spohr.debian.org sid InRelease
-Hit http://spohr.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://spohr.debian.org sid InRelease [186 kB]
+Get:2 http://spohr.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:3 http://incoming.debian.org sid InRelease [186 kB]
Ign http://incoming.debian.org InRelease
Hit http://spohr.debian.org sid/contrib Sources/DiffIndex
-Hit http://spohr.debian.org sid/main hppa Packages/DiffIndex
-Hit http://spohr.debian.org sid/contrib hppa Packages/DiffIndex
+Get:4 http://spohr.debian.org sid/main hppa Packages/DiffIndex [2038 B]
+Get:5 http://spohr.debian.org sid/contrib hppa Packages/DiffIndex [2023 B]
Ign http://spohr.debian.org sid/contrib TranslationIndex
Hit http://spohr.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release.gpg
+Get:6 http://spohr.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://spohr.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
+Get:9 http://spohr.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
Ign http://spohr.debian.org sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
+Get:10 http://spohr.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
+Get:11 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main hppa Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib hppa Packages/DiffIndex
+Get:12 http://incoming.debian.org sid/main hppa Packages/DiffIndex [2038 B]
+Get:13 http://incoming.debian.org sid/contrib hppa Packages/DiffIndex [2023 B]
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Ign http://incoming.debian.org sid/main 2011-03-02-0827.59.pdiff
-Ign http://incoming.debian.org sid/contrib 2011-03-02-0827.59.pdiff
-Ign http://incoming.debian.org sid/main hppa 2011-03-02-0827.59.pdiff
-Hit http://incoming.debian.org sid/main
-Hit http://incoming.debian.org sid/contrib
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Hit http://incoming.debian.org sid/main hppa
+Get:14 http://incoming.debian.org Release [1604 B]
+Get:15 http://incoming.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
+Get:16 http://incoming.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
+Get:17 http://incoming.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
+Get:18 http://spohr.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
+Get:19 http://incoming.debian.org Sources [31.2 kB]
+Get:20 http://incoming.debian.org Packages [637 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
+Get:21 http://spohr.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
+Get:22 http://incoming.debian.org sid/main 2011-03-29-0818.12.pdiff [2203 B]
+Get:23 http://incoming.debian.org sid/main hppa 2011-03-29-0818.12.pdiff [4027 B]
+Get:24 http://incoming.debian.org sid/contrib hppa 2011-03-29-0818.12.pdiff [361 B]
+Fetched 1067 kB in 26s (40.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,58 +91,114 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (310 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://spohr.debian.org/debian/ sid/main samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://spohr.debian.org/debian/ sid/main samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://spohr.debian.org/debian/ sid/main samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 0s (5127 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.15-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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)
+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)
+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 (2.11.2-10)
+gcc: already installed (4:4.5.2-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-3 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
-libncurses5-dev: already installed (5.7+20100313-5)
+libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: debhelper cdbs zlib1g-dev
+Checking for dependency conflicts...
+Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- gettext gettext-base groff-base html2text intltool-debian libcroco3
- libglib2.0-0 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:
- devscripts doc-base dh-make gettext-doc groff less www-browser
- libmail-box-perl
+ wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
+ groff 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 gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libpcre3 libpipeline1 libunistring0 libxml2 man-db
- po-debconf zlib1g-dev
+ bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 16 newly installed, 0 to remove and 9 not upgraded.
-Need to get 0 B/10.3 MB of archives.
-After this operation, 27.1 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/11.4 MB of archives.
+After this operation, 31.6 MB of additional disk space will be used.
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10143 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_hppa.deb) ...
Selecting previously deselected package groff-base.
-(Reading database ... 11588 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-4_hppa.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_hppa.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_hppa.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_hppa.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_hppa.deb) ...
+Selecting previously deselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.04-5_hppa.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../archives/file_5.04-5_hppa.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hppa.deb) ...
Selecting previously deselected package libpcre3.
@@ -147,7 +208,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hppa.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_hppa.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_hppa.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_hppa.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hppa.deb) ...
Selecting previously deselected package libunistring0.
@@ -155,24 +216,31 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hppa.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_hppa.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_hppa.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_hppa.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_hppa.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Selecting previously deselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_hppa.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hppa.deb) ...
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up 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 (2.5.9-4) ...
Building database of manual pages ...
+Setting up libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+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) ...
@@ -181,12 +249,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.32-5-parisc64 hppa (parisc64)
-Toolchain package versions: libc6-dev_2.11.2-10 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: apt_0.8.11.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.48-5 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-10 libc-dev-bin_2.11.2-10 libc6_2.11.2-10 libc6-dev_2.11.2-10 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.48-5 libdpkg-perl_1.15.8.10 libextutils-parsexs-perl_2.220600-1 libgc1c2_1:6.8-1.2 libgcc4_4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmodule-build-perl_0.360700-1 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-6 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.2-1 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libreadline5_5.2-7 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4+b1 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_166-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 libyaml-perl_0.71-1 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-parisc hppa (parisc)
+Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 libc6-dev_2.11.2-10 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 linux-libc-dev_2.6.37-2
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 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_4:4.5.2-3 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-3 g++-4.5_4.5.2-7 gcc_4:4.5.2-3 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 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-13.1 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_2.11.2-10 libc-dev-bin_2.11.2-10 libc6_2.11.2-10 libc6-dev_2.11.2-10 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_1.15.8.10 libelfg0_0.8.13-1 libgcc4_4.5.2-7 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_4.5.2-7 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+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 libppl-c4_0.11.2-2 libppl9_0.11.2-2 libpwl5_0.11.2-2 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4+b1 libss2_1.41.12-2 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 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 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -196,14 +269,14 @@ Package versions: apt_0.8.11.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
+gpgv: keyblock resource `~/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -212,41 +285,50 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture hppa
- /usr/bin/fakeroot debian/rules clean
+ 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_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
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_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
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
@@ -265,9 +347,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/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
@@ -278,10 +361,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/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
@@ -300,24 +383,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/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
@@ -327,14 +410,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -363,9 +446,13 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ 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
@@ -397,7 +484,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -422,7 +509,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-hppa-xspK0E/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-hppa-LuAVpm/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -437,73 +524,66 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_hppa.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_hppa.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_hppa.deb'.
- dpkg-genchanges -B -mhppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd.debian.org> >../samtools_0.1.13-1_hppa.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_hppa.deb'.
+ dpkg-genchanges -B -mhppa Build Daemon (peri) <buildd_hppa-peri at buildd.debian.org> >../samtools_0.1.14-1_hppa.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0936
+Build finished at 20110329-0918
-samtools_0.1.13-1_hppa.changes:
+samtools_0.1.14-1_hppa.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hppa
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
-Maintainer: hppa Build Daemon (penalosa) <buildd_hppa-penalosa at buildd.debian.org>
+Maintainer: hppa Build Daemon (peri) <buildd_hppa-peri at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- cb9201266b913e4ed094a286e11982576b85ed97 590730 samtools_0.1.13-1_hppa.deb
- d3d9d98576fcfec2c090f56df2adfada8defe0fa 171726 libbam-dev_0.1.13-1_hppa.deb
+ 124dd3e62f424d74082f970406e253d42366db4d 610592 samtools_0.1.14-1_hppa.deb
+ c4bacf0729abff07775a5cc8cc4d2d5a8ac8c952 176994 libbam-dev_0.1.14-1_hppa.deb
Checksums-Sha256:
- 1f4630f35ed5ab5a470009d5a4b4f487a7298f5112afb71aa60a2daf4b31745f 590730 samtools_0.1.13-1_hppa.deb
- 2e98a5cc4ef84cb8d43b9fcb24c97e7e4b23ec37a5210f33332fce0783bfce3a 171726 libbam-dev_0.1.13-1_hppa.deb
+ b50a3deb9524928b432f67f947204c2054e157f41225dd6479e3712fafa695bb 610592 samtools_0.1.14-1_hppa.deb
+ e9cbfc41cc47f3a4bb943b300b656f4c12bb08c37d6309cb212fd3829e08fc65 176994 libbam-dev_0.1.14-1_hppa.deb
Files:
- 7a357d381c941ea9f318b88749ec858f 590730 science optional samtools_0.1.13-1_hppa.deb
- 0de29d01bb923a4a125b4dc3e43d9e5c 171726 libdevel optional libbam-dev_0.1.13-1_hppa.deb
+ af9de90faf88c403f44d59ba1404ec3b 610592 science optional samtools_0.1.14-1_hppa.deb
+ 49146b2f8ac2ea23a7390c154de5ae6a 176994 libdevel optional libbam-dev_0.1.14-1_hppa.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_hppa.deb
+samtools_0.1.14-1_hppa.deb
──────────────────────────
new debian package, version 2.0.
- size 590730 bytes: control archive= 1783 bytes.
- 792 bytes, 16 lines control
+ size 610592 bytes: control archive= 1789 bytes.
+ 786 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: hppa
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1076
- Depends: libc6 (>= 2.11), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1132
+ Depends: libc6 (>= 2.11), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -515,71 +595,71 @@ samtools_0.1.13-1_hppa.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/bin/
--rwxr-xr-x root/root 104028 2011-03-02 09:36 ./usr/bin/bcftools
--rwxr-xr-x root/root 380924 2011-03-02 09:36 ./usr/bin/samtools
--rwxr-xr-x root/root 26564 2011-03-02 09:36 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/lib/samtools/
--rwxr-xr-x root/root 11744 2011-03-02 09:36 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7880 2011-03-02 09:36 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 18492 2011-03-02 09:36 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8744 2011-03-02 09:36 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7880 2011-03-02 09:36 ./usr/lib/samtools/maq2sam-short
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2011-03-02 09:36 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2011-03-02 09:36 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/man/man1/
--rw-r--r-- root/root 1229 2011-03-02 09:36 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-03-02 09:36 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-02 09:36 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2011-03-02 09:36 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/samtools/
-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 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 5778 2011-03-29 09:18 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-
-
-libbam-dev_0.1.13-1_hppa.deb
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-03-29 09:18 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 09:18 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-29 09:18 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 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 126609 2011-03-29 09:17 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1966 2011-03-29 09:18 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/bin/
+-rwxr-xr-x root/root 398484 2011-03-29 09:18 ./usr/bin/samtools
+-rwxr-xr-x root/root 114496 2011-03-29 09:18 ./usr/bin/bcftools
+-rwxr-xr-x root/root 26928 2011-03-29 09:18 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/lib/samtools/
+-rwxr-xr-x root/root 22684 2011-03-29 09:18 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9932 2011-03-29 09:18 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 10072 2011-03-29 09:18 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10072 2011-03-29 09:18 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 14100 2011-03-29 09:18 ./usr/lib/samtools/md5fa
+
+
+libbam-dev_0.1.14-1_hppa.deb
────────────────────────────
new debian package, version 2.0.
- size 171726 bytes: control archive= 894 bytes.
+ size 176994 bytes: control archive= 899 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: hppa
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 420
+ Installed-Size: 436
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -590,23 +670,23 @@ libbam-dev_0.1.13-1_hppa.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/include/
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/lib/
--rw-r--r-- root/root 271240 2011-03-02 09:36 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/include/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-03-29 09:18 ./usr/lib/
+-rw-r--r-- root/root 286382 2011-03-29 09:18 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -615,34 +695,76 @@ drwxr-xr-x root/root 0 2011-03-02 09:36 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-hppa-sbuild-e02e2472-e461-4194-b7d0-5bc4f17318db/build/buildd-samtools_0.1.13-1-hppa-xspK0E
-(Reading database ... 12843 files and directories currently installed.)
-Removing zlib1g-dev ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-hppa-sbuild-03c9b932-c06f-434d-911e-297794d47a06/build/buildd-samtools_0.1.14-1-hppa-LuAVpm
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ bsdmainutils* cdbs* debhelper* 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 0 not upgraded.
+After this operation, 31.6 MB disk space will be freed.
+(Reading database ... 11580 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
-Removing po-debconf ...
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 gettext ...
Removing html2text ...
Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
+Removing 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: hppa
+Build-Space: 10284
+Build-Time: 171
+Distribution: sid
+Install-Time: 46
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 265
+Source-Version: 0.1.14-1
+Space: 10284
+Status: successful
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0936
-Build needed 00:03:48, 9412k disc space
+Finished at 20110329-0918
+Build needed 00:04:25, 10284k disc space
diff --git a/hurd-i386.log b/hurd-i386.log
index 7d4891c..215e39f 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,65 +1,67 @@
-From buildd at rossini.debian.net Sun Mar 06 06:00:11 2011
-Return-path: <buildd at rossini.debian.net>
-Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
+From buildd at mozart.debian.net Tue Mar 29 12:10:36 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 1Pw70k-0002lI-He
- for logs at buildd.debian.org; Sun, 06 Mar 2011 06:00:10 +0000
-Received: from hurd.ethz.ch ([192.33.98.55] helo=rossini.debian.net)
- by io.debian.net with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
- id 1Pw70f-000DSP-EB; Sun, 06 Mar 2011 07:00:05 +0100
-Received: from buildd by rossini.debian.net with local (Exim 4.72)
- (envelope-from <buildd at rossini.debian.net>)
- id 1Pw70f-0002ks-1O; Sun, 06 Mar 2011 06:00:05 +0000
-Date: Sun, 06 Mar 2011 06:00:05 +0000
-Message-Id: <E1Pw70f-0002ks-1O at rossini.debian.net>
-From: Build Daemon <buildd at rossini.debian.net>
-To: samuel.thibault at labri.fr, mbanck at debian.org, logs at debian-ports.org,
+ (Exim 4.69) (envelope-from <buildd at mozart.debian.net>)
+ id 1Q4Xko-0006zs-I2
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 12:10:35 +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 1Q4Xki-0002jX-8f; Tue, 29 Mar 2011 13:10:28 +0100
+Received: from buildd by mozart.debian.net with local (Exim 4.72)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1Q4Xki-0002yz-AA; Tue, 29 Mar 2011 12:10:28 +0000
+Date: Tue, 29 Mar 2011 12:10:28 +0000
+Message-Id: <E1Q4Xki-0002yz-AA at mozart.debian.net>
+From: Build Daemon <buildd at mozart.debian.net>
+To: samuel.thibault at labri.fr, mbanck at gmx.net, logs at debian-ports.org,
logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for attempted build of samtools_0.1.13-1 on hurd-i386 (dist=sid)
+Subject: Log for successful build of samtools_0.1.14-1 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 0.1.13-1 (hurd-i386) 06 Mar 2011 05:56 ║
+║ samtools 0.1.14-1 (hurd-i386) 29 mars 2011 12:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-gNFKIo
-Start Time: 20110306-0556
+Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE
+Start Time: 20110329-1205
Ign file: ./ InRelease
Ign file: ./ Release.gpg
Ign file: ./ Release
Ign file: ./ Translation-en
Ign http://ftp.debian-ports.org unreleased InRelease
-Hit http://ftp.fr.debian.org unstable InRelease
-Hit http://ftp.fr.debian.org experimental InRelease
Hit http://ftp.debian-ports.org unreleased Release.gpg
-Ign http://incoming.debian.org InRelease
Hit http://ftp.debian-ports.org unreleased Release
-Get:1 http://incoming.debian.org Release.gpg [835 B]
-Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid InRelease
+Ign http://incoming.debian.org InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
+Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
+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
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Hit http://ftp.fr.debian.org unstable/main TranslationIndex
-Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
-Get:3 http://incoming.debian.org Sources [36.0 kB]
+Get:3 http://incoming.debian.org Sources [35.0 kB]
Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Get:4 http://incoming.debian.org Packages [200 kB]
+Get:4 http://incoming.debian.org Packages [643 kB]
+Ign http://ftp.uk.debian.org sid/contrib Translation-en
+Ign http://ftp.uk.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 239 kB in 1min 4s (3715 B/s)
+Fetched 680 kB in 47s (14.3 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,11 +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 374 kB of source archives.
-Get:1 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (325 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://ftp.uk.debian.org/debian/ sid/main samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://ftp.uk.debian.org/debian/ sid/main samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://ftp.uk.debian.org/debian/ sid/main samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 0s (1051 kB/s)
Download complete and in download only mode
Check arch
@@ -98,97 +100,43 @@ Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
└──────────────────────────────────────────────────────────────────────────────┘
Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.1.2
+debhelper: already installed (8.1.2 >= 8 is satisfied)
cdbs: missing
libncurses5-dev: missing
-zlib1g-dev: missing
+zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
Checking for source dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
+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:
- libident liblzo2-2
+ libboost-iostreams1.42.0 libusb-0.1-4p
Use 'apt-get autoremove' to remove them.
-The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libexpat1
- libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
Suggested packages:
- devscripts doc-base dh-make gettext-doc libmail-box-perl
+ devscripts doc-base 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
-0 upgraded, 16 newly installed, 0 to remove and 20 not upgraded.
-Need to get 0 B/9452 kB of archives.
-After this operation, 28.8 MB of additional disk space will be used.
+ cdbs libncurses5-dev
+0 upgraded, 2 newly installed, 0 to remove and 67 not upgraded.
+Need to get 0 B/1733 kB of archives.
+After this operation, 3084 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3
- libexpat1 libunistring0 gettext intltool-debian po-debconf debhelper cdbs
- libncurses5-dev zlib1g-dev
+ cdbs libncurses5-dev
Authentication warning overridden.
-Selecting previously deselected package libmagic1.
-(Reading database ... 11608 files and directories currently installed.)
-Unpacking libmagic1 (from .../libmagic1_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hurd-i386.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_hurd-i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
-Selecting previously deselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hurd-i386.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
+(Reading database ... 14520 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_hurd-i386.deb) ...
Processing triggers for man-db ...
-Processing triggers for install-info ...
-Setting up libmagic1 (5.03-5+b1) ...
-Setting up file (5.03-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libexpat1 (2.0.1-7) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5+b1) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.15.8.10 hurd-dev_20110303-1~0 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
-Package versions: adduser_3.112+nmu2 apt_0.8.11.5+b1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.6-2 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15+b1 hurd_20110303-1~0 hurd-dev_20110303-1~0 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.1 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.3-1+hurd.1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libident_0.22-3 libidn11_1.20-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 liblzo2-2_2.04-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5+b1 libncurses5-dev_5.7+20100313-5+b1 libncursesw5_5.7+20100313-5+b1 libnewt0.52_0.52.11-2 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.2-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsasl2-modules_2.1.23.dfsg1-7 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-8 libxml2_2.7.8.dfsg-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5+b1 netbase_4.45 netcat-traditional_1.10-39 openssl_0.9.8o-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-2 tzdata_2011a-1 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.15.8.10 hurd-dev_20110303-1~1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.21.0.20110302-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
+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_2.21.0.20110302-2 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-4 cpp-4.4_4.4.5-10 cron_3.0pl1-115 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.1.2 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_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.1 fontconfig-config_2.8.0-2.1 g++_4:4.4.4-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-4 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_4.4.5-10 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 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-iostreams1.42.0_1.42.0-4+b1 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 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdigest-sha1-perl_2.13-1 libdpkg-perl_1.15.8.10 libept-dev_1.0.3+b2 libept1_1.0.3+b2 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.1 libfreetype6_2.4.4-1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgfortran3_4.4.5-10 libglib2.0-0_2.28.2-1 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_4.4.5-10 libgpg-error0_1.10-0.3 libidn11_1.20-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.03-5+b1 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 libncursesw5_5.8+20110307-1 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.2-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 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_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-10 libtagcoll2-dev_2.0.11-1.1 libtasn1-3_2.9-2 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 libwibble-dev_0.1.26-1 libwrap0_7.6.dbs-8 libxapian-dev_1.2.3-2 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2 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_5.8+20110307-1 netbase_4.42 netcat-traditional_1.10-38 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 pkg-config_0.25-1 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 random-egd_0.5-0+hurd.1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-dejavu-core_2.31-1 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -200,261 +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 Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-/usr/sbin/chroot: failed to run command `/bin/su': Computer bought the farm
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110306-0559
-FAILED [dpkg-buildpackage died]
-────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-gNFKIo
-(Reading database ... 13552 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing zlib1g-dev ...
-Removing cdbs ...
-Removing debhelper ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing file ...
-Purging configuration files for file ...
-Removing libexpat1 ...
-Purging configuration files for libexpat1 ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Processing triggers for man-db ...
-Processing triggers for install-info ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110306-0559
-Build needed 00:03:24, 1576k disc space
-
-From buildd at rossini.debian.net Wed Mar 09 11:43:32 2011
-Return-path: <buildd at rossini.debian.net>
-Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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- id 1PxHnf-0007Qh-OJ; Wed, 09 Mar 2011 11:43:31 +0000
-Date: Wed, 09 Mar 2011 11:43:31 +0000
-Message-Id: <E1PxHnf-0007Qh-OJ at rossini.debian.net>
-From: Build Daemon <buildd at rossini.debian.net>
-To: samuel.thibault at labri.fr, mbanck at debian.org, logs at debian-ports.org,
- logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on hurd-i386 (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on rossini.debian.net
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (hurd-i386) 09 Mar 2011 11:32 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.13-1
-Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn
-Start Time: 20110309-1132
-Ign file: ./ InRelease
-Ign file: ./ Release.gpg
-Ign file: ./ Release
-Ign file: ./ Translation-en
-Ign http://ftp.debian-ports.org unreleased InRelease
-Hit http://ftp.fr.debian.org unstable InRelease
-Hit http://ftp.fr.debian.org experimental InRelease
-Hit http://ftp.debian-ports.org unreleased Release.gpg
-Ign http://incoming.debian.org InRelease
-Hit http://ftp.debian-ports.org unreleased Release
-Hit http://incoming.debian.org Release.gpg
-Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
-Hit http://incoming.debian.org Release
-Hit http://ftp.fr.debian.org unstable/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/non-free Sources/DiffIndex
-Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.fr.debian.org unstable/main TranslationIndex
-Hit http://ftp.fr.debian.org experimental/main Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/contrib Sources/DiffIndex
-Hit http://ftp.fr.debian.org experimental/non-free Sources/DiffIndex
-Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
-Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org Translation-en
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://ftp.fr.debian.org/debian/ unstable/main samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (279 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Checking for already installed source dependencies...
-debhelper: missing
-Using default version 8.1.2
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for source dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libexpat1
- libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf
-Suggested packages:
- devscripts doc-base dh-make gettext-doc ncurses-doc libmail-box-perl
-Recommended packages:
- autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
-The following NEW packages will be installed:
- cdbs debhelper file gettext gettext-base html2text intltool-debian libcroco3
- libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2
- po-debconf zlib1g-dev
-0 upgraded, 16 newly installed, 0 to remove and 25 not upgraded.
-Need to get 0 B/8347 kB of archives.
-After this operation, 23.5 MB of additional disk space will be used.
-WARNING: The following packages cannot be authenticated!
- libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3
- libexpat1 libunistring0 gettext intltool-debian po-debconf debhelper cdbs
- libncurses5-dev zlib1g-dev
-Authentication warning overridden.
-Selecting previously deselected package libmagic1.
-(Reading database ... 11608 files and directories currently installed.)
-Unpacking libmagic1 (from .../libmagic1_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.03-5+b1_hurd-i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_hurd-i386.deb) ...
-Selecting previously deselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_hurd-i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_hurd-i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
-Selecting previously deselected package libexpat1.
-Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_hurd-i386.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_hurd-i386.deb) ...
-Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.8-1_hurd-i386.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
-Processing triggers for man-db ...
-Processing triggers for install-info ...
-Setting up libmagic1 (5.03-5+b1) ...
-Setting up file (5.03-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-2) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libexpat1 (2.0.1-7) ...
-Setting up libunistring0 (0.9.3-3) ...
-Setting up gettext (0.18.1.1-3) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.2) ...
-Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.8-1) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.15.8.10 hurd-dev_20110303-1~1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.5.2-4
-Package versions: adduser_3.112+nmu2 apt_0.8.11.5+b1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 ca-certificates_20090814+nmu2 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.6-2 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.3 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.12.4 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gawk_1:3.1.7.dfsg-5 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gnupg-curl_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15+b1 hurd_20110303-1~1 hurd-dev_20110303-1~1 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.1 insserv_1.14.0-2 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.3-1+hurd.1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.4.5-10 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.4-2 libgomp1_4.4.5-10 libgpg-error0_1.10-0.3 libident_0.22-3 libidn11_1.20-1 libldap-2.4-2_2.4.17-1 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 liblzo2-2_2.04-1 libmagic1_5.03-5+b1 libmpfr4_3.0.0-7 libncurses5_5.8-1 libncurses5-dev_5.8-1 libncursesw5_5.8-1 libnewt0.52_0.52.11-2 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.2-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libpopt0_1.16-1 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsasl2-modules_2.1.23.dfsg1-7 libslang2_2.1.4-3 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-10 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libwrap0_7.6.dbs-8 libxml2_2.7.8.dfsg-2 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.8-1 netbase_4.45 netcat-traditional_1.10-39 openssl_0.9.8o-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-2 tzdata_2011a-1 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -465,39 +164,39 @@ dpkg-buildpackage
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
- dpkg-source --before-build samtools-0.1.13
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.13-1
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
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_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
rm -f debian/stamp-makefile-check
dh_clean
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
debian/rules build
+rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
/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_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
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
@@ -516,9 +215,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/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
@@ -529,10 +229,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/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
@@ -551,24 +251,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/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
@@ -578,15 +278,15 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14'
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
[sam_header_read2] 2 sequences loaded.
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
@@ -614,9 +314,9 @@ 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_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/examples'
- /usr/bin/fakeroot debian/rules binary-arch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
+ /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -648,7 +348,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -673,7 +373,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -688,72 +388,65 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_hurd-i386.deb'.
- dpkg-genchanges -B -mhurd-i386 Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../samtools_0.1.13-1_hurd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../samtools_0.1.14-1_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-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110309-1142
+Build finished at 20110329-1210
-samtools_0.1.13-1_hurd-i386.changes:
+samtools_0.1.14-1_hurd-i386.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.13-1
+Version: 0.1.14-1
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: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 63e225a0aa19088164afcc1621327058a2123ea4 573676 samtools_0.1.13-1_hurd-i386.deb
- 66010e2872537411b1ac3e423585fdec17b1dcba 163446 libbam-dev_0.1.13-1_hurd-i386.deb
+ 0d91d72190bf868ecec9648ba27c8e63ef9745ee 584046 samtools_0.1.14-1_hurd-i386.deb
+ db3b2019d85c298a6a8c85e57a682d1f1b402843 165090 libbam-dev_0.1.14-1_hurd-i386.deb
Checksums-Sha256:
- ebe68e1457e38485a77b1c39a5225231a3fe6fc80928e7598b2792eb77c811ac 573676 samtools_0.1.13-1_hurd-i386.deb
- f13e62fad0d97eb6bbc33b4ab42265d8ba45211de96b62b66b96caca33173c98 163446 libbam-dev_0.1.13-1_hurd-i386.deb
+ 2b87d92e9d3f06d6d1884bf62f56c7ee13f9e2a2c88882cc04c2bcf1c13c4f61 584046 samtools_0.1.14-1_hurd-i386.deb
+ a247725321c5b88c1b5328fa2715ab8584de6cd479b70c4fe302751bce5ce6b8 165090 libbam-dev_0.1.14-1_hurd-i386.deb
Files:
- ab0f5cbe484b78c9d29559f3fd5239ce 573676 science optional samtools_0.1.13-1_hurd-i386.deb
- 313550a03c4c714b2c750bfdbd672cdb 163446 libdevel optional libbam-dev_0.1.13-1_hurd-i386.deb
+ f88872b6051a468ca99bb0489daa19d6 584046 science optional samtools_0.1.14-1_hurd-i386.deb
+ d0034d3677faf9a5afd7edab577ffd72 165090 libdevel optional libbam-dev_0.1.14-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_hurd-i386.deb
+samtools_0.1.14-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 573676 bytes: control archive= 1797 bytes.
+ size 584046 bytes: control archive= 1793 bytes.
793 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1028
+ Installed-Size: 1052
Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -766,36 +459,36 @@ samtools_0.1.13-1_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 2011-03-09 11:39 ./
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-09 11:38 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-29 12:08 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-09 11:39 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-09 11:39 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-09 11:39 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 1229 2011-03-09 11:39 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-09 11:41 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-03-29 12:08 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-29 12:08 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 12:08 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 12:08 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 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
@@ -804,33 +497,33 @@ drwxr-xr-x root/root 0 2011-03-09 11:41 ./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 2011-03-09 11:41 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/bin/
--rwxr-xr-x root/root 88260 2011-03-09 11:40 ./usr/bin/bcftools
--rwxr-xr-x root/root 23788 2011-03-09 11:40 ./usr/bin/razip
--rwxr-xr-x root/root 353772 2011-03-09 11:40 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/lib/samtools/
--rwxr-xr-x root/root 17488 2011-03-09 11:40 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6336 2011-03-09 11:40 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6320 2011-03-09 11:40 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10084 2011-03-09 11:40 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6920 2011-03-09 11:40 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.13-1_hurd-i386.deb
+-rwxr-xr-x root/root 5778 2011-03-29 12:09 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/bin/
+-rwxr-xr-x root/root 97540 2011-03-29 12:09 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23788 2011-03-29 12:09 ./usr/bin/razip
+-rwxr-xr-x root/root 357868 2011-03-29 12:09 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17488 2011-03-29 12:09 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6336 2011-03-29 12:09 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6320 2011-03-29 12:09 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10084 2011-03-29 12:09 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6920 2011-03-29 12:09 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.14-1_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 163446 bytes: control archive= 903 bytes.
+ size 165090 bytes: control archive= 904 bytes.
678 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 392
+ Installed-Size: 404
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -841,21 +534,21 @@ libbam-dev_0.1.13-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./
-drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-09 11:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-09 11:41 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 12:08 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-09 11:41 ./usr/lib/
--rw-r--r-- root/root 245022 2011-03-09 11:41 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/lib/
+-rw-r--r-- root/root 249922 2011-03-29 12:09 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 12:09 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./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
@@ -866,35 +559,12 @@ drwxr-xr-x root/root 0 2011-03-09 11:40 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.13-1-hurd-i386-O5YkVn
-(Reading database ... 12544 files and directories currently installed.)
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.14-1-hurd-i386-kHSALE
+(Reading database ... 14625 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 20110309-1142
-Build needed 00:10:57, 8808k disc space
+Finished at 20110329-1210
+Build needed 00:05:01, 8968k disc space
diff --git a/i386.log b/i386.log
index 6fc8f91..98e8dc2 100644
--- a/i386.log
+++ b/i386.log
@@ -1,67 +1,68 @@
-From buildd at biber.debian.org Wed Mar 02 05:23:36 2011
+From buildd at biber.debian.org Tue Mar 29 05:18:46 2011
Return-path: <buildd at biber.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+Received: from kokkonen.debian.org ([82.195.75.97])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at biber.debian.org>)
- id 1PueXA-0001wG-7m
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:23:36 +0000
+ id 1Q4RKI-0006ND-Az
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:18:46 +0000
Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at biber.debian.org>)
- id 1PueX7-0001A0-VK; Wed, 02 Mar 2011 05:23:34 +0000
-Received: from buildd by biber.debian.org with local (Exim 4.69)
+ id 1Q4RKE-0003t4-UZ; Tue, 29 Mar 2011 05:18:43 +0000
+Received: from buildd by biber.debian.org with local (Exim 4.72)
(envelope-from <buildd at biber.debian.org>)
- id 1PueX6-0002pc-BM; Wed, 02 Mar 2011 05:23:32 +0000
+ id 1Q4RKC-0002d9-DS; Tue, 29 Mar 2011 05:18:40 +0000
+Message-Id: <E1Q4RKC-0002d9-DS 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, 29 Mar 2011 05:18:40 +0000
From: buildd on biber <buildd at biber.debian.org>
To: kurt at roeckx.be,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on i386 (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1PueX6-0002pc-BM at biber.debian.org>
-Date: Wed, 02 Mar 2011 05:23:32 +0000
+Subject: Log for successful build of samtools_0.1.14-1 on i386 (dist=sid)
+Key-Id: 44C3EAC7
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on biber.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (i386) 02 Mar 2011 05:20 ║
+║ samtools 0.1.14-1 (i386) 29 Mar 2011 05:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: i386
-Chroot Build Dir: /var/lib/schroot/mount/sid-i386-sbuild-0ea7fe83-726a-4c1d-a06d-ec5b060e0a7e/build/buildd-samtools_0.1.13-1-i386-TcVkK4
-Start Time: 20110302-0520
-Get:1 http://ftp.gr.debian.org unstable InRelease [147 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [4156 kB]
-Get:3 http://incoming.debian.org unstable InRelease [147 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [38.5 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [82.8 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [6999 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [61.0 kB]
+Get:1 http://ftp.gr.debian.org unstable InRelease [184 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [5169 kB]
+Get:3 http://incoming.debian.org unstable InRelease [185 kB]
+Get:4 http://ftp.gr.debian.org unstable/contrib Sources [47.0 kB]
+Get:5 http://ftp.gr.debian.org unstable/non-free Sources [99.0 kB]
+Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7046 kB]
+Ign http://incoming.debian.org InRelease
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [61.6 kB]
Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2232 B]
Ign http://ftp.gr.debian.org unstable/contrib Translation-en
-Ign http://incoming.debian.org InRelease
-Get:9 http://incoming.debian.org Release.gpg [835 B]
-Get:10 http://incoming.debian.org unstable/main Sources [4156 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [6999 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [61.0 kB]
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [5142 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [7051 kB]
+Get:14 http://incoming.debian.org unstable/contrib i386 Packages [61.6 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [19.2 kB]
-Get:18 http://incoming.debian.org Packages [373 kB]
+Get:17 http://incoming.debian.org Sources [30.5 kB]
+Get:18 http://incoming.debian.org Packages [618 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 23.4 MB in 20s (1141 kB/s)
+Fetched 25.8 MB in 17s (1506 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,30 +83,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (229 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 1s (213 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 8 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.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source 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-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)
+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)
+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)
+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 (4:4.5.2-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-2 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -116,7 +166,7 @@ The following extra packages will be installed:
man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ 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
@@ -124,12 +174,12 @@ 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 0 not upgraded.
-Need to get 11.8 MB of archives.
-After this operation, 35.2 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 8 not upgraded.
+Need to get 10.7 MB of archives.
+After this operation, 29.8 MB of additional disk space will be used.
Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.2 [200 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-4 [1130 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.1.0-1 [35.2 kB]
+Get: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 2.5.9-4 [980 kB]
Get:5 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5 [234 kB]
Get:6 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5 [49.1 kB]
@@ -137,25 +187,25 @@ Get:7 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-
Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2 [827 kB]
Get:10 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
-Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.1-1+b1 [1487 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.2-1 [1495 kB]
Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-3 [433 kB]
Get:14 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
-Get:15 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.7+20100313-5 [1597 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian i386 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf i386 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper i386 8.1.2 [553 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs i386 0.4.92 [1268 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.8+20110307-1 [466 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 11.8 MB in 1s (9326 kB/s)
+Fetched 10.7 MB in 0s (11.3 MB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10235 files and directories currently installed.)
+(Reading database ... 10333 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_1.21-4_i386.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_i386.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_i386.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_i386.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_i386.deb) ...
Selecting previously deselected package libmagic1.
@@ -171,7 +221,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
Selecting previously deselected package libunistring0.
@@ -179,22 +229,22 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_i386.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_i386.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_i386.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_i386.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_i386.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_i386.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -203,7 +253,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
@@ -212,13 +262,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.26-2-amd64 i386 (x86_64)
-Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-2 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libstdc++6_4.5.2-4
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
+Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 libc6-dev_2.11.2-11 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 linux-libc-dev_2.6.38-1
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110322-1 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_4:4.5.2-2 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-2 g++-4.5_4.5.2-7 gcc_4:4.5.2-2 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 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-13.1 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_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.5.2-7 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+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 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-7 libstdc++6-4.5-dev_4.5.2-7 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 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_2.5.9-4 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_5.10.1-18 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -228,14 +282,13 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -250,25 +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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture i386
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
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
@@ -277,8 +330,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
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
@@ -297,9 +350,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/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
@@ -310,10 +364,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/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
@@ -332,24 +386,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/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
@@ -359,14 +413,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -395,9 +449,9 @@ 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_0.1.13-1-i386-TcVkK4/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -429,7 +483,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -454,7 +508,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-i386-TcVkK4/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-i386-hlIVkN/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -469,27 +523,27 @@ 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_0.1.13-1_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.13-1_i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.14-1_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-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0523
+Build finished at 20110329-0518
-samtools_0.1.13-1_i386.changes:
+samtools_0.1.14-1_i386.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
@@ -497,45 +551,38 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- ade2eb3236c4b6ac7d3e591c1ce6a35ef3a0398c 572508 samtools_0.1.13-1_i386.deb
- 99f19933e954aa396f16555d1e01476cc49cd590 163322 libbam-dev_0.1.13-1_i386.deb
+ 3f377fc586893e47b4e71c72a0337725f9f1122b 581312 samtools_0.1.14-1_i386.deb
+ bc7b0695cd71ab87a7a1e629b72e26be4b3c1542 164874 libbam-dev_0.1.14-1_i386.deb
Checksums-Sha256:
- 664b163f71501b9fa3e8e9d8d4e980d4fbe8fa17001ec70084cc6c35ada4aacd 572508 samtools_0.1.13-1_i386.deb
- 575d0af686c6327c19fbd7cddd9b3022bb396da31f83c63e24bff45c55af9067 163322 libbam-dev_0.1.13-1_i386.deb
+ 1c3921ce6639cccac9e053cbfc3253b3388548fabf15cee3be0852d8291282d7 581312 samtools_0.1.14-1_i386.deb
+ da4ebaa4d71684734323da8741f2d34ced3c5c1bef1715366be99bb89e0e5d0c 164874 libbam-dev_0.1.14-1_i386.deb
Files:
- 225ee85994601154b340e480a74716ab 572508 science optional samtools_0.1.13-1_i386.deb
- b6ace1ccf9f7e0448af80832ab0fb930 163322 libdevel optional libbam-dev_0.1.13-1_i386.deb
+ 7ba7f76e3366c743f20d66601e061a36 581312 science optional samtools_0.1.14-1_i386.deb
+ 1c8570523c06425347a7da29409bdb1f 164874 libdevel optional libbam-dev_0.1.14-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_i386.deb
+samtools_0.1.14-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 572508 bytes: control archive= 1783 bytes.
- 791 bytes, 16 lines control
+ size 581312 bytes: control archive= 1787 bytes.
+ 785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1028
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1056
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -547,50 +594,50 @@ samtools_0.1.13-1_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 2011-03-02 05:23 ./
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/lib/samtools/
--rwxr-xr-x root/root 6680 2011-03-02 05:23 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6176 2011-03-02 05:23 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6160 2011-03-02 05:23 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9908 2011-03-02 05:23 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17224 2011-03-02 05:23 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/bin/
--rwxr-xr-x root/root 88260 2011-03-02 05:23 ./usr/bin/bcftools
--rwxr-xr-x root/root 23692 2011-03-02 05:23 ./usr/bin/razip
--rwxr-xr-x root/root 353772 2011-03-02 05:23 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/samtools/
+-rwxr-xr-x root/root 6664 2011-03-29 05:18 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6144 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6112 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10116 2011-03-29 05:18 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17384 2011-03-29 05:18 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/bin/
+-rwxr-xr-x root/root 96964 2011-03-29 05:18 ./usr/bin/bcftools
+-rwxr-xr-x root/root 22584 2011-03-29 05:18 ./usr/bin/razip
+-rwxr-xr-x root/root 361964 2011-03-29 05:18 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./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 2011-03-02 04:30 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./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 2011-03-02 05:23 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-29 05:18 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2011-03-02 05:23 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/man/man1/
--rw-r--r-- root/root 1229 2011-03-02 05:23 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8164 2011-03-02 05:23 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-03-02 05:23 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/samtools/
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-03-29 05:18 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-03-29 05:18 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 05:18 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-29 05:18 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-03-02 05:23 ./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 2011-03-29 05:18 ./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
@@ -599,19 +646,19 @@ drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/samtools/
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-libbam-dev_0.1.13-1_i386.deb
+libbam-dev_0.1.14-1_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 163322 bytes: control archive= 899 bytes.
+ size 164874 bytes: control archive= 899 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 392
+ Installed-Size: 404
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -622,22 +669,22 @@ libbam-dev_0.1.13-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/lib/
--rw-r--r-- root/root 245070 2011-03-02 05:23 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
+-rw-r--r-- root/root 252230 2011-03-29 05:18 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./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 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/include/
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/include/
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
@@ -647,9 +694,31 @@ drwxr-xr-x root/root 0 2011-03-02 05:23 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-i386-sbuild-0ea7fe83-726a-4c1d-a06d-ec5b060e0a7e/build/buildd-samtools_0.1.13-1-i386-TcVkK4
-Not removing build depends: cloned chroot in use
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0523
-Build needed 00:02:56, 8808k disc space
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-i386-sbuild-ff35df57-9fa1-48d1-9b3c-7aa763415fff/build/buildd-samtools_0.1.14-1-i386-hlIVkN
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: i386
+Build-Space: 9732
+Build-Time: 46
+Distribution: sid
+Install-Time: 36
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 111
+Source-Version: 0.1.14-1
+Space: 9732
+Status: successful
+Version: 0.1.14-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110329-0518
+Build needed 00:01:51, 9732k disc space
+Signature with key '44C3EAC7' requested:
diff --git a/ia64.log b/ia64.log
index b4ef90e..c4fd58d 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,68 +1,67 @@
-From buildd at alkman.debian.org Wed Mar 02 05:28:59 2011
+From buildd at alkman.debian.org Tue Mar 29 05:18:34 2011
Return-path: <buildd at alkman.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from kokkonen.debian.org ([82.195.75.97])
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 alkman.debian.org>)
- id 1PuecM-00030H-RA
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:28:59 +0000
+ id 1Q4RK5-0006Lm-O5
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:18:34 +0000
Received: from alkman.debian.org ([192.25.206.63])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at alkman.debian.org>)
- id 1Puebx-0006DF-P5
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:28:55 +0000
-Received: from buildd by alkman.debian.org with local (Exim 4.69)
+ id 1Q4RK1-0003r2-QZ
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:18:30 +0000
+Received: from buildd by alkman.debian.org with local (Exim 4.72)
(envelope-from <buildd at alkman.debian.org>)
- id 1Puebq-0001dc-6B; Wed, 02 Mar 2011 05:28:26 +0000
+ id 1Q4RJx-0000zl-Vp; Tue, 29 Mar 2011 05:18:26 +0000
+Date: Tue, 29 Mar 2011 05:18:25 +0000
+Message-Id: <E1Q4RJx-0000zl-Vp at alkman.debian.org>
From: buildd on alkman <buildd at alkman.debian.org>
To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on ia64 (dist=sid)
+Subject: Log for successful build of samtools_0.1.14-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Puebq-0001dc-6B at alkman.debian.org>
-Date: Wed, 02 Mar 2011 05:28:26 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on alkman.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (ia64) 02 Mar 2011 05:24 ║
+║ samtools 0.1.14-1 (ia64) 29 Mar 2011 05:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: ia64
-Chroot Build Dir: /var/lib/schroot/mount/sid-ia64-sbuild-921a377a-9305-4edc-bc84-5d1036145ce6/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK
-Start Time: 20110302-0524
-Get:1 http://spohr.debian.org unstable InRelease [147 kB]
-Get:2 http://incoming.debian.org unstable InRelease [147 kB]
-Get:3 http://spohr.debian.org unstable/main Sources [4156 kB]
-Get:4 http://spohr.debian.org unstable/contrib Sources [38.5 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [82.8 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [6790 kB]
+Get:1 http://spohr.debian.org unstable InRelease [185 kB]
+Get:2 http://spohr.debian.org unstable/main Sources [5142 kB]
+Get:3 http://incoming.debian.org unstable InRelease [185 kB]
+Get:4 http://spohr.debian.org unstable/contrib Sources [47.4 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [99.4 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [6847 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [835 B]
-Get:8 http://incoming.debian.org unstable/main Sources [4156 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [51.4 kB]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org unstable/main Sources [5142 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [14 B]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
Get:10 http://spohr.debian.org unstable/main TranslationIndex [2232 B]
Ign http://spohr.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [6790 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [51.4 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [6847 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [14 B]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [19.2 kB]
-Get:18 http://incoming.debian.org Packages [373 kB]
+Get:17 http://incoming.debian.org Sources [30.5 kB]
+Get:18 http://incoming.debian.org Packages [618 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 22.9 MB in 20s (1104 kB/s)
+Fetched 25.3 MB in 22s (1103 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,30 +82,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 0s (419 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 0s (485 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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 (6.1)
+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)
+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 (5.10.1-17)
+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)
+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 (4:4.4.5-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-4 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -117,7 +165,7 @@ The following extra packages will be installed:
man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ 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
@@ -125,12 +173,12 @@ 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 19 not upgraded.
-Need to get 14.0 MB of archives.
-After this operation, 47.4 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 23 not upgraded.
+Need to get 13.0 MB of archives.
+After this operation, 42.6 MB of additional disk space will be used.
Get:1 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.2 [236 kB]
-Get:2 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-4 [1400 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.1.0-1 [46.5 kB]
+Get: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 2.5.9-4 [1154 kB]
Get:5 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.04-5 [263 kB]
Get:6 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5 [51.9 kB]
@@ -138,25 +186,25 @@ Get:7 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-3
Get:8 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-3 [316 kB]
Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-2 [1181 kB]
Get:10 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.1-1+b1 [1963 kB]
+Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.2-1 [1969 kB]
Get:12 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
Get:13 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-3 [469 kB]
Get:14 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-3 [2453 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:19 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.7+20100313-5 [1716 kB]
+Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian ia64 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf ia64 1.0.16+nmu1 [223 kB]
+Get:17 http://spohr.debian.org/debian/ unstable/main debhelper ia64 8.1.2 [553 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main cdbs ia64 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 14.0 MB in 4s (3116 kB/s)
+Fetched 13.0 MB in 0s (14.3 MB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10123 files and directories currently installed.)
+(Reading database ... 10169 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_1.21-4_ia64.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_ia64.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_ia64.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_ia64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_ia64.deb) ...
Selecting previously deselected package libmagic1.
@@ -172,7 +220,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_ia64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_ia64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
Selecting previously deselected package libunistring0.
@@ -180,22 +228,22 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_ia64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_ia64.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_ia64.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_ia64.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_ia64.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_ia64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_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) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -204,7 +252,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
@@ -213,13 +261,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: libc6.1-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.32-30 gcc-4.4_4.4.5-10 g++-4.4_4.4.5-10 binutils_2.20.1-16 libstdc++6-4.4-dev_4.4.5-10 libstdc++6_4.4.5-10
-Package versions: apt_0.8.11.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6.1_2.11.2-11 libc6.1-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.2-2 libpam0g_1.1.1-6.1 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-30 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-2 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
+Toolchain package versions: binutils_2.21.0.20110302-1 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-13 gcc-4.4_4.4.5-13 libc6.1-dev_2.11.2-13 libstdc++6_4.5.2-5 libstdc++6-4.4-dev_4.4.5-13 linux-libc-dev_2.6.37-2
+Package versions: apt_0.8.12 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110302-1 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_4:4.4.5-4 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-4 g++-4.4_4.4.5-13 gcc_4:4.4.5-4 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-5 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 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc6.1_2.11.2-13 libc6.1-dev_2.11.2-13 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-6 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-5 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 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_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-5 libstdc++6-4.4-dev_4.4.5-13 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 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_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 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_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011c-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 │
@@ -229,14 +281,13 @@ Package versions: apt_0.8.11.3 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -251,25 +302,25 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture ia64
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
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
@@ -278,8 +329,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
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
@@ -298,9 +349,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/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
@@ -311,10 +363,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/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
@@ -333,24 +385,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/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
@@ -360,14 +412,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -396,9 +448,9 @@ 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_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -430,7 +482,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -455,7 +507,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-ia64-7ZMmCK/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-ia64-3DXQWn/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -470,27 +522,27 @@ 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_0.1.13-1_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.13-1_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.14-1_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-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0528
+Build finished at 20110329-0518
-samtools_0.1.13-1_ia64.changes:
+samtools_0.1.14-1_ia64.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
@@ -498,45 +550,38 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 1084bf1f41cc43c6da647f501e5413c710f7b67e 713526 samtools_0.1.13-1_ia64.deb
- ed2687461eba5fcb36c546914e1a1d9cf9068707 212932 libbam-dev_0.1.13-1_ia64.deb
+ c5b13aa76194e732e45a2038c03fad3751ca5562 727514 samtools_0.1.14-1_ia64.deb
+ 6931effef784cd0ace2a7fc5e1433d0af2cf7ed5 215156 libbam-dev_0.1.14-1_ia64.deb
Checksums-Sha256:
- ee7d12486e7e6805716ee2f650ac832ab98b50bb8b97b4714a1f4b5b72576b5c 713526 samtools_0.1.13-1_ia64.deb
- ec80d4dd8147f85363109220ee897f195a3f984ac518f57f6849c10500fd238d 212932 libbam-dev_0.1.13-1_ia64.deb
+ 09bfead42bdf5029c8b8797734dc01c75bd13bce3f00ebe1b58abfe806ccf772 727514 samtools_0.1.14-1_ia64.deb
+ 58d10aaa3d1cc7a927c5d62ddaa8c4dee7242190b572112553b98d38b17a359c 215156 libbam-dev_0.1.14-1_ia64.deb
Files:
- f53a25adc191c81783e610278f9c6c9f 713526 science optional samtools_0.1.13-1_ia64.deb
- c6592ca4b578749b158f4ae1c0bc29d2 212932 libdevel optional libbam-dev_0.1.13-1_ia64.deb
+ d901a8353f01c6b0b93b48016a963dee 727514 science optional samtools_0.1.14-1_ia64.deb
+ 66273a0ee8e92f9793b0728ff4c0a9c4 215156 libdevel optional libbam-dev_0.1.14-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_ia64.deb
+samtools_0.1.14-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 713526 bytes: control archive= 1789 bytes.
- 793 bytes, 16 lines control
+ size 727514 bytes: control archive= 1781 bytes.
+ 787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1936
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1984
+ Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -548,22 +593,22 @@ samtools_0.1.13-1_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 2011-03-02 05:28 ./
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/samtools/
--rwxr-xr-x root/root 30712 2011-03-02 05:28 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13360 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13296 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 22384 2011-03-02 05:28 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2011-03-02 05:28 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/bin/
--rwxr-xr-x root/root 226632 2011-03-02 05:28 ./usr/bin/bcftools
--rwxr-xr-x root/root 52520 2011-03-02 05:28 ./usr/bin/razip
--rwxr-xr-x root/root 792192 2011-03-02 05:28 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-03-02 05:28 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30712 2011-03-29 05:18 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13360 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13296 2011-03-29 05:18 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 22384 2011-03-29 05:18 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2011-03-29 05:18 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/bin/
+-rwxr-xr-x root/root 250336 2011-03-29 05:18 ./usr/bin/bcftools
+-rwxr-xr-x root/root 52520 2011-03-29 05:18 ./usr/bin/razip
+-rwxr-xr-x root/root 801864 2011-03-29 05:18 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-03-29 05:18 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
@@ -572,47 +617,47 @@ drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/samtools/
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/man1/
--rw-r--r-- root/root 1229 2011-03-02 05:28 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-03-02 05:28 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-02 05:28 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/samtools/
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-03-29 05:18 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-03-29 05:18 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 05:18 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-02 05:28 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2011-03-02 05:28 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2011-03-29 05:18 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2011-03-29 05:18 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-libbam-dev_0.1.13-1_ia64.deb
+libbam-dev_0.1.14-1_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 212932 bytes: control archive= 895 bytes.
+ size 215156 bytes: control archive= 896 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 752
+ Installed-Size: 768
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -623,22 +668,22 @@ libbam-dev_0.1.13-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/include/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/include/
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
--rw-r--r-- root/root 521844 2011-03-02 05:28 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/lib/
+-rw-r--r-- root/root 530970 2011-03-29 05:18 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:18 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
@@ -648,9 +693,31 @@ drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-921a377a-9305-4edc-bc84-5d1036145ce6/build/buildd-samtools_0.1.13-1-ia64-7ZMmCK
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-5dd52ac5-1458-47e7-98e4-b9ee548aeb2f/build/buildd-samtools_0.1.14-1-ia64-3DXQWn
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: ia64
+Build-Space: 15780
+Build-Time: 115
+Distribution: sid
+Install-Time: 59
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 227
+Source-Version: 0.1.14-1
+Space: 15780
+Status: successful
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0528
-Build needed 00:03:35, 15492k disc space
+Finished at 20110329-0518
+Build needed 00:03:47, 15780k disc space
diff --git a/info b/info
index ab88a03..c685384 100644
--- a/info
+++ b/info
@@ -1,14 +1,14 @@
-s390~1299043371~sid~successful
-i386~1299043417~sid~successful
-powerpc~1299043539~sid~successful
-sparc~1299043573~sid~failed
-armel~1299043663~sid~failed
-ia64~1299043739~sid~successful
-kfreebsd-i386~1299043749~sid~successful
-mipsel~1299044792~sid~successful
-alpha~1299047331~sid~successful
-mips~1299054657~sid~successful
-hppa~1299058650~sid~successful
-kfreebsd-amd64~1299139939~sid~successful
-hurd-i386~1299391211~sid~failed
-hurd-i386~1299671012~sid~successful
+powerpc~1301374901~sid~successful
+kfreebsd-i386~1301374936~sid~successful
+s390~1301375007~sid~successful
+alpha~1301375148~sid~successful
+ia64~1301375914~sid~successful
+i386~1301375927~sid~successful
+kfreebsd-amd64~1301376172~sid~successful
+sparc~1301383013~sid~failed
+mipsel~1301388816~sid~successful
+hppa~1301390346~sid~successful
+hurd-i386~1301400643~sid~successful
+armel~1301467862~sid~failed
+armel~1301710029~sid~failed
+mips~1301743651~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index ad9474c..7adf97d 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,51 +1,59 @@
-From buildd at fano.debian.org Thu Mar 03 08:12:19 2011
+From buildd at fano.debian.org Tue Mar 29 05:22:52 2011
Return-path: <buildd at fano.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+Received: from kokkonen.debian.org ([82.195.75.97])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at fano.debian.org>)
- id 1Pv3dy-0002f4-Q8
- for logs at buildd.debian.org; Thu, 03 Mar 2011 08:12:19 +0000
+ id 1Q4ROF-00077a-PS
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:22:52 +0000
Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at fano.debian.org>)
- id 1Pv3dv-0003M1-RA; Thu, 03 Mar 2011 08:12:16 +0000
+ id 1Q4ROC-0003zh-0n; Tue, 29 Mar 2011 05:22:48 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1Pv3dp-0002mV-Pp; Thu, 03 Mar 2011 08:12:09 +0000
-Date: Thu, 03 Mar 2011 08:12:09 +0000
-Message-Id: <E1Pv3dp-0002mV-Pp at fano.debian.org>
+ id 1Q4RO8-00091Q-6P; Tue, 29 Mar 2011 05:22:44 +0000
+Date: Tue, 29 Mar 2011 05:22:44 +0000
+Message-Id: <E1Q4RO8-00091Q-6P at fano.debian.org>
From: buildd on fano <buildd at fano.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
-Subject: Log for successful build of samtools_0.1.13-1 on kfreebsd-amd64
+Subject: Log for successful build of samtools_0.1.14-1 on kfreebsd-amd64
(dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on fano.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (kfreebsd-amd64) 03 Mar 2011 08:10 ║
+║ samtools 0.1.14-1 (kfreebsd-amd64) 29 Mar 2011 05:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: kfreebsd-amd64
-Chroot Build Dir: /var/lib/schroot/mount/sid-ka-sbuild-1299139834-9072/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd
-Start Time: 20110303-0810
-Hit http://ftp.ca.debian.org sid InRelease
+Hit http://mirror-ubc.debian.org sid InRelease
+Hit http://mirror-ubc.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
+Hit http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+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
+Hit http://mirror-ubc.debian.org sid/main TranslationIndex
+Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Hit http://ftp.ca.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org Release.gpg
+Get:1 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [79.9 kB]
+Ign http://mirror-ubc.debian.org sid/contrib Translation-en
+Ign http://mirror-ubc.debian.org sid/non-free Translation-en
+Get:2 http://incoming.debian.org Release.gpg [836 B]
Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://ftp.ca.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.ca.debian.org sid/main TranslationIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
@@ -54,13 +62,14 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
+Get:3 http://incoming.debian.org Release [1604 B]
+Get:4 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [79.9 kB]
+Get:5 http://incoming.debian.org Sources [30.9 kB]
+Get:6 http://incoming.debian.org Packages [623 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 816 kB in 7s (113 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,30 +90,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://ftp.ca.debian.org/debian/ sid/main samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (318 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 3s (123 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.15-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.1)
+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)
+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-bin: already installed (5.8+20110307-1)
+perl-base: already installed (5.10.1-18)
+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)
+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 (4:4.5.2-3 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-3 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -114,7 +172,8 @@ 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 less www-browser
+ devscripts doc-base dh-make gettext-doc groff ncurses-doc less www-browser
+debconf: delaying package configuration, since apt-utils is not installed
libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
@@ -123,15 +182,14 @@ 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
-debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/12.0 MB of archives.
-After this operation, 33.7 MB of additional disk space will be used.
+Need to get 0 B/10.9 MB of archives.
+After this operation, 28.9 MB of additional disk space will be used.
Selecting previously deselected package groff-base.
-(Reading database ... 11844 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-4_kfreebsd-amd64.deb) ...
+(Reading database ... 11962 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_1.1.0-1_kfreebsd-amd64.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_kfreebsd-amd64.deb) ...
Selecting previously deselected package libmagic1.
@@ -147,7 +205,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libunistring0.
@@ -155,19 +213,19 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_kfreebsd-amd64.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_kfreebsd-amd64.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_kfreebsd-amd64.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../cdbs_0.4.92_kfreebsd-amd64.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_kfreebsd-amd64.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_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) ...
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -176,7 +234,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
@@ -185,13 +243,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.5.2-4 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libc0.1-dev_2.11.2-13 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1+b1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.2-base_4.2.4-6 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.5-1 libgomp1_4.5.2-4 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011b-2 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 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_4:4.5.2-3 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.5.2-3 g++-4.5_4.5.2-7 gcc_4:4.5.2-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.5-14 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 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 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_1.15.8.10 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1 libgomp1_4.6.0-1 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 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_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 perl-base_5.10.1-18 perl-modules_5.10.1-18 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_2011d-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 │
@@ -201,14 +263,13 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -223,25 +284,25 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture kfreebsd-amd64
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
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
@@ -250,8 +311,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
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
@@ -270,9 +331,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/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
@@ -283,10 +345,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/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
@@ -305,24 +367,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/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
@@ -332,14 +394,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -368,9 +430,9 @@ 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_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -402,7 +464,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -427,7 +489,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -442,27 +504,27 @@ 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_0.1.13-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.13-1_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.14-1_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-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110303-0811
+Build finished at 20110329-0522
-samtools_0.1.13-1_kfreebsd-amd64.changes:
+samtools_0.1.14-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
@@ -470,45 +532,38 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- fe45b44e2603d5ef8c612bd631a2d8afc65e2db0 582914 samtools_0.1.13-1_kfreebsd-amd64.deb
- f8b231d35ce6fe977645a4cf67fd466365886700 161392 libbam-dev_0.1.13-1_kfreebsd-amd64.deb
+ 2810422722b454637df6606051abef73fb3dfe12 595312 samtools_0.1.14-1_kfreebsd-amd64.deb
+ 53922ebf32d5e742178be8656687e0e5ffc86b38 165302 libbam-dev_0.1.14-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 80b584d252e31830bbcb68be5ffb8aae03261c18c95b9dc2ca72e92da19dc6d4 582914 samtools_0.1.13-1_kfreebsd-amd64.deb
- 9d98b0214ffbd8be51eb703fb31a0d515592b7c414ecfe68b38b6f4620abb073 161392 libbam-dev_0.1.13-1_kfreebsd-amd64.deb
+ d8153dd8d4518f5eb1ce5515059492ec68a36e1a7bcde9553a1ee6d4f8b4e2e9 595312 samtools_0.1.14-1_kfreebsd-amd64.deb
+ 6bf8ccf2a6f3462deaa19bba8c6c701fe785d7ba696ff9683e3ff7527beb3926 165302 libbam-dev_0.1.14-1_kfreebsd-amd64.deb
Files:
- f37e340d80c90e52c0a535ab32f235a4 582914 science optional samtools_0.1.13-1_kfreebsd-amd64.deb
- 3b32618835f90c4680bf7354661b61cd 161392 libdevel optional libbam-dev_0.1.13-1_kfreebsd-amd64.deb
+ dce1169db2836395bce68bafb8b6a2c4 595312 science optional samtools_0.1.14-1_kfreebsd-amd64.deb
+ 5265f735e09d1c4b623010c30c96a1ba 165302 libdevel optional libbam-dev_0.1.14-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_kfreebsd-amd64.deb
+samtools_0.1.14-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 582914 bytes: control archive= 1791 bytes.
- 802 bytes, 16 lines control
+ size 595312 bytes: control archive= 1788 bytes.
+ 797 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 984
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1018
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -520,36 +575,36 @@ samtools_0.1.13-1_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 2011-03-03 08:11 ./
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-03 08:11 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-29 05:22 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-03 08:11 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-03 08:11 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-03 08:11 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 1229 2011-03-03 08:11 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-03-29 05:22 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-29 05:22 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 05:22 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 05:22 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 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
@@ -558,33 +613,33 @@ drwxr-xr-x root/root 0 2011-03-03 08:11 ./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 2011-03-03 08:11 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/bin/
--rwxr-xr-x root/root 93576 2011-03-03 08:11 ./usr/bin/bcftools
--rwxr-xr-x root/root 24864 2011-03-03 08:11 ./usr/bin/razip
--rwxr-xr-x root/root 356560 2011-03-03 08:11 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/lib/samtools/
--rwxr-xr-x root/root 19248 2011-03-03 08:11 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8248 2011-03-03 08:11 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8200 2011-03-03 08:11 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11712 2011-03-03 08:11 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8520 2011-03-03 08:11 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.13-1_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2011-03-29 05:22 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/bin/
+-rwxr-xr-x root/root 106312 2011-03-29 05:22 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24800 2011-03-29 05:22 ./usr/bin/razip
+-rwxr-xr-x root/root 376080 2011-03-29 05:22 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19248 2011-03-29 05:22 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8288 2011-03-29 05:22 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8192 2011-03-29 05:22 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11912 2011-03-29 05:22 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8608 2011-03-29 05:22 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.14-1_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 161392 bytes: control archive= 901 bytes.
+ size 165302 bytes: control archive= 904 bytes.
683 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 440
+ Installed-Size: 458
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -595,21 +650,21 @@ libbam-dev_0.1.13-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/lib/
--rw-r--r-- root/root 296260 2011-03-03 08:11 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/lib/
+-rw-r--r-- root/root 314106 2011-03-29 05:22 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 05:22 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./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
@@ -620,38 +675,74 @@ drwxr-xr-x root/root 0 2011-03-03 08:11 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1299139834-9072/build/buildd-samtools_0.1.13-1-kfreebsd-amd64-J3KHdd
-(Reading database ... 14181 files and directories currently installed.)
-Removing zlib1g-dev ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1301376062-33060/build/buildd-samtools_0.1.14-1-kfreebsd-amd64-TntfUU
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ 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 0 not upgraded.
+After this operation, 28.9 MB disk space will be freed.
+(Reading database ... 13291 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
+Removing file ...
Removing po-debconf ...
-Removing libncurses5-dev ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
Removing man-db ...
Purging configuration files for man-db ...
-Removing intltool-debian ...
Removing groff-base ...
Purging configuration files for groff-base ...
-Removing gettext ...
-Removing file ...
Removing html2text ...
Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
+Removing 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 libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
+Removing zlib1g-dev ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: kfreebsd-amd64
+Build-Space: 11528
+Build-Time: 41
+Distribution: sid
+Install-Time: 29
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 87
+Source-Version: 0.1.14-1
+Space: 11528
+Status: successful
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110303-0811
-Build needed 00:01:22, 10174k disc space
+Finished at 20110329-0522
+Build needed 00:01:27, 11528k disc space
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index e1505ea..45230f7 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,58 +1,57 @@
-From buildd at field.debian.org Wed Mar 02 05:29:08 2011
-Return-path: <buildd at field.debian.org>
+From buildd at finzi.debian.org Tue Mar 29 05:02:16 2011
+Return-path: <buildd at finzi.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at field.debian.org>)
- id 1PuecW-00031Q-Ad
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:29:08 +0000
-Received: from field.debian.org ([194.177.211.210])
+ (Exim 4.69) (envelope-from <buildd at finzi.debian.org>)
+ id 1Q4R4J-0002tN-LR
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:02:16 +0000
+Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
+ CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at field.debian.org>)
- id 1PuecS-0001IA-Ri; Wed, 02 Mar 2011 05:29:05 +0000
-Received: from buildd by field.debian.org with local (Exim 4.72)
- (envelope-from <buildd at field.debian.org>)
- id 1PuecR-0007eK-81; Wed, 02 Mar 2011 05:29:03 +0000
-Date: Wed, 02 Mar 2011 05:29:03 +0000
-Message-Id: <E1PuecR-0007eK-81 at field.debian.org>
-From: buildd on field <buildd at field.debian.org>
+ (Exim 4.69) (envelope-from <buildd at finzi.debian.org>)
+ id 1Q4R4F-0003Ue-Ql; Tue, 29 Mar 2011 05:02:12 +0000
+Received: from buildd by finzi.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at finzi.debian.org>)
+ id 1Q4R4B-000PSC-Ng; Tue, 29 Mar 2011 05:02:07 +0000
+Date: Tue, 29 Mar 2011 05:02:07 +0000
+Message-Id: <E1Q4R4B-000PSC-Ng at finzi.debian.org>
+From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,kibi at debian-ports.org
-Subject: Log for successful build of samtools_0.1.13-1 on kfreebsd-i386
+Subject: Log for successful build of samtools_0.1.14-1 on kfreebsd-i386
(dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on field.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (kfreebsd-i386) 02 Mar 2011 05:25 ║
+║ samtools 0.1.14-1 (kfreebsd-i386) 29 Mar 2011 05:00 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: kfreebsd-i386
-Chroot Build Dir: /var/lib/schroot/mount/sid-ki-sbuild-1299043555-27708/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx
-Start Time: 20110302-0525
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid InRelease
+Hit http://mirror-ubc.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Hit http://ftp.gr.debian.org sid/main TranslationIndex
-Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Get:1 http://incoming.debian.org Release.gpg [835 B]
-Ign http://ftp.gr.debian.org sid/contrib Translation-en
-Ign http://ftp.gr.debian.org sid/non-free Translation-en
+Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
+Hit http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
+Hit http://mirror-ubc.debian.org sid/main TranslationIndex
+Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
+Ign http://mirror-ubc.debian.org sid/contrib Translation-en
+Ign http://mirror-ubc.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org Release.gpg
Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
@@ -62,13 +61,13 @@ 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 [19.2 kB]
-Get:4 http://incoming.debian.org Packages [373 kB]
+Hit http://incoming.debian.org Release
+Get:1 http://incoming.debian.org Sources [30.5 kB]
+Get:2 http://incoming.debian.org Packages [608 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 395 kB in 4s (81.1 kB/s)
+Fetched 638 kB in 8s (73.2 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -89,30 +88,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (197 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 2s (140 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.15-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.1)
+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)
+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-bin: already installed (5.8+20110307-1)
+perl-base: already installed (5.10.1-18)
+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)
+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 (4:4.5.2-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-2 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -122,24 +170,24 @@ 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 less www-browser
+ devscripts doc-base 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
+ curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
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 0 not upgraded.
-Need to get 0 B/11.5 MB of archives.
-After this operation, 32.1 MB of additional disk space will be used.
+0 upgraded, 19 newly installed, 0 to remove and 3 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.
Selecting previously deselected package groff-base.
-(Reading database ... 11789 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-4_kfreebsd-i386.deb) ...
+(Reading database ... 13556 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_1.1.0-1_kfreebsd-i386.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
@@ -155,7 +203,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_kfreebsd-i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libunistring0.
@@ -171,11 +219,11 @@ Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_kfreebsd-i386.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_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 (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -184,7 +232,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
@@ -193,13 +241,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: libc6-dev_ =*=NOT INSTALLED=*= dpkg-dev_1.15.8.10 libstdc++6_4.5.2-4 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libc0.1-dev_2.11.2-13 kfreebsd-kernel-headers_0.53
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-1+b1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.1_2.11.2-13 libc0.1-dev_2.11.2-13 libcam0_8.1-5 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.10.5-1 libgomp1_4.5.2-4 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpng12-0_1.2.44-1 libreadline6_6.1-3 libsasl2-2_2.1.23.dfsg1-7 libsbuf0_8.1-5 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 type-handling_0.2.23 tzdata_2011b-2 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
+Checking correctness of dependencies...
+Kernel: GNU/kFreeBSD 8.1-1-686 kfreebsd-i386 (i686)
+Toolchain package versions: binutils_2.21.0.20110327-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-7 gcc-4.5_4.5.2-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.11.2-13 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7
+Package versions: apt_0.8.13 autotools-dev_20100122.1 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 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_4:4.5.2-2 cpp-4.5_4.5.2-7 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15-1 file_5.04-5 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.5.2-2 g++-4.5_4.5.2-7 gcc_4:4.5.2-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.5-14 gcc-4.5_4.5.2-7 gcc-4.5-base_4.5.2-7 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 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_1.15.8.10 libedit2_2.11-20080614-2 libelfg0_0.8.13-1 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-1 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1 libgomp1_4.6.0-1 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.23-7 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.8+20110307-1 libncurses5-dev_5.8+20110307-1 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_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.6.0-1 libstdc++6-4.5-dev_4.5.2-7 libtasn1-3_2.9-2 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 netbase_4.45 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 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_2011d-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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -209,14 +261,13 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -231,25 +282,25 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture kfreebsd-i386
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
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
@@ -258,8 +309,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
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
@@ -278,9 +329,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/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
@@ -291,10 +343,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/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
@@ -313,24 +365,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/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
@@ -340,14 +392,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -376,9 +428,9 @@ 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_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -410,7 +462,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -435,7 +487,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -450,73 +502,66 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.13-1_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.14-1_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-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0528
+Build finished at 20110329-0501
-samtools_0.1.13-1_kfreebsd-i386.changes:
+samtools_0.1.14-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 428bb527c130930bd9664c727b920e5cec99b126 572384 samtools_0.1.13-1_kfreebsd-i386.deb
- 377f032405891e1669dcc434ecf3abe268dce306 163380 libbam-dev_0.1.13-1_kfreebsd-i386.deb
+ db1751cbe6d180f3573a100d81181e7a3b860afb 582452 samtools_0.1.14-1_kfreebsd-i386.deb
+ 390dc919f44e2888f4717b0ae2b7bce1d06ac8f3 165382 libbam-dev_0.1.14-1_kfreebsd-i386.deb
Checksums-Sha256:
- 8c5b32ef9c0d5f660ec13b2aab72bbbf402abdd02f9f40afd2949b3d5ec449f6 572384 samtools_0.1.13-1_kfreebsd-i386.deb
- e975100d3d3596af04c618ef3ea436e5a2c6df72596849d491d01a0dcfff65a3 163380 libbam-dev_0.1.13-1_kfreebsd-i386.deb
+ d2b07e3dd509a6b3f8ce644f2c876ca061b61a94c8f95b8d07a3ad60fd21a577 582452 samtools_0.1.14-1_kfreebsd-i386.deb
+ 434488f487129b42b7c693218ab51eb6d84a8ac3cbba92b9ce8ef2da2ea7d66e 165382 libbam-dev_0.1.14-1_kfreebsd-i386.deb
Files:
- f227797b77fab3d79c5d11a62274ce31 572384 science optional samtools_0.1.13-1_kfreebsd-i386.deb
- 6fc6111d6f389e43b3df8d4c33e14937 163380 libdevel optional libbam-dev_0.1.13-1_kfreebsd-i386.deb
+ ca3cb78bc60213a2ac7a4bba896ef19e 582452 science optional samtools_0.1.14-1_kfreebsd-i386.deb
+ 0a3ac24ba10128c1550043ac0474513d 165382 libdevel optional libbam-dev_0.1.14-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_kfreebsd-i386.deb
+samtools_0.1.14-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 572384 bytes: control archive= 1791 bytes.
- 801 bytes, 16 lines control
+ size 582452 bytes: control archive= 1788 bytes.
+ 795 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 966
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 996
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -528,36 +573,36 @@ samtools_0.1.13-1_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 2011-03-02 05:28 ./
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-02 05:28 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-29 05:01 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-02 05:28 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-02 05:28 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-02 05:28 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 1229 2011-03-02 05:28 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/samtools/
+-rw-r--r-- root/root 1966 2011-03-29 05:01 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-29 05:01 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 05:01 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 05:01 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/samtools/
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 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
@@ -566,33 +611,33 @@ drwxr-xr-x root/root 0 2011-03-02 05:28 ./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 2011-03-02 05:28 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/bin/
--rwxr-xr-x root/root 88260 2011-03-02 05:28 ./usr/bin/bcftools
--rwxr-xr-x root/root 23612 2011-03-02 05:28 ./usr/bin/razip
--rwxr-xr-x root/root 353772 2011-03-02 05:28 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/samtools/
--rwxr-xr-x root/root 17296 2011-03-02 05:28 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6160 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6144 2011-03-02 05:28 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9876 2011-03-02 05:28 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6632 2011-03-02 05:28 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.13-1_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2011-03-29 05:01 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/bin/
+-rwxr-xr-x root/root 96964 2011-03-29 05:01 ./usr/bin/bcftools
+-rwxr-xr-x root/root 23352 2011-03-29 05:01 ./usr/bin/razip
+-rwxr-xr-x root/root 361964 2011-03-29 05:01 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17424 2011-03-29 05:01 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6128 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6096 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10084 2011-03-29 05:01 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 6616 2011-03-29 05:01 ./usr/lib/samtools/md5sum-lite
+
+
+libbam-dev_0.1.14-1_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 163380 bytes: control archive= 900 bytes.
+ size 165382 bytes: control archive= 904 bytes.
682 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 376
+ Installed-Size: 394
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -603,21 +648,21 @@ libbam-dev_0.1.13-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/lib/
--rw-r--r-- root/root 245054 2011-03-02 05:28 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
+-rw-r--r-- root/root 253062 2011-03-29 05:01 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./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
@@ -628,38 +673,74 @@ drwxr-xr-x root/root 0 2011-03-02 05:28 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1299043555-27708/build/buildd-samtools_0.1.13-1-kfreebsd-i386-iEIVnx
-(Reading database ... 14126 files and directories currently installed.)
-Removing zlib1g-dev ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1301374820-96255/build/buildd-samtools_0.1.14-1-kfreebsd-i386-QA8sZR
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 3 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 3 not upgraded.
+After this operation, 27.2 MB disk space will be freed.
+(Reading database ... 14883 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
+Removing file ...
Removing po-debconf ...
-Removing libncurses5-dev ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
Removing man-db ...
Purging configuration files for man-db ...
-Removing intltool-debian ...
Removing groff-base ...
Purging configuration files for groff-base ...
-Removing gettext ...
-Removing file ...
Removing html2text ...
Purging configuration files for html2text ...
-Removing gettext-base ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
Removing libcroco3 ...
Purging configuration files for libcroco3 ...
+Removing 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 libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
+Removing zlib1g-dev ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: kfreebsd-i386
+Build-Space: 9446
+Build-Time: 47
+Distribution: sid
+Install-Time: 29
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 94
+Source-Version: 0.1.14-1
+Space: 9446
+Status: successful
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0528
-Build needed 00:02:29, 8490k disc space
+Finished at 20110329-0501
+Build needed 00:01:34, 9446k disc space
diff --git a/mips.log b/mips.log
index 1983aa9..8f1590f 100644
--- a/mips.log
+++ b/mips.log
@@ -1,67 +1,67 @@
-From buildd at ball.debian.org Wed Mar 02 08:30:56 2011
-Return-path: <buildd at ball.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at lucatelli.debian.org Sat Apr 02 11:27:31 2011
+Return-path: <buildd at lucatelli.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 ball.debian.org>)
- id 1PuhSS-0002Mt-4Z
- for logs at buildd.debian.org; Wed, 02 Mar 2011 08:30:56 +0000
-Received: from ball.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d09])
+ (Exim 4.69) (envelope-from <buildd at lucatelli.debian.org>)
+ id 1Q5yzL-0004SJ-46
+ for logs at buildd.debian.org; Sat, 02 Apr 2011 11:27:31 +0000
+Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=ball.debian.org, EMAIL=hostmaster at ball.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at ball.debian.org>)
- id 1PuhSO-0001pk-MY
- for logs at buildd.debian.org; Wed, 02 Mar 2011 08:30:52 +0000
-Received: from buildd by ball.debian.org with local (Exim 4.69)
- (envelope-from <buildd at ball.debian.org>)
- id 1PuhSN-000452-Px; Wed, 02 Mar 2011 08:30:51 +0000
-From: buildd on ball <buildd at ball.debian.org>
-To: logs at buildd.debian.org,buildd-porters at ball.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on mips (dist=sid)
+ CN=lucatelli.debian.org,
+ EMAIL=hostmaster at lucatelli.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 1Q5yzG-0001p9-4c; Sat, 02 Apr 2011 11:27:26 +0000
+Received: from buildd by lucatelli.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at lucatelli.debian.org>)
+ id 1Q5yz6-00038J-NA; Sat, 02 Apr 2011 11:27:16 +0000
+From: buildd on lucatelli <buildd at lucatelli.debian.org>
+To: aba at debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.14-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PuhSN-000452-Px at ball.debian.org>
-Date: Wed, 02 Mar 2011 08:30:51 +0000
+Message-Id: <E1Q5yz6-00038J-NA at lucatelli.debian.org>
+Date: Sat, 02 Apr 2011 11:27:16 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on ball.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (mips) 02 Mar 2011 08:23 ║
+║ samtools 0.1.14-1 (mips) 02 Apr 2011 10:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: mips
-Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-e12386c2-4fa2-477c-a347-07dc3227f8c5/build/buildd-samtools_0.1.13-1-mips-vcsZoS
-Start Time: 20110302-0823
-Get:1 http://debian.netcologne.de unstable Release.gpg [835B]
-Ign http://debian.netcologne.de/debian/ unstable/contrib Translation-en
-Ign http://debian.netcologne.de/debian/ unstable/main Translation-en
-Get:2 http://debian.netcologne.de unstable Release [146kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [835B]
-Ign http://incoming.debian.org/debian/ unstable/contrib Translation-en
-Ign http://incoming.debian.org/debian/ unstable/main Translation-en
-Get:4 http://incoming.debian.org Release.gpg [835B]
-Ign http://incoming.debian.org/buildd-unstable/ Translation-en
-Get:5 http://incoming.debian.org unstable Release [146kB]
-Get:6 http://debian.netcologne.de unstable/main Sources [4155kB]
-Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://debian.netcologne.de unstable/contrib Sources [38.5kB]
-Get:9 http://debian.netcologne.de unstable/non-free Sources [82.8kB]
-Get:10 http://incoming.debian.org unstable/main Sources [4156kB]
-Get:11 http://debian.netcologne.de unstable/main mips Packages [6811kB]
-Get:12 http://debian.netcologne.de unstable/contrib mips Packages [51.5kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.5kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [82.8kB]
-Get:15 http://incoming.debian.org unstable/main mips Packages [6812kB]
-Get:16 http://incoming.debian.org unstable/contrib mips Packages [51.4kB]
-Get:17 http://incoming.debian.org Sources [19.5kB]
-Get:18 http://incoming.debian.org Packages [373kB]
-Fetched 23.0MB in 46s (495kB/s)
+Get:1 http://mirror-ubc.debian.org unstable InRelease [186 kB]
+Get:2 http://incoming.debian.org unstable InRelease [186 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5192 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 [5192 kB]
+Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [48.7 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [98.4 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [6876 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [52.9 kB]
+Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
+Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2232 B]
+Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [48.7 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [98.4 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [6876 kB]
+Get:14 http://incoming.debian.org unstable/contrib mips Packages [52.9 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [34.0 kB]
+Get:18 http://incoming.debian.org Packages [481 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Ign http://incoming.debian.org Translation-en
+Fetched 25.4 MB in 54s (466 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -79,93 +79,132 @@ Download source files with APT
Reading package lists...
Building dependency tree...
+Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523B]
-Fetched 374kB in 0s (402kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 0s (3371 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.15-1)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source 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-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)
+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)
+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)
+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)
+make: already installed (3.81-8)
+dpkg-dev: already installed (1.16.0 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
+Reading state information...
The following extra packages will be installed:
bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5 libpcre3 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 less www-browser libmail-box-perl
+ 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 64 not upgraded.
-Need to get 12.7MB of archives.
-After this operation, 38.0MB of additional disk space will be used.
-Get:1 http://debian.netcologne.de/debian/ unstable/main ncurses-bin mips 5.7+20100313-5 [317kB]
-Get:2 http://debian.netcologne.de/debian/ unstable/main libncurses5 mips 5.7+20100313-5 [349kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mips 8.2.2 [210kB]
-Get:4 http://debian.netcologne.de/debian/ unstable/main groff-base mips 1.21-4 [1203kB]
-Get:5 http://debian.netcologne.de/debian/ unstable/main libpipeline1 mips 1.1.0-1 [35.1kB]
-Get:6 http://debian.netcologne.de/debian/ unstable/main man-db mips 2.5.9-4 [997kB]
-Get:7 http://debian.netcologne.de/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
-Get:8 http://debian.netcologne.de/debian/ unstable/main file mips 5.04-5 [49.7kB]
-Get:9 http://debian.netcologne.de/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153kB]
-Get:10 http://debian.netcologne.de/debian/ unstable/main libpcre3 mips 8.12-3 [262kB]
-Get:11 http://debian.netcologne.de/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2 [837kB]
-Get:12 http://debian.netcologne.de/debian/ unstable/main html2text mips 1.3.2a-15 [103kB]
-Get:13 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 mips 2.28.1-1+b1 [1501kB]
-Get:14 http://debian.netcologne.de/debian/ unstable/main libcroco3 mips 0.6.2-1 [110kB]
-Get:15 http://debian.netcologne.de/debian/ unstable/main libunistring0 mips 0.9.3-3 [415kB]
-Get:16 http://debian.netcologne.de/debian/ unstable/main gettext mips 0.18.1.1-3 [2037kB]
-Get:17 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8kB]
-Get:18 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223kB]
-Get:19 http://debian.netcologne.de/debian/ unstable/main debhelper all 8.1.2 [553kB]
-Get:20 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.92 [1268kB]
-Get:21 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev mips 5.7+20100313-5 [1643kB]
-Get:22 http://debian.netcologne.de/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
+0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
+Need to get 10.9 MB of archives.
+After this operation, 32.6 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.2 [210 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-5 [1203 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-1 [35.7 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.5.9-4 [997 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5 [239 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5 [49.7 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2 [837 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.4-1 [1505 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-3 [415 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian mips 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf mips 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper mips 8.1.2 [553 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs mips 0.4.92 [1268 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.8+20110307-1 [510 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.7MB in 3s (3230kB/s)
-(Reading database ... 10123 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-5_mips.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.7+20100313-5) ...
-(Reading database ... 10123 files and directories currently installed.)
-Preparing to replace libncurses5 5.7+20100313-3 (using .../libncurses5_5.7+20100313-5_mips.deb) ...
-Unpacking replacement libncurses5 ...
-Setting up libncurses5 (5.7+20100313-5) ...
+Fetched 10.9 MB in 2s (5355 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10123 files and directories currently installed.)
+(Reading database ... 10112 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_1.21-4_mips.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_mips.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_mips.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mips.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_mips.deb) ...
Selecting previously deselected package libmagic1.
@@ -181,7 +220,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_mips.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_mips.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
Selecting previously deselected package libunistring0.
@@ -189,22 +228,22 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mips.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_mips.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_mips.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_mips.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_mips.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_mips.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_mips.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -213,7 +252,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+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) ...
@@ -222,13 +261,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
-Kernel: Linux 2.6.32.2-dsa-mips-swarm mips (mips64)
-Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.4-15 g++-4.4_4.4.4-15 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-15 libstdc++6_4.4.4-15
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.2.2 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-15 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-15 gcc_4:4.4.4-2 gcc-4.4_4.4.4-15 gcc-4.4-base_4.4.4-15 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-15 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-15 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-15 libstdc++6-4.4-dev_4.4.4-15 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-1 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
+Toolchain package versions: binutils_2.21.0.20110327-1 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_2.6.37-2
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-1 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_8.1.2 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 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 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_5.8+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_2.2.2-4 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_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8+20110307-1 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-18 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_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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -238,14 +281,14 @@ Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutil
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
+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 Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -254,41 +297,50 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture mips
- /usr/bin/fakeroot debian/rules clean
+ 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_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
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_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
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
@@ -307,9 +359,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/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
@@ -320,10 +373,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/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
@@ -342,24 +395,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/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
@@ -369,14 +422,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -405,9 +458,13 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ 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
@@ -439,7 +496,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -464,7 +521,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-mips-vcsZoS/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-mips-NRXuaA/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -479,73 +536,66 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_mips.deb'.
- dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../samtools_0.1.13-1_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.14-1_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-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0830
+Build finished at 20110402-1127
-samtools_0.1.13-1_mips.changes:
+samtools_0.1.14-1_mips.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
-Maintainer: Debian Build Daemon <buildd_mips-ball at buildd.debian.org>
+Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 19429914145f75322b5ea497e562d8671cfffd9a 612004 samtools_0.1.13-1_mips.deb
- c4f35b4344a0bacedecefe1346d9e10ca97f7b9a 178466 libbam-dev_0.1.13-1_mips.deb
+ c4a0df6c32a891ed1dadca5dc6614de6d53f722f 599612 samtools_0.1.14-1_mips.deb
+ c88b5ebcdb748eaa4e135e990a5422b04ca458c8 180344 libbam-dev_0.1.14-1_mips.deb
Checksums-Sha256:
- 9886d680a19a3f8facf21a093f195b501fdb3160397a08af91e5696c3c8f3fb8 612004 samtools_0.1.13-1_mips.deb
- 1c8b1ec23abcf52f0e22274329742c43c6fd065437637cdd8e5a50a8303d77c7 178466 libbam-dev_0.1.13-1_mips.deb
+ 2e79390623f3d483cf0ad9386e452c8adc0a0738f641c50e1525b12747caf22a 599612 samtools_0.1.14-1_mips.deb
+ c07b30fac7a34cda1af1de542db2bc2f37e390b26cd078c2370ffd0469af20cd 180344 libbam-dev_0.1.14-1_mips.deb
Files:
- 7c9aaf4dba7f011e454956aca53f312e 612004 science optional samtools_0.1.13-1_mips.deb
- 726c409ca321426acfbf088e4afada7b 178466 libdevel optional libbam-dev_0.1.13-1_mips.deb
+ 005f72cf2e67eb843919a839b950bbce 599612 science optional samtools_0.1.14-1_mips.deb
+ cc9a12c2ad91a0d762033fbb9e786104 180344 libdevel optional libbam-dev_0.1.14-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_mips.deb
+samtools_0.1.14-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 612004 bytes: control archive= 1787 bytes.
- 791 bytes, 16 lines control
+ size 599612 bytes: control archive= 1790 bytes.
+ 785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1180
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1208
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -557,71 +607,71 @@ samtools_0.1.13-1_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 2011-03-02 08:30 ./
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/samtools/
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-02 08:30 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-03-02 08:29 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/man/man1/
--rw-r--r-- root/root 1229 2011-03-02 08:30 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8164 2011-03-02 08:30 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-03-02 08:30 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/samtools/
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2011-03-02 08:30 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/lib/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7764 2011-04-02 11:26 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9768 2011-04-02 11:26 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 13268 2011-04-02 11:26 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-04-02 11:26 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 19944 2011-04-02 11:26 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/bin/
+-rwxr-xr-x root/root 133584 2011-04-02 11:26 ./usr/bin/bcftools
+-rwxr-xr-x root/root 465228 2011-04-02 11:26 ./usr/bin/samtools
+-rwxr-xr-x root/root 30712 2011-04-02 11:26 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/samtools/
-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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/bin/
--rwxr-xr-x root/root 30712 2011-03-02 08:30 ./usr/bin/razip
--rwxr-xr-x root/root 460960 2011-03-02 08:30 ./usr/bin/samtools
--rwxr-xr-x root/root 121204 2011-03-02 08:30 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/lib/samtools/
--rwxr-xr-x root/root 19928 2011-03-02 08:30 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9768 2011-03-02 08:30 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2011-03-02 08:30 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13268 2011-03-02 08:30 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2011-03-02 08:30 ./usr/lib/samtools/maq2sam-short
-
-
-libbam-dev_0.1.13-1_mips.deb
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2011-04-02 11:26 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 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 2011-04-02 11:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2011-04-02 10:52 ./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 1296 2011-03-29 04:14 ./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 2011-04-02 11:26 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/man/man1/
+-rw-r--r-- root/root 2005 2011-04-02 11:26 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-04-02 11:26 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 8393 2011-04-02 11:26 ./usr/share/man/man1/samtools.1.gz
+
+
+libbam-dev_0.1.14-1_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 178466 bytes: control archive= 898 bytes.
+ size 180344 bytes: control archive= 904 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 452
+ Installed-Size: 460
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -632,23 +682,23 @@ libbam-dev_0.1.13-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/lib/
+-rw-r--r-- root/root 309706 2011-04-02 11:26 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/include/
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./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 2011-04-02 11:26 ./usr/share/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-04-02 11:26 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/include/
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/lib/
--rw-r--r-- root/root 304468 2011-03-02 08:30 ./usr/lib/libbam.a
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -657,74 +707,97 @@ drwxr-xr-x root/root 0 2011-03-02 08:30 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mips-sbuild-e12386c2-4fa2-477c-a347-07dc3227f8c5/build/buildd-samtools_0.1.13-1-mips-vcsZoS
-Not removing build depends: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mips-sbuild-d66e71cd-c930-45f5-a382-5f876f353c80/build/buildd-samtools_0.1.14-1-mips-NRXuaA
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mips
+Build-Space: 9928
+Build-Time: 2466
+Distribution: sid
+Install-Time: 63
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 2625
+Source-Version: 0.1.14-1
+Space: 9928
+Status: successful
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0830
+Finished at 20110402-1127
+Build needed 00:43:45, 9928k disc space
-From buildd at mayer.debian.org Wed Mar 02 05:46:32 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at rem.debian.org Tue Mar 29 08:53:36 2011
+Return-path: <buildd at rem.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 mayer.debian.org>)
- id 1PuetL-0005cK-M5
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:32 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.69) (envelope-from <buildd at rem.debian.org>)
+ id 1Q4UgB-0005mD-5O
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 08:53:35 +0000
+Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
- id 1PuetI-0001iN-RD
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:29 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>)
- id 1PuetF-0002Hy-Rz; Wed, 02 Mar 2011 05:46:25 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
-To: buildd-porters at mayer.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on mipsel (dist=sid)
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1Q4Ug5-0003w9-Cp; Tue, 29 Mar 2011 08:53:29 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>)
+ id 1Q4Ug4-0004pX-IW; Tue, 29 Mar 2011 08:53:28 +0000
+Date: Tue, 29 Mar 2011 08:53:28 +0000
+Message-Id: <E1Q4Ug4-0004pX-IW at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
+To: aba+buildd_rem at not.so.argh.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.14-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PuetF-0002Hy-Rz at mayer.debian.org>
-Date: Wed, 02 Mar 2011 05:46:25 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (mipsel) 02 Mar 2011 05:41 ║
+║ samtools 0.1.14-1 (mipsel) 29 Mar 2011 08:47 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
-Start Time: 20110302-0541
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://mirror.ayous.org unstable InRelease [185 kB]
+Get:2 http://incoming.debian.org unstable InRelease [186 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [5142 kB]
+Get:4 http://mirror.ayous.org unstable/contrib Sources [47.4 kB]
+Get:5 http://mirror.ayous.org unstable/non-free Sources [99.4 kB]
+Get:6 http://mirror.ayous.org unstable/main mipsel Packages [6872 kB]
Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [835 B]
-Hit http://debian.oregonstate.edu sid InRelease
-Hit http://debian.oregonstate.edu sid/main Sources
-Hit http://debian.oregonstate.edu sid/contrib Sources
-Hit http://debian.oregonstate.edu sid/main mipsel Packages
-Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [19.5 kB]
-Get:4 http://incoming.debian.org Packages [373 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org Release [1604 B]
+Get:9 http://incoming.debian.org unstable/main Sources [5140 kB]
+Get:10 http://mirror.ayous.org unstable/contrib mipsel Packages [52.2 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:11 http://mirror.ayous.org unstable/main TranslationIndex [2232 B]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:12 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:14 http://incoming.debian.org unstable/main mipsel Packages [6869 kB]
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [52.2 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:17 http://incoming.debian.org Sources [29.5 kB]
+Get:18 http://incoming.debian.org Packages [637 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 395 kB in 2s (177 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 25.5 MB in 44s (567 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -742,62 +815,207 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 0s (410 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 1s (343 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
-debhelper: already installed (8.1.2 >= 8 is satisfied)
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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 (3.05)
+ncurses-base: already installed (5.7+20100313-5)
+ncurses-bin: already installed (5.7+20100313-5)
+perl-base: already installed (5.10.1-17)
+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)
+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 (4:4.4.5-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-2 >= 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)
+debhelper: missing
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev
+zlib1g-dev: missing
+Checking for dependency conflicts...
+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:
- libpopt0 pkg-config udev zlib1g-dev
-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
Suggested packages:
- devscripts doc-base
+ wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
+ groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev
+ bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ 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 27 not upgraded.
+Need to get 11.5 MB of archives.
+After this operation, 32.7 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main ncurses-bin mipsel 5.8+20110307-1 [328 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libncurses5 mipsel 5.8+20110307-1 [358 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.2 [207 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-5 [1154 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-1 [35.1 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.9-4 [980 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.2-1 [1496 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.8+20110307-1 [505 kB]
+Get:22 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 2 newly installed, 0 to remove and 10 not upgraded.
-Need to get 0 B/2907 kB of archives.
-After this operation, 8671 kB of additional disk space will be used.
+Fetched 11.5 MB in 1s (8242 kB/s)
+(Reading database ... 10176 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.7+20100313-5 (using .../ncurses-bin_5.8+20110307-1_mipsel.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.8+20110307-1) ...
+(Reading database ... 10177 files and directories currently installed.)
+Preparing to replace libncurses5 5.7+20100313-5 (using .../libncurses5_5.8+20110307-1_mipsel.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.8+20110307-1) ...
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10176 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mipsel.deb) ...
+Selecting previously deselected package groff-base.
+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_2.5.9-4_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_2.28.2-1_mipsel.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mipsel.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
+Selecting previously deselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously deselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 11889 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_mipsel.deb) ...
-Processing triggers for man-db ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_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 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 (2.5.9-4) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
+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 (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
+Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.4.5-12
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.63-1 libdpkg-perl_1.15.8.10 libgcc1_1:4.4.5-12 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-12 liblocale-gettext-perl_1.05-6 liblzma1_4.999.9beta+20091116-1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpopt0_1.16-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-12 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_166-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 pkg-config_0.25-1.1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 udev_166-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.20.1-16 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-10 gcc-4.4_4.4.5-10 libc6-dev_2.11.2-11 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 linux-libc-dev_2.6.37-1
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-6 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_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -807,14 +1025,13 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -829,25 +1046,25 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
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
@@ -856,8 +1073,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
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
@@ -876,9 +1093,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/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
@@ -889,10 +1107,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/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
@@ -911,24 +1129,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/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
@@ -938,14 +1156,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -974,9 +1192,9 @@ 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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -1008,7 +1226,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1033,7 +1251,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -1048,73 +1266,66 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.13-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.14-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0546
+Build finished at 20110329-0853
-samtools_0.1.13-1_mipsel.changes:
+samtools_0.1.14-1_mipsel.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
+Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 5901d8131d2a5ab7f91d6d5ec34a7590df033c49 614580 samtools_0.1.13-1_mipsel.deb
- c48e2280335b48710f8035593d4058fc84068915 179140 libbam-dev_0.1.13-1_mipsel.deb
+ 9e4876fbec4a8ba07353e394d60e72d6da104720 628462 samtools_0.1.14-1_mipsel.deb
+ 80c9f71040529d13aa4b9f6e3012e56dc60d2688 180964 libbam-dev_0.1.14-1_mipsel.deb
Checksums-Sha256:
- adc39bd662310f6d06d8dd0ced4d22c62748fc57d19d2307694b0e52acda5058 614580 samtools_0.1.13-1_mipsel.deb
- 8f66c76baf784bfdff627e21eb06bab4ef5d317e01862615634e1fba3deaa0ce 179140 libbam-dev_0.1.13-1_mipsel.deb
+ d51b6a383c05ef3dfbd9f229300fa99faea0d5a98a86b808be5cd60da486ad2a 628462 samtools_0.1.14-1_mipsel.deb
+ 3b9e78a078eb961b6f1f99c28f610ddef53093bd61788d22eb208173450fb20f 180964 libbam-dev_0.1.14-1_mipsel.deb
Files:
- 9ee93dbf8080e7350d75f35f0e602351 614580 science optional samtools_0.1.13-1_mipsel.deb
- 2e123c18f5c6ce1e892587f822e885fe 179140 libdevel optional libbam-dev_0.1.13-1_mipsel.deb
+ 373e112e5c09eea2a44f8b96ae9a19a5 628462 science optional samtools_0.1.14-1_mipsel.deb
+ 31c974e3d03e4840586b0ba41f8259c8 180964 libdevel optional libbam-dev_0.1.14-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_mipsel.deb
+samtools_0.1.14-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 614580 bytes: control archive= 1788 bytes.
- 793 bytes, 16 lines control
+ size 628462 bytes: control archive= 1787 bytes.
+ 787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1180
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1208
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -1126,71 +1337,71 @@ samtools_0.1.13-1_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 2011-03-02 05:45 ./
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-02 05:45 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-02 05:45 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-02 05:45 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-02 05:45 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 1229 2011-03-02 05:45 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9768 2011-03-29 08:53 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 19944 2011-03-29 08:53 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13268 2011-03-29 08:53 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-29 08:52 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 08:52 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 08:52 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-03-29 08:53 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 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 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-03-02 05:45 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/bin/
--rwxr-xr-x root/root 121204 2011-03-02 05:45 ./usr/bin/bcftools
--rwxr-xr-x root/root 30584 2011-03-02 05:45 ./usr/bin/razip
--rwxr-xr-x root/root 460960 2011-03-02 05:45 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/samtools/
--rwxr-xr-x root/root 19960 2011-03-02 05:45 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13268 2011-03-02 05:45 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9768 2011-03-02 05:45 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.13-1_mipsel.deb
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2011-03-29 08:52 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2011-03-29 08:52 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./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 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/bin/
+-rwxr-xr-x root/root 465228 2011-03-29 08:53 ./usr/bin/samtools
+-rwxr-xr-x root/root 133584 2011-03-29 08:53 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-03-29 08:53 ./usr/bin/razip
+
+
+libbam-dev_0.1.14-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 179140 bytes: control archive= 896 bytes.
+ size 180964 bytes: control archive= 906 bytes.
675 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 452
+ Installed-Size: 460
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -1201,23 +1412,23 @@ libbam-dev_0.1.13-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:46 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/include/
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/
+-rw-r--r-- root/root 309810 2011-03-29 08:53 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 05:46 ./usr/lib/
--rw-r--r-- root/root 304188 2011-03-02 05:46 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1226,12 +1437,31 @@ drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
-(Reading database ... 12996 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing cdbs ...
-Processing triggers for man-db ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-16618150-cfe1-42f6-875a-1aca472b2e4a/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 9952
+Build-Time: 237
+Distribution: sid
+Install-Time: 61
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 374
+Source-Version: 0.1.14-1
+Space: 9952
+Status: successful
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0546
-Build needed 00:04:43, 9760k disc space
+Finished at 20110329-0853
+Build needed 00:06:14, 9952k disc space
diff --git a/mipsel.log b/mipsel.log
index ffd9775..633972e 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,66 +1,66 @@
-From buildd at mayer.debian.org Wed Mar 02 05:46:32 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at rem.debian.org Tue Mar 29 08:53:36 2011
+Return-path: <buildd at rem.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 mayer.debian.org>)
- id 1PuetL-0005cK-M5
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:32 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.69) (envelope-from <buildd at rem.debian.org>)
+ id 1Q4UgB-0005mD-5O
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 08:53:35 +0000
+Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at mayer.debian.org>)
- id 1PuetI-0001iN-RD
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:46:29 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>)
- id 1PuetF-0002Hy-Rz; Wed, 02 Mar 2011 05:46:25 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
-To: buildd-porters at mayer.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on mipsel (dist=sid)
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1Q4Ug5-0003w9-Cp; Tue, 29 Mar 2011 08:53:29 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>)
+ id 1Q4Ug4-0004pX-IW; Tue, 29 Mar 2011 08:53:28 +0000
+Date: Tue, 29 Mar 2011 08:53:28 +0000
+Message-Id: <E1Q4Ug4-0004pX-IW at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
+To: aba+buildd_rem at not.so.argh.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.14-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1PuetF-0002Hy-Rz at mayer.debian.org>
-Date: Wed, 02 Mar 2011 05:46:25 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (mipsel) 02 Mar 2011 05:41 ║
+║ samtools 0.1.14-1 (mipsel) 29 Mar 2011 08:47 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: mipsel
-Chroot Build Dir: /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
-Start Time: 20110302-0541
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://mirror.ayous.org unstable InRelease [185 kB]
+Get:2 http://incoming.debian.org unstable InRelease [186 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [5142 kB]
+Get:4 http://mirror.ayous.org unstable/contrib Sources [47.4 kB]
+Get:5 http://mirror.ayous.org unstable/non-free Sources [99.4 kB]
+Get:6 http://mirror.ayous.org unstable/main mipsel Packages [6872 kB]
Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [835 B]
-Hit http://debian.oregonstate.edu sid InRelease
-Hit http://debian.oregonstate.edu sid/main Sources
-Hit http://debian.oregonstate.edu sid/contrib Sources
-Hit http://debian.oregonstate.edu sid/main mipsel Packages
-Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:2 http://incoming.debian.org Release [1604 B]
-Get:3 http://incoming.debian.org Sources [19.5 kB]
-Get:4 http://incoming.debian.org Packages [373 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org Release [1604 B]
+Get:9 http://incoming.debian.org unstable/main Sources [5140 kB]
+Get:10 http://mirror.ayous.org unstable/contrib mipsel Packages [52.2 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:11 http://mirror.ayous.org unstable/main TranslationIndex [2232 B]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:12 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:14 http://incoming.debian.org unstable/main mipsel Packages [6869 kB]
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [52.2 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
+Get:17 http://incoming.debian.org Sources [29.5 kB]
+Get:18 http://incoming.debian.org Packages [637 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 395 kB in 2s (177 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 25.5 MB in 44s (567 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,62 +78,207 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 0s (410 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/debian/ unstable/main samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 1s (343 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
-debhelper: already installed (8.1.2 >= 8 is satisfied)
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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 (3.05)
+ncurses-base: already installed (5.7+20100313-5)
+ncurses-bin: already installed (5.7+20100313-5)
+perl-base: already installed (5.10.1-17)
+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)
+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 (4:4.4.5-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-2 >= 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)
+debhelper: missing
+Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev
+zlib1g-dev: missing
+Checking for dependency conflicts...
+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:
- libpopt0 pkg-config udev zlib1g-dev
-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
Suggested packages:
- devscripts doc-base
+ wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
+ groff ncurses-doc less www-browser libmail-box-perl
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ libgpm2 xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev
+ bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
+ 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 27 not upgraded.
+Need to get 11.5 MB of archives.
+After this operation, 32.7 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main ncurses-bin mipsel 5.8+20110307-1 [328 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libncurses5 mipsel 5.8+20110307-1 [358 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.2 [207 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-5 [1154 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-1 [35.1 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.5.9-4 [980 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5 [238 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5 [49.5 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-2 [833 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.2-1 [1496 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-3 [411 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.8+20110307-1 [505 kB]
+Get:22 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 2 newly installed, 0 to remove and 10 not upgraded.
-Need to get 0 B/2907 kB of archives.
-After this operation, 8671 kB of additional disk space will be used.
+Fetched 11.5 MB in 1s (8242 kB/s)
+(Reading database ... 10176 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.7+20100313-5 (using .../ncurses-bin_5.8+20110307-1_mipsel.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.8+20110307-1) ...
+(Reading database ... 10177 files and directories currently installed.)
+Preparing to replace libncurses5 5.7+20100313-5 (using .../libncurses5_5.8+20110307-1_mipsel.deb) ...
+Unpacking replacement libncurses5 ...
+Setting up libncurses5 (5.8+20110307-1) ...
+Selecting previously deselected package bsdmainutils.
+(Reading database ... 10176 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mipsel.deb) ...
+Selecting previously deselected package groff-base.
+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_2.5.9-4_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_2.28.2-1_mipsel.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-3_mipsel.deb) ...
+Selecting previously deselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-3_mipsel.deb) ...
+Selecting previously deselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously deselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously deselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 11889 files and directories currently installed.)
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_mipsel.deb) ...
-Processing triggers for man-db ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_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 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 (2.5.9-4) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5) ...
+Setting up file (5.04-5) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-2) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
+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 (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
+Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.4.5-12
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.3-base_4.3.5-4 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdevmapper1.02.1_2:1.02.63-1 libdpkg-perl_1.15.8.10 libgcc1_1:4.4.5-12 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-12 liblocale-gettext-perl_1.05-6 liblzma1_4.999.9beta+20091116-1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libncursesw5_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libpopt0_1.16-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-12 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libudev0_166-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 pkg-config_0.25-1.1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 udev_166-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.20.1-16 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-10 gcc-4.4_4.4.5-10 libc6-dev_2.11.2-11 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 linux-libc-dev_2.6.37-1
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-16 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-10 gcc_4:4.4.5-2 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.5-10 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-6 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_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.8+20110307-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -143,14 +288,13 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -165,25 +309,25 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture mipsel
- /usr/bin/fakeroot debian/rules clean
+ fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
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
@@ -192,8 +336,8 @@ test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
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
@@ -212,9 +356,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/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
@@ -225,10 +370,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/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
@@ -247,24 +392,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/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
@@ -274,14 +419,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -310,9 +455,9 @@ 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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -344,7 +489,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -369,7 +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_0.1.13-1-mipsel-6gQP9i/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-mipsel-_HS1qn/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -384,73 +529,66 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.13-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.13-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.13-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.14-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0546
+Build finished at 20110329-0853
-samtools_0.1.13-1_mipsel.changes:
+samtools_0.1.14-1_mipsel.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
+Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 5901d8131d2a5ab7f91d6d5ec34a7590df033c49 614580 samtools_0.1.13-1_mipsel.deb
- c48e2280335b48710f8035593d4058fc84068915 179140 libbam-dev_0.1.13-1_mipsel.deb
+ 9e4876fbec4a8ba07353e394d60e72d6da104720 628462 samtools_0.1.14-1_mipsel.deb
+ 80c9f71040529d13aa4b9f6e3012e56dc60d2688 180964 libbam-dev_0.1.14-1_mipsel.deb
Checksums-Sha256:
- adc39bd662310f6d06d8dd0ced4d22c62748fc57d19d2307694b0e52acda5058 614580 samtools_0.1.13-1_mipsel.deb
- 8f66c76baf784bfdff627e21eb06bab4ef5d317e01862615634e1fba3deaa0ce 179140 libbam-dev_0.1.13-1_mipsel.deb
+ d51b6a383c05ef3dfbd9f229300fa99faea0d5a98a86b808be5cd60da486ad2a 628462 samtools_0.1.14-1_mipsel.deb
+ 3b9e78a078eb961b6f1f99c28f610ddef53093bd61788d22eb208173450fb20f 180964 libbam-dev_0.1.14-1_mipsel.deb
Files:
- 9ee93dbf8080e7350d75f35f0e602351 614580 science optional samtools_0.1.13-1_mipsel.deb
- 2e123c18f5c6ce1e892587f822e885fe 179140 libdevel optional libbam-dev_0.1.13-1_mipsel.deb
+ 373e112e5c09eea2a44f8b96ae9a19a5 628462 science optional samtools_0.1.14-1_mipsel.deb
+ 31c974e3d03e4840586b0ba41f8259c8 180964 libdevel optional libbam-dev_0.1.14-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_mipsel.deb
+samtools_0.1.14-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 614580 bytes: control archive= 1788 bytes.
- 793 bytes, 16 lines control
+ size 628462 bytes: control archive= 1787 bytes.
+ 787 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1180
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1208
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -462,71 +600,71 @@ samtools_0.1.13-1_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 2011-03-02 05:45 ./
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-03-02 05:45 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-03-02 05:45 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-03-02 05:45 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8164 2011-03-02 05:45 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 1229 2011-03-02 05:45 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9768 2011-03-29 08:53 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 19944 2011-03-29 08:53 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13268 2011-03-29 08:53 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2011-03-29 08:53 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-03-29 08:52 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 08:52 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 8393 2011-03-29 08:52 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-03-29 08:53 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 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 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-03-02 05:45 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/bin/
--rwxr-xr-x root/root 121204 2011-03-02 05:45 ./usr/bin/bcftools
--rwxr-xr-x root/root 30584 2011-03-02 05:45 ./usr/bin/razip
--rwxr-xr-x root/root 460960 2011-03-02 05:45 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/lib/samtools/
--rwxr-xr-x root/root 19960 2011-03-02 05:45 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7764 2011-03-02 05:45 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13268 2011-03-02 05:45 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9768 2011-03-02 05:45 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.13-1_mipsel.deb
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2011-03-29 08:52 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2011-03-29 08:52 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./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 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/bin/
+-rwxr-xr-x root/root 465228 2011-03-29 08:53 ./usr/bin/samtools
+-rwxr-xr-x root/root 133584 2011-03-29 08:53 ./usr/bin/bcftools
+-rwxr-xr-x root/root 30584 2011-03-29 08:53 ./usr/bin/razip
+
+
+libbam-dev_0.1.14-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 179140 bytes: control archive= 896 bytes.
+ size 180964 bytes: control archive= 906 bytes.
675 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 452
+ Installed-Size: 460
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -537,23 +675,23 @@ libbam-dev_0.1.13-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:46 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/include/
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/lib/
+-rw-r--r-- root/root 309810 2011-03-29 08:53 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 08:52 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 08:53 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-03-02 05:46 ./usr/lib/
--rw-r--r-- root/root 304188 2011-03-02 05:46 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -562,12 +700,31 @@ drwxr-xr-x root/root 0 2011-03-02 05:45 ./usr/include/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-34b0f464-07a4-4cfa-9177-9ea76bc1a353/build/buildd-samtools_0.1.13-1-mipsel-6gQP9i
-(Reading database ... 12996 files and directories currently installed.)
-Removing libncurses5-dev ...
-Removing cdbs ...
-Processing triggers for man-db ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-16618150-cfe1-42f6-875a-1aca472b2e4a/build/buildd-samtools_0.1.14-1-mipsel-_HS1qn
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: mipsel
+Build-Space: 9952
+Build-Time: 237
+Distribution: sid
+Install-Time: 61
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 374
+Source-Version: 0.1.14-1
+Space: 9952
+Status: successful
+Version: 0.1.14-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0546
-Build needed 00:04:43, 9760k disc space
+Finished at 20110329-0853
+Build needed 00:06:14, 9952k disc space
diff --git a/powerpc.log b/powerpc.log
index bf0fc85..0fbfd9e 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,68 +1,69 @@
-From buildd at poulenc.debian.org Wed Mar 02 05:25:39 2011
+From buildd at poulenc.debian.org Tue Mar 29 05:01:41 2011
Return-path: <buildd at poulenc.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 poulenc.debian.org>)
- id 1PueZ8-0002Xg-Tr
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:25:39 +0000
+ id 1Q4R3l-0002mh-1V
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:01:41 +0000
Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
helo=poulenc.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=poulenc.debian.org, EMAIL=hostmaster at poulenc.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 4.69) (envelope-from <buildd at poulenc.debian.org>)
- id 1PueZ5-0006Af-Dp; Wed, 02 Mar 2011 05:25:35 +0000
+ id 1Q4R3h-0003Ua-Lv; Tue, 29 Mar 2011 05:01:37 +0000
Received: from buildd by poulenc.debian.org with local (Exim 4.69)
(envelope-from <buildd at poulenc.debian.org>)
- id 1PueZ4-0007wN-Uv; Wed, 02 Mar 2011 05:25:34 +0000
+ id 1Q4R3f-0003qN-CA; Tue, 29 Mar 2011 05:01:35 +0000
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
+Date: Tue, 29 Mar 2011 05:01:35 +0000
From: buildd on poulenc <buildd at poulenc.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on powerpc (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1PueZ4-0007wN-Uv at poulenc.debian.org>
-Date: Wed, 02 Mar 2011 05:25:34 +0000
+Subject: Log for successful build of samtools_0.1.14-1 on powerpc (dist=sid)
+Key-Id: 205E9E83
+Message-Id: <E1Q4R3f-0003qN-CA at poulenc.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on poulenc.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on poulenc.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (powerpc) 02 Mar 2011 05:22 ║
+║ samtools 0.1.14-1 (powerpc) 29 Mar 2011 04:58 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: powerpc
-Chroot Build Dir: /var/lib/schroot/mount/sid-powerpc-sbuild-dc383189-78ef-48ae-9752-00541d455a5a/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY
-Start Time: 20110302-0522
-Get:1 http://ftp.uk.debian.org unstable InRelease [147 kB]
-Get:2 http://incoming.debian.org unstable InRelease [147 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [4155 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [184 kB]
+Get:2 http://ftp.uk.debian.org unstable/main Sources [5169 kB]
+Get:3 http://incoming.debian.org unstable InRelease [185 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [835 B]
-Get:5 http://incoming.debian.org unstable/main Sources [4156 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [38.5 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [82.8 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [6906 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [51.2 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [5142 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [47.0 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [99.0 kB]
+Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [6965 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [51.4 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2232 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [6908 kB]
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [51.2 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [6970 kB]
+Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [51.4 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [19.2 kB]
-Get:18 http://incoming.debian.org Packages [373 kB]
+Get:17 http://incoming.debian.org Sources [30.5 kB]
+Get:18 http://incoming.debian.org Packages [608 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 23.2 MB in 24s (955 kB/s)
+Fetched 25.7 MB in 30s (851 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,30 +84,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (310 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 1s (325 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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 (5.10.1-17)
+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)
+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 (4:4.5.2-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.5.2-2 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -117,7 +167,7 @@ The following extra packages will be installed:
man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ 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
@@ -125,12 +175,12 @@ 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 5 not upgraded.
-Need to get 12.1 MB of archives.
-After this operation, 37.0 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 28 not upgraded.
+Need to get 11.0 MB of archives.
+After this operation, 31.6 MB of additional disk space will be used.
Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.2 [209 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-4 [1168 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.1.0-1 [36.9 kB]
+Get: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 2.5.9-4 [1001 kB]
Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5 [241 kB]
Get:6 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5 [49.9 kB]
@@ -138,7 +188,7 @@ Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1
Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-3 [258 kB]
Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-2 [849 kB]
Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.1-1+b1 [1594 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.2-1 [1598 kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-3 [422 kB]
Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
@@ -146,17 +196,17 @@ Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0
Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.7+20100313-5 [1633 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.8-1 [500 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 12.1 MB in 4s (2988 kB/s)
+Fetched 11.0 MB in 1s (6030 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10202 files and directories currently installed.)
+(Reading database ... 10319 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_1.21-4_powerpc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_powerpc.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_powerpc.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_powerpc.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_powerpc.deb) ...
Selecting previously deselected package libmagic1.
@@ -172,7 +222,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_powerpc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_powerpc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.2-1_powerpc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
Selecting previously deselected package libunistring0.
@@ -188,14 +238,14 @@ Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
Selecting previously deselected package cdbs.
Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_powerpc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8-1_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) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -204,7 +254,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+Setting up libglib2.0-0 (2.28.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
@@ -213,13 +263,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+Checking correctness of dependencies...
Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-1 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.5.2-4
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110302-1 dpkg-dev_1.15.8.10 g++-4.5_4.5.2-5 gcc-4.5_4.5.2-5 libc6-dev_2.11.2-11 libstdc++6_4.5.2-5 libstdc++6-4.5-dev_4.5.2-5 linux-libc-dev_2.6.37-2
+Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110302-1 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_4:4.5.2-2 cpp-4.5_4.5.2-5 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-2 g++-4.5_4.5.2-5 gcc_4:4.5.2-2 gcc-4.4-base_4.4.5-13 gcc-4.5_4.5.2-5 gcc-4.5-base_4.5.2-5 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 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_1.15.8.10 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.2-1 libgmp10_2:5.0.1+dfsg-6 libgmp3c2_2:4.3.2+dfsg-1 libgmpxx4ldbl_2:5.0.1+dfsg-6 libgomp1_4.5.2-5 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-1 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_0.11.2-1 libppl7_0.10.2-9 libppl9_0.11.2-1 libpwl5_0.11.2-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-5 libstdc++6-4.5-dev_4.5.2-5 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.8-1 ncurses-bin_5.8-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011c-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 │
@@ -229,14 +283,14 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
+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 Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -245,41 +299,50 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture powerpc
- /usr/bin/fakeroot debian/rules clean
+ 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_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
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_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
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
@@ -298,9 +361,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/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
@@ -311,10 +375,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/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
@@ -333,24 +397,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/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
@@ -360,14 +424,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -380,8 +444,8 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/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
-[bam_rmdup_core] processing reference seq1...
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
+[bam_rmdup_core] processing reference seq1...
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
@@ -396,9 +460,13 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/examples'
+ fakeroot debian/rules binary-arch
touch debian/stamp-makefile-check
- /usr/bin/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
@@ -430,7 +498,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -455,7 +523,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-powerpc-LUjtNL/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -470,27 +538,27 @@ 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_0.1.13-1_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.13-1_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.14-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0525
+Build finished at 20110329-0501
-samtools_0.1.13-1_powerpc.changes:
+samtools_0.1.14-1_powerpc.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
@@ -498,45 +566,38 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- ec854a8fd08c95b6eef5d027e164e7a424b577ba 596096 samtools_0.1.13-1_powerpc.deb
- 64e036078167da575fc8f378d5d106cd51485f17 167942 libbam-dev_0.1.13-1_powerpc.deb
+ 23f92911b4f4f57644ffd0f2e6b7249a2489217a 609078 samtools_0.1.14-1_powerpc.deb
+ 155eed0613b949db7c19842579721f9745defab3 169584 libbam-dev_0.1.14-1_powerpc.deb
Checksums-Sha256:
- 014deaaeb06a67a27db7d52215604397974d60b5def385b009236c22b605e492 596096 samtools_0.1.13-1_powerpc.deb
- dd35627bfbf8f9808e7bc43f19e10f8dc046ed24b0d5c8ad76514390f75f9aa5 167942 libbam-dev_0.1.13-1_powerpc.deb
+ 038c075d8da67f36a5a3e2d0e91a9d8d2ea1d53084f1c0f786dc5b1665c40935 609078 samtools_0.1.14-1_powerpc.deb
+ 3b19a3483170e5d5186f72c3e3ea8e8ea2c19a6a120451a0206aa925ab9ce468 169584 libbam-dev_0.1.14-1_powerpc.deb
Files:
- c0c3acfb780b67494a4284202432cfca 596096 science optional samtools_0.1.13-1_powerpc.deb
- 439cf6a8cebeea3997943ab032ab689d 167942 libdevel optional libbam-dev_0.1.13-1_powerpc.deb
+ 7e04dd9c3b726829131ba2c5de342e2f 609078 science optional samtools_0.1.14-1_powerpc.deb
+ 1296c5bfc7f112820687d8b006d4f477 169584 libdevel optional libbam-dev_0.1.14-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_powerpc.deb
+samtools_0.1.14-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 596096 bytes: control archive= 1789 bytes.
- 794 bytes, 16 lines control
+ size 609078 bytes: control archive= 1788 bytes.
+ 788 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1072
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1100
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -548,18 +609,18 @@ samtools_0.1.13-1_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 2011-03-02 05:25 ./
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/man/man1/
--rw-r--r-- root/root 8164 2011-03-02 05:25 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 1229 2011-03-02 05:25 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-03-02 05:25 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/samtools/
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/man/man1/
+-rw-r--r-- root/root 8393 2011-03-29 05:01 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 05:01 ./usr/share/man/man1/bcftools.1.gz
+-rw-r--r-- root/root 430 2011-03-29 05:01 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/samtools/
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 5778 2011-03-02 05:25 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-03-29 05:01 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
@@ -570,49 +631,49 @@ drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/samtools/
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 1966 2011-03-02 05:25 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1966 2011-03-29 05:01 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2011-03-02 05:25 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-29 05:01 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/lib/samtools/
--rwxr-xr-x root/root 7352 2011-03-02 05:25 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11116 2011-03-02 05:25 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8008 2011-03-02 05:25 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7352 2011-03-02 05:25 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 19404 2011-03-02 05:25 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/bin/
--rwxr-xr-x root/root 384456 2011-03-02 05:25 ./usr/bin/samtools
--rwxr-xr-x root/root 26828 2011-03-02 05:25 ./usr/bin/razip
--rwxr-xr-x root/root 101192 2011-03-02 05:25 ./usr/bin/bcftools
-
-
-libbam-dev_0.1.13-1_powerpc.deb
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7368 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11148 2011-03-29 05:01 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7992 2011-03-29 05:01 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7384 2011-03-29 05:01 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 19668 2011-03-29 05:01 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/bin/
+-rwxr-xr-x root/root 392096 2011-03-29 05:01 ./usr/bin/samtools
+-rwxr-xr-x root/root 26824 2011-03-29 05:01 ./usr/bin/razip
+-rwxr-xr-x root/root 109892 2011-03-29 05:01 ./usr/bin/bcftools
+
+
+libbam-dev_0.1.14-1_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 167942 bytes: control archive= 901 bytes.
+ size 169584 bytes: control archive= 906 bytes.
676 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 412
+ Installed-Size: 420
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -623,23 +684,23 @@ libbam-dev_0.1.13-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/include/
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/include/
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/khash.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./usr/include/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/lib/
--rw-r--r-- root/root 262160 2011-03-02 05:25 ./usr/lib/libbam.a
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+drwxr-xr-x root/root 0 2011-03-29 05:01 ./usr/lib/
+-rw-r--r-- root/root 269610 2011-03-29 05:01 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -648,9 +709,31 @@ drwxr-xr-x root/root 0 2011-03-02 05:25 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-dc383189-78ef-48ae-9752-00541d455a5a/build/buildd-samtools_0.1.13-1-powerpc-ZXJaAY
-Not removing build depends: cloned chroot in use
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0525
-Build needed 00:02:56, 9344k disc space
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-7ce15bea-2f5e-46ec-b54c-eef9e9ac79e5/build/buildd-samtools_0.1.14-1-powerpc-LUjtNL
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: powerpc
+Build-Space: 10164
+Build-Time: 78
+Distribution: sid
+Install-Time: 63
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 187
+Source-Version: 0.1.14-1
+Space: 10164
+Status: successful
+Version: 0.1.14-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110329-0501
+Build needed 00:03:07, 10164k disc space
+Signature with key '205E9E83' requested:
diff --git a/s390.log b/s390.log
index 8477c09..986893e 100644
--- a/s390.log
+++ b/s390.log
@@ -1,4 +1,4 @@
-From buildd at zandonai.debian.org Wed Mar 02 05:22:51 2011
+From buildd at zandonai.debian.org Tue Mar 29 05:03:26 2011
Return-path: <buildd at zandonai.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,63 +6,64 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
- id 1PueWQ-0001hb-T1
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:22:51 +0000
+ id 1Q4R5S-000346-GR
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 05:03:26 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.69) (envelope-from <buildd at zandonai.debian.org>)
- id 1PueWO-00019m-QS; Wed, 02 Mar 2011 05:22:48 +0000
+ id 1Q4R5P-0003W3-7h; Tue, 29 Mar 2011 05:03:23 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.69)
(envelope-from <buildd at zandonai.debian.org>)
- id 1PueWN-0002FS-EF; Wed, 02 Mar 2011 05:22:47 +0000
+ id 1Q4R5N-0004zZ-6m; Tue, 29 Mar 2011 05:03:21 +0000
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
+Date: Tue, 29 Mar 2011 05:03:21 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.13-1 on s390 (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1PueWN-0002FS-EF at zandonai.debian.org>
-Date: Wed, 02 Mar 2011 05:22:47 +0000
+Subject: Log for successful build of samtools_0.1.14-1 on s390 (dist=sid)
+Key-Id: 9BD94C88
+Message-Id: <E1Q4R5N-0004zZ-6m at zandonai.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on zandonai.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (s390) 02 Mar 2011 05:21 ║
+║ samtools 0.1.14-1 (s390) 29 Mar 2011 05:01 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: s390
-Chroot Build Dir: /var/lib/schroot/mount/sid-s390-sbuild-043a721a-9346-4640-90d0-b639032ed477/build/buildd-samtools_0.1.13-1-s390-Msk1pi
-Start Time: 20110302-0521
-Get:1 http://ftp.de.debian.org unstable InRelease [147 kB]
-Get:2 http://incoming.debian.org unstable InRelease [147 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [4156 kB]
+Get:1 http://ftp.de.debian.org unstable InRelease [184 kB]
+Get:2 http://incoming.debian.org unstable InRelease [185 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5169 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [835 B]
-Get:5 http://incoming.debian.org unstable/main Sources [4156 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [38.5 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [82.8 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [6828 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [49.9 kB]
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [5142 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [47.0 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [99.0 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [6883 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [50.4 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2232 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [6828 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [49.9 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [6888 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [50.4 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [19.2 kB]
-Get:18 http://incoming.debian.org Packages [373 kB]
+Get:17 http://incoming.debian.org Sources [30.5 kB]
+Get:18 http://incoming.debian.org Packages [608 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 23.0 MB in 26s (855 kB/s)
+Fetched 25.5 MB in 32s (786 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,30 +84,79 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (287 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 1s (289 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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)
+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)
+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 (4:4.4.5-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-4 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -117,7 +167,7 @@ The following extra packages will be installed:
man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ 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
@@ -125,38 +175,38 @@ 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 0 not upgraded.
-Need to get 12.2 MB of archives.
-After this operation, 36.5 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 9 not upgraded.
+Need to get 11.1 MB of archives.
+After this operation, 31.2 MB of additional disk space will be used.
Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.2 [208 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-4 [1158 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.1.0-1 [38.0 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.5.9-4 [1015 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.1-1+b1 [1629 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-5 [1158 kB]
+Get:3 http://incoming.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.4-1 [1635 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-1 [38.7 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.5.9-4 [1015 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5 [243 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5 [50.0 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2 [873 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-3 [431 kB]
Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.7+20100313-5 [1634 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian s390 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf s390 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper s390 8.1.2 [553 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs s390 0.4.92 [1268 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.8+20110307-1 [503 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 12.2 MB in 3s (3519 kB/s)
+Fetched 11.1 MB in 3s (3234 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10125 files and directories currently installed.)
+(Reading database ... 10127 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_1.21-4_s390.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_s390.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_s390.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_s390.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_s390.deb) ...
Selecting previously deselected package libmagic1.
@@ -172,7 +222,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_s390.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_s390.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_s390.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
Selecting previously deselected package libunistring0.
@@ -180,22 +230,22 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_s390.deb) ...
Selecting previously deselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_s390.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_s390.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_s390.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_s390.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_s390.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_s390.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -204,7 +254,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+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) ...
@@ -213,13 +263,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-s390x s390 (s390x)
-Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-2 gcc-4.4_4.4.5-13 g++-4.4_4.4.5-13 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-13 libstdc++6_4.5.2-4
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-13 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-2 g++-4.4_4.4.5-13 gcc_4:4.4.5-2 gcc-4.4_4.4.5-13 gcc-4.4-base_4.4.5-13 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-13 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-14 gcc-4.4_4.4.5-14 libc6-dev_2.11.2-11 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 linux-libc-dev_2.6.38-1
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110322-1 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_4:4.4.5-4 cpp-4.4_4.4.5-14 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-4 g++-4.4_4.4.5-14 gcc_4:4.4.5-4 gcc-4.4_4.4.5-14 gcc-4.4-base_4.4.5-14 gcc-4.5-base_4.5.2-6 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-13.1 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_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.5.2-6 liblocale-gettext-perl_1.05-6 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_2.0.96-1 libsepol1_2.0.42-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 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_2.5.9-4 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_5.10.1-18 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -229,14 +283,14 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
+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 Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -245,41 +299,50 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture s390
- /usr/bin/fakeroot debian/rules clean
+ 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_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
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_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
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
@@ -298,9 +361,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/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
@@ -311,10 +375,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/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
@@ -333,24 +397,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/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
@@ -360,14 +424,14 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -396,9 +460,13 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/examples'
touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
+ 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
@@ -430,7 +498,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -455,7 +523,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.13-1-s390-Msk1pi/samtools-0.1.13/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.14-1-s390-jqHPik/samtools-0.1.14/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -470,27 +538,27 @@ 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_0.1.13-1_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.14-1_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_0.1.13-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.13-1_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.14-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.14-1_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-0.1.13
+ dpkg-source --after-build samtools-0.1.14
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0522
+Build finished at 20110329-0503
-samtools_0.1.13-1_s390.changes:
+samtools_0.1.14-1_s390.changes:
Format: 1.8
-Date: Wed, 02 Mar 2011 13:54:34 +0900
+Date: Tue, 29 Mar 2011 13:13:54 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.13-1
+Version: 0.1.14-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -498,45 +566,38 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 606004 616025
Changes:
- samtools (0.1.13-1) unstable; urgency=low
+ samtools (0.1.14-1) unstable; urgency=low
.
- * New upstream release:
- - backward incompatible with VCF/BCF generated by samtools older
- than r921 inclusive (0.1.12a is r862);
- - buildable with with ld --as-needed (Closes: #606004);
- - the helper tool bcf-fix.pl was removed.
- * Install the manual page of bcftools (debian/rules,
- debian/samtools.manpages). Closes: #616025.
+ * New upstream release.
Checksums-Sha1:
- 46e902da61e714377fe849430ef98c069f158890 592758 samtools_0.1.13-1_s390.deb
- 6c100382b345290d249c94504122c864636f3e80 169590 libbam-dev_0.1.13-1_s390.deb
+ 7a0121edd4478eb920016cf54511717e3093b70a 599798 samtools_0.1.14-1_s390.deb
+ d0e46a3d85499e7d3859187c878eae339a5149cb 170978 libbam-dev_0.1.14-1_s390.deb
Checksums-Sha256:
- 2396f980b7c9a6bbe8104b1cffc8918221794b14a2fa4f16fd4416df1eda84d9 592758 samtools_0.1.13-1_s390.deb
- 13987d40937564a92cb650132863f65cf9d21295b3c748efc6d3069ba1a1ffff 169590 libbam-dev_0.1.13-1_s390.deb
+ 2209fbe1bac794ee42c3889dd722398bf37daa9e3bc312a0901dd84555a41044 599798 samtools_0.1.14-1_s390.deb
+ 542b3a1200f89417ed82a791d09f315d0c3e6e5e895ad17671c1f60a44c6b06b 170978 libbam-dev_0.1.14-1_s390.deb
Files:
- 7dce94745af66705410759840c4bb6cc 592758 science optional samtools_0.1.13-1_s390.deb
- ce14ed862c383d2110c6655b4dd2c9e7 169590 libdevel optional libbam-dev_0.1.13-1_s390.deb
+ efd3eff690deee25ef7db33b611c913d 599798 science optional samtools_0.1.14-1_s390.deb
+ 16711d7315c1328e8d55379e62f7cb37 170978 libdevel optional libbam-dev_0.1.14-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.13-1_s390.deb
+samtools_0.1.14-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 592758 bytes: control archive= 1783 bytes.
- 791 bytes, 16 lines control
+ size 599798 bytes: control archive= 1779 bytes.
+ 785 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1092
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1116
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -548,27 +609,27 @@ samtools_0.1.13-1_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 2011-03-02 05:22 ./
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/bin/
--rwxr-xr-x root/root 104532 2011-03-02 05:22 ./usr/bin/bcftools
--rwxr-xr-x root/root 399072 2011-03-02 05:22 ./usr/bin/samtools
--rwxr-xr-x root/root 27380 2011-03-02 05:22 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/lib/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/lib/samtools/
--rwxr-xr-x root/root 11324 2011-03-02 05:22 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7188 2011-03-02 05:22 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7188 2011-03-02 05:22 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7932 2011-03-02 05:22 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 18564 2011-03-02 05:22 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/man/man1/
--rw-r--r-- root/root 8164 2011-03-02 05:22 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-03-02 05:22 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 1229 2011-03-02 05:22 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/samtools/
--rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/bin/
+-rwxr-xr-x root/root 113080 2011-03-29 05:03 ./usr/bin/bcftools
+-rwxr-xr-x root/root 403648 2011-03-29 05:03 ./usr/bin/samtools
+-rwxr-xr-x root/root 27380 2011-03-29 05:03 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/lib/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11324 2011-03-29 05:03 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7188 2011-03-29 05:03 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7188 2011-03-29 05:03 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7932 2011-03-29 05:03 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18564 2011-03-29 05:03 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/man/man1/
+-rw-r--r-- root/root 8393 2011-03-29 05:03 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-03-29 05:03 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 2005 2011-03-29 05:03 ./usr/share/man/man1/bcftools.1.gz
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./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
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
@@ -577,42 +638,42 @@ drwxr-xr-x root/root 0 2011-03-02 05:22 ./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 2011-03-02 05:22 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-03-29 05:03 ./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 2011-03-02 05:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/samtools/
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2011-03-02 04:30 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2011-03-29 03:51 ./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 2011-03-02 04:30 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2011-03-02 05:22 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-03-29 03:51 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2011-03-29 05:03 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1280 2011-03-02 04:54 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./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 2011-03-02 05:22 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-03-29 05:03 ./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
-libbam-dev_0.1.13-1_s390.deb
+libbam-dev_0.1.14-1_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 169590 bytes: control archive= 891 bytes.
+ size 170978 bytes: control archive= 896 bytes.
673 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.13-1
+ Version: 0.1.14-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 408
+ Installed-Size: 416
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -623,23 +684,23 @@ libbam-dev_0.1.13-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/include/
--rw-r--r-- root/root 24165 2011-03-01 19:50 ./usr/include/bam.h
--rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/include/
+-rw-r--r-- root/root 24165 2011-03-22 03:09 ./usr/include/bam.h
+-rw-r--r-- root/root 4580 2011-03-22 03:09 ./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 2011-03-02 05:22 ./usr/lib/
--rw-r--r-- root/root 258332 2011-03-02 05:22 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 7887 2011-03-01 19:50 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/lib/
+-rw-r--r-- root/root 263338 2011-03-29 05:03 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-03-29 05:03 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 8225 2011-03-22 03:09 ./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 1280 2011-03-02 04:54 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5171 2011-03-02 04:37 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1296 2011-03-29 04:14 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5287 2011-03-29 04:05 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -648,9 +709,31 @@ drwxr-xr-x root/root 0 2011-03-02 05:22 ./usr/share/doc/libbam-dev/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390-sbuild-043a721a-9346-4640-90d0-b639032ed477/build/buildd-samtools_0.1.13-1-s390-Msk1pi
-Not removing build depends: cloned chroot in use
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0522
-Build needed 00:01:38, 9672k disc space
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-s390-sbuild-d1dabdcc-44f9-445d-84cf-4e96fe5d167b/build/buildd-samtools_0.1.14-1-s390-jqHPik
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: s390
+Build-Space: 9836
+Build-Time: 43
+Distribution: sid
+Install-Time: 18
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 102
+Source-Version: 0.1.14-1
+Space: 9836
+Status: successful
+Version: 0.1.14-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110329-0503
+Build needed 00:01:42, 9836k disc space
+Signature with key '9BD94C88' requested:
diff --git a/sparc.log b/sparc.log
index 1139afa..aa43417 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,68 +1,70 @@
-From buildd at lebrun.debian.org Wed Mar 02 05:26:12 2011
-Return-path: <buildd at lebrun.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at schroeder.debian.org Tue Mar 29 07:16:52 2011
+Return-path: <buildd at schroeder.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 lebrun.debian.org>)
- id 1PueZg-0002ja-3h
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:26:12 +0000
-Received: from lebrun.debian.org ([193.198.184.10])
+ (Exim 4.69) (envelope-from <buildd at schroeder.debian.org>)
+ id 1Q4TAa-0004hN-DD
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 07:16:52 +0000
+Received: from schroeder.debian.org ([193.198.184.11])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.69) (envelope-from <buildd at lebrun.debian.org>)
- id 1PueZd-0001F3-Kw
- for logs at buildd.debian.org; Wed, 02 Mar 2011 05:26:10 +0000
-Received: from buildd by lebrun.debian.org with local (Exim 4.69)
- (envelope-from <buildd at lebrun.debian.org>)
- id 1PueZb-0005Ep-LC; Wed, 02 Mar 2011 05:26:07 +0000
-From: buildd on lebrun <buildd at lebrun.debian.org>
-To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
-Subject: Log for attempted build of samtools_0.1.13-1 on sparc (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1PueZb-0005Ep-LC at lebrun.debian.org>
-Date: Wed, 02 Mar 2011 05:26:07 +0000
+ 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 1Q4TAU-0001OQ-PK
+ for logs at buildd.debian.org; Tue, 29 Mar 2011 07:16:46 +0000
+Received: from buildd by schroeder.debian.org with local (Exim 4.69)
+ (envelope-from <buildd at schroeder.debian.org>)
+ id 1Q4TAU-0006tp-1t; Tue, 29 Mar 2011 07:16:46 +0000
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
+Date: Tue, 29 Mar 2011 07:16:45 +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_0.1.14-1 on sparc (dist=sid)
+Key-Id: 9BBB678A
+Message-Id: <E1Q4TAU-0006tp-1t at schroeder.debian.org>
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on lebrun.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.13-1 (sparc) 02 Mar 2011 05:22 ║
+║ samtools 0.1.14-1 (sparc) 29 Mar 2011 07:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.13-1
+Version: 0.1.14-1
+Source Version: 0.1.14-1
Architecture: sparc
-Chroot Build Dir: /var/lib/schroot/mount/sid-sparc-sbuild-30bb6ad2-5de7-4de9-950a-9c1381aa6c71/build/buildd-samtools_0.1.13-1-sparc-0vH7vX
-Start Time: 20110302-0522
-Get:1 http://debian.carnet.hr unstable InRelease [147 kB]
-Get:2 http://incoming.debian.org unstable InRelease [147 kB]
-Get:3 http://debian.carnet.hr unstable/main Sources [4156 kB]
-Get:4 http://debian.carnet.hr unstable/contrib Sources [38.5 kB]
+Get:1 http://ftp.carnet.hr unstable InRelease [185 kB]
+Get:2 http://incoming.debian.org unstable InRelease [185 kB]
+Get:3 http://ftp.carnet.hr unstable/main Sources [5142 kB]
+Get:4 http://ftp.carnet.hr unstable/contrib Sources [47.4 kB]
Ign http://incoming.debian.org InRelease
-Get:5 http://incoming.debian.org Release.gpg [835 B]
-Get:6 http://incoming.debian.org unstable/main Sources [4156 kB]
-Get:7 http://debian.carnet.hr unstable/non-free Sources [82.8 kB]
-Get:8 http://debian.carnet.hr unstable/main sparc Packages [6855 kB]
-Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [51.2 kB]
-Ign http://debian.carnet.hr unstable/contrib TranslationIndex
-Get:10 http://debian.carnet.hr unstable/main TranslationIndex [2232 B]
-Get:11 http://incoming.debian.org unstable/contrib Sources [38.5 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [82.8 kB]
-Get:13 http://incoming.debian.org unstable/main sparc Packages [6855 kB]
-Get:14 http://incoming.debian.org unstable/contrib sparc Packages [51.2 kB]
+Get:5 http://incoming.debian.org Release.gpg [836 B]
+Get:6 http://incoming.debian.org unstable/main Sources [5142 kB]
+Get:7 http://ftp.carnet.hr unstable/non-free Sources [99.4 kB]
+Get:8 http://ftp.carnet.hr unstable/main sparc Packages [6905 kB]
+Get:9 http://ftp.carnet.hr unstable/contrib sparc Packages [51.5 kB]
+Ign http://ftp.carnet.hr unstable/contrib TranslationIndex
+Get:10 http://ftp.carnet.hr unstable/main TranslationIndex [2232 B]
+Get:11 http://incoming.debian.org unstable/contrib Sources [47.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
+Get:13 http://incoming.debian.org unstable/main sparc Packages [6905 kB]
+Get:14 http://incoming.debian.org unstable/contrib sparc Packages [51.5 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2232 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Ign http://debian.carnet.hr unstable/contrib Translation-en
-Get:17 http://incoming.debian.org Sources [19.2 kB]
-Get:18 http://incoming.debian.org Packages [373 kB]
+Ign http://ftp.carnet.hr unstable/contrib Translation-en
+Get:17 http://incoming.debian.org Sources [30.7 kB]
+Get:18 http://incoming.debian.org Packages [630 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 23.1 MB in 24s (929 kB/s)
+Fetched 25.5 MB in 26s (956 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,30 +85,80 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 374 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (tar) [365 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.13-1 (diff) [6523 B]
-Fetched 374 kB in 1s (255 kB/s)
+Need to get 379 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (dsc) [1939 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (tar) [370 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.14-1 (diff) [6869 B]
+Fetched 379 kB in 1s (309 kB/s)
Download complete and in download only mode
Check arch
──────────
-** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.14.5-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+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-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)
+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 (5.10.1-18)
+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)
+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 (4:4.4.5-4 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.4.5-4 >= 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)
debhelper: missing
Using default version 8.1.2
cdbs: missing
libncurses5-dev: missing
zlib1g-dev: missing
-Checking for source dependency conflicts...
+Checking for dependency conflicts...
Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
@@ -117,7 +169,7 @@ The following extra packages will be installed:
man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff less www-browser libmail-box-perl
+ 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
@@ -125,38 +177,38 @@ 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 5 not upgraded.
-Need to get 12.0 MB of archives.
-After this operation, 36.3 MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.2 [205 kB]
-Get:2 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-4 [1155 kB]
-Get:3 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.1.0-1 [35.0 kB]
-Get:4 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.5.9-4 [1007 kB]
-Get:5 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5 [239 kB]
-Get:6 http://debian.carnet.hr/debian/ unstable/main file sparc 5.04-5 [49.5 kB]
-Get:7 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
-Get:8 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
-Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-2 [840 kB]
-Get:10 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.1-1+b1 [1546 kB]
-Get:12 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-3 [424 kB]
-Get:14 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
-Get:15 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.1.2 [553 kB]
-Get:18 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.92 [1268 kB]
-Get:19 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.7+20100313-5 [1611 kB]
-Get:20 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+0 upgraded, 20 newly installed, 0 to remove and 9 not upgraded.
+Need to get 10.9 MB of archives.
+After this operation, 30.9 MB of additional disk space will be used.
+Get:1 http://ftp.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.2 [205 kB]
+Get:2 http://incoming.debian.org/buildd-unstable/ libglib2.0-0 2.28.4-1 [1553 kB]
+Get:3 http://ftp.carnet.hr/debian/ unstable/main groff-base sparc 1.21-5 [1152 kB]
+Get:4 http://ftp.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-1 [35.8 kB]
+Get:5 http://ftp.carnet.hr/debian/ unstable/main man-db sparc 2.5.9-4 [1007 kB]
+Get:6 http://ftp.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5 [239 kB]
+Get:7 http://ftp.carnet.hr/debian/ unstable/main file sparc 5.04-5 [49.5 kB]
+Get:8 http://ftp.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
+Get:9 http://ftp.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
+Get:10 http://ftp.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-2 [840 kB]
+Get:11 http://ftp.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:12 http://ftp.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
+Get:13 http://ftp.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-3 [424 kB]
+Get:14 http://ftp.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
+Get:15 http://ftp.carnet.hr/debian/ unstable/main intltool-debian sparc 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.carnet.hr/debian/ unstable/main po-debconf sparc 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.carnet.hr/debian/ unstable/main debhelper sparc 8.1.2 [553 kB]
+Get:18 http://ftp.carnet.hr/debian/ unstable/main cdbs sparc 0.4.92 [1268 kB]
+Get:19 http://ftp.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.8+20110307-1 [481 kB]
+Get:20 http://ftp.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.0 MB in 7s (1516 kB/s)
+Fetched 10.9 MB in 7s (1436 kB/s)
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10479 files and directories currently installed.)
+(Reading database ... 10488 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_1.21-4_sparc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-5_sparc.deb) ...
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.1.0-1_sparc.deb) ...
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_sparc.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.5.9-4_sparc.deb) ...
Selecting previously deselected package libmagic1.
@@ -172,7 +224,7 @@ Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.1-1+b1_sparc.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_sparc.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
Selecting previously deselected package libunistring0.
@@ -180,22 +232,22 @@ Unpacking libunistring0 (from .../libunistring0_0.9.3-3_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_all.deb) ...
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_sparc.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_sparc.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.2_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.2_sparc.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.92_sparc.deb) ...
Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-5_sparc.deb) ...
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.8+20110307-1_sparc.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
Setting up bsdmainutils (8.2.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-4) ...
-Setting up libpipeline1 (1.1.0-1) ...
+Setting up groff-base (1.21-5) ...
+Setting up libpipeline1 (1.2.0-1) ...
Setting up man-db (2.5.9-4) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5) ...
@@ -204,7 +256,7 @@ Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
Setting up libxml2 (2.7.8.dfsg-2) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.1-1+b1) ...
+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) ...
@@ -213,13 +265,17 @@ Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.1.2) ...
Setting up cdbs (0.4.92) ...
-Setting up libncurses5-dev (5.7+20100313-5) ...
+Setting up libncurses5-dev (5.8+20110307-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
-Checking correctness of source dependencies...
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc (sparc64)
-Toolchain package versions: libc6-dev_2.11.2-11 dpkg-dev_1.15.8.10 linux-libc-dev_2.6.37-2 gcc-4.4_4.4.5-12 g++-4.4_4.4.5-12 binutils_2.21.0.20110216-2 libstdc++6-4.4-dev_4.4.5-12 libstdc++6_4.5.2-4
-Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.0.20110216-2 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.4.5-2 cpp-4.4_4.4.5-12 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b2 g++_4:4.4.5-2 g++-4.4_4.4.5-12 gcc_4:4.4.5-2 gcc-4.4_4.4.5-12 gcc-4.4-base_4.4.5-12 gcc-4.5-base_4.5.2-4 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-4 gzip_1.3.12-9 hostname_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13.1 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-11 libc-dev-bin_2.11.2-11 libc6_2.11.2-11 libc6-dev_2.11.2-11 libc6-dev-sparc64_2.11.2-11 libc6-sparc64_2.11.2-11 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-4 libdpkg-perl_1.15.8.10 libgc1c2_1:7.1-6 libgcc1_1:4.5.2-4 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.1-1+b1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.5.2-4 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr4_3.0.0-7 libncurses5_5.7+20100313-5 libncurses5-dev_5.7+20100313-5 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.1.0-1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.42-1 libss2_1.41.12-2 libstdc++6_4.5.2-4 libstdc++6-4.4-dev_4.4.5-12 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.37-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.7+20100313-5 ncurses-bin_5.7+20100313-5 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.10.1-17 perl-base_5.10.1-17 perl-modules_5.10.1-17 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011b-2 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.0.20110322-1 dpkg-dev_1.15.8.10 g++-4.4_4.4.5-14 gcc-4.4_4.4.5-14 libc6-dev_2.11.2-11 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 linux-libc-dev_2.6.38-1
+Package versions: apt_0.8.13 base-files_6.1 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.0.20110322-1 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_4:4.4.5-4 cpp-4.4_4.4.5-14 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.2 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.15.8.10 dpkg-dev_1.15.8.10 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.5-2 file_5.04-5 findutils_4.4.2-1+b2 g++_4:4.4.5-4 g++-4.4_4.4.5-14 gcc_4:4.4.5-4 gcc-4.4_4.4.5-14 gcc-4.4-base_4.4.5-14 gcc-4.5-base_4.5.2-6 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-13.1 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_1.15.8.10 libgc1c2_1:7.1-7 libgcc1_1:4.5.2-6 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.5.2-6 liblocale-gettext-perl_1.05-6+b1 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_2.0.96-1 libsepol1_2.0.42-1 libss2_1.41.12-2 libstdc++6_4.5.2-6 libstdc++6-4.4-dev_4.4.5-14 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8 man-db_2.5.9-4 mawk_1.3.3-15+b1 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_5.10.1-18 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -229,14 +285,14 @@ Package versions: apt_0.8.11.5 base-files_6.1 base-passwd_3.5.22+b1 bash_4.1-3 b
Unpack source
─────────────
-dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
+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 Wed Mar 2 05:08:33 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Mar 29 04:36:06 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.13-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.13
-dpkg-source: info: unpacking samtools_0.1.13.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.13-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.14-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.14
+dpkg-source: info: unpacking samtools_0.1.14.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.14-1.debian.tar.gz
Check disc space
────────────────
@@ -245,41 +301,50 @@ 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 0.1.13-1
- dpkg-source --before-build samtools-0.1.13
+dpkg-buildpackage: source version 0.1.14-1
+ dpkg-source --before-build samtools-0.1.14
dpkg-buildpackage: host architecture sparc
- /usr/bin/fakeroot debian/rules clean
+ 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_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
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_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
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
@@ -298,9 +363,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. 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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/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
@@ -311,10 +377,10 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/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
@@ -333,24 +399,24 @@ gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_K
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
gcc -g -O2 -g -O2 -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/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
@@ -360,29 +426,47 @@ gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/misc'
gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/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_0.1.13-1-sparc-0vH7vX/samtools-0.1.13/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2/samtools-0.1.14/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110302-0526
+Build finished at 20110329-0716
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-30bb6ad2-5de7-4de9-950a-9c1381aa6c71/build/buildd-samtools_0.1.13-1-sparc-0vH7vX
-Not removing build depends: cloned chroot in use
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110302-0526
-Build needed 00:03:28, 5524k disc space
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-1f17b091-dc18-40ea-9d8a-12962f92cec8/build/buildd-samtools_0.1.14-1-sparc-TQ4pX2
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+Architecture: sparc
+Build-Space: 5648
+Build-Time: 98
+Distribution: sid
+Fail-Stage: build
+Install-Time: 68
+Job: samtools_0.1.14-1
+Package: samtools
+Package-Time: 215
+Source-Version: 0.1.14-1
+Space: 5648
+Status: attempted
+Version: 0.1.14-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110329-0716
+Build needed 00:03:35, 5648k disc space
+Signature with key '9BBB678A' requested:
--
Processing of sequence alignments in SAM and BAM formats.
More information about the debian-med-commit
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