[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.16-1-3-g3df22f3
Charles Plessy
plessy at debian.org
Tue Sep 6 08:39:14 UTC 2011
The following commit has been merged in the meta branch:
commit 3328e003a447350b43ad550bf253f01392f396b3
Author: Charles Plessy <plessy at debian.org>
Date: Tue Sep 6 16:01:06 2011 +0900
Collected build logs for 0.1.17-1.
diff --git a/armel.log b/armel.log
index b339e87..11e0b72 100644
--- a/armel.log
+++ b/armel.log
@@ -1,4 +1,4 @@
-From buildd at ancina.debian.org Thu May 19 04:48:22 2011
+From buildd at ancina.debian.org Tue Jul 12 17:59:18 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,
@@ -6,70 +6,62 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
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+ id 1QghEr-0007Vh-VT
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 17:59:18 +0000
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+ id 1QghEq-0000dR-On
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 17:59:16 +0000
Received: from buildd by ancina.debian.org with local (Exim 4.69)
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- id 1QMv9j-0005ww-02; Thu, 19 May 2011 04:48:15 +0000
+ id 1QghEk-0003rF-Mu; Tue, 12 Jul 2011 17:59:10 +0000
MIME-Version: 1.0
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-Date: Thu, 19 May 2011 04:48:14 +0000
+Date: Tue, 12 Jul 2011 17:59:10 +0000
From: Build Daemon <buildd at ancina.debian.org>
To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.16-1 on armel (dist=sid)
+Subject: Log for attempted build of samtools_0.1.17-1 on armel (dist=sid)
Key-Id: A1EAA0BB
-Message-Id: <E1QMv9j-0005ww-02 at ancina.debian.org>
+Message-Id: <E1QghEk-0003rF-Mu 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 0.1.16-1 (armel) 19 May 2011 04:42 ║
+║ samtools 0.1.17-1 (armel) 12 Jul 2011 17:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: armel
-Get:1 http://ftp.de.debian.org sid InRelease [146 kB]
-Get:2 http://incoming.debian.org sid InRelease [146 kB]
-Get:3 http://ftp.de.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://ftp.de.debian.org sid InRelease
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
+Get:2 http://incoming.debian.org Release [1604 B]
Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Get:4 http://ftp.de.debian.org sid/main armel Packages/DiffIndex [2038 B]
+Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Get:5 http://ftp.de.debian.org sid/main TranslationIndex [2264 B]
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://ftp.de.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Get:8 http://ftp.de.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
-Get:9 http://ftp.de.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Get:10 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://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
-Get:11 http://incoming.debian.org sid/main armel Packages/DiffIndex [2038 B]
+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
-Get:12 http://incoming.debian.org sid/main TranslationIndex [2264 B]
-Get:13 http://ftp.de.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
+Hit http://incoming.debian.org sid/main TranslationIndex
+Hit http://incoming.debian.org Sources
+Get:3 http://incoming.debian.org Packages [526 kB]
Ign http://ftp.de.debian.org sid/contrib Translation-en
-Get:14 http://incoming.debian.org Release [1604 B]
-Get:15 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Get:16 http://incoming.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
-Get:17 http://incoming.debian.org Sources [26.8 kB]
-Get:18 http://incoming.debian.org Packages [270 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Get:19 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Get:20 http://incoming.debian.org sid/main armel 2011-05-19-0211.17.pdiff [10.3 kB]
-Fetched 635 kB in 21s (29.5 kB/s)
+Ign http://incoming.debian.org sid/contrib Translation-en
+Fetched 528 kB in 13s (39.8 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -90,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (378 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://ftp.de.debian.org/debian/ sid/main samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 0s (1007 kB/s)
Download complete and in download only mode
Check arch
@@ -108,99 +100,99 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- groff-base libpipeline1 libssl0.9.8 man-db
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- groff-base libpipeline1 libssl0.9.8 man-db
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.2)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
tar: already installed (1.25-3)
-bsdutils: already installed (1:2.17.2-9.1)
+bsdutils: already installed (1:2.19.1-2)
mount: already installed (2.17.2-9.1)
-util-linux: already installed (2.17.2-9.1)
-libc6-dev: already installed (2.13-2)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-7)
+gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libssl0.9.8
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
- libmagic1 libunistring0 libxml2 po-debconf
+ diffstat file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf
Suggested packages:
- devscripts dh-make gettext-doc ncurses-doc libmail-box-perl
+ devscripts dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl procmail graphviz
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
- libglib2.0-0 libmagic1 libncurses5-dev libunistring0 libxml2 po-debconf
- zlib1g-dev
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 15 newly installed, 0 to remove and 20 not upgraded.
-Need to get 0 B/6919 kB of archives.
-After this operation, 21.2 MB of additional disk space will be used.
+0 upgraded, 20 newly installed, 0 to remove and 15 not upgraded.
+Need to get 0 B/9391 kB of archives.
+After this operation, 28.0 MB of additional disk space will be used.
+Selecting previously deselected package libpipeline1.
+(Reading database ... 11252 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_armel.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-1_armel.deb) ...
Selecting previously deselected package libmagic1.
-(Reading database ... 11632 files and directories currently installed.)
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_armel.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_armel.deb) ...
Selecting previously deselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_armel.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_armel.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_armel.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -216,18 +208,25 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_armel.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_armel.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
-Processing triggers for man-db ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-1) ...
+Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -236,22 +235,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libssl0.9.8
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-3
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-5 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.7_4.7.25-18 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.4 libldap-2.4-2_2.4.25-1+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libsasl2-2_2.1.23.dfsg1-8 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libssl0.9.8_0.9.8o-7 libssl1.0.0_1.0.0d-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libudev0_168-2 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 nullmailer_1:1.05-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 wget_1.12-3.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-3 gcc-4.6_4.6.1-3 libc6-dev_2.13-7 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 linux-libc-dev_2.6.39-2
+Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-3 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-3 gcc-4.6-base_4.6.1-3 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6_2.13-7 libc6-dev_2.13-7 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-3 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-2 libgomp1_4.6.1-3 libgpg-error0_1.10-0.3 libgpm2_1.20.4-3.4 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 libtasn1-3_2.9-4 libtimedate-perl_1.2000-1 libudev0_171-3 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libvolume-id1_0.141-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 nullmailer_1:1.05-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.14-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 wget_1.12-3.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -261,14 +259,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -277,50 +275,68 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/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_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/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_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
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 -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -341,7 +357,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -355,28 +370,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -395,25 +410,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -423,55 +438,57 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-armel-pTW4iV/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/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_0.1.16-1-armel-pTW4iV/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-armel-Waxu30/samtools-0.1.17/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0448
+Build finished at 20110712-1758
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-07f266a1-570b-4ca5-950b-e0c54b32a6a0/build/buildd-samtools_0.1.16-1-armel-pTW4iV
+Purging /var/lib/schroot/mount/sid-armel-sbuild-5d53a889-878a-46d1-913e-aa08f7672685/build/buildd-samtools_0.1.17-1-armel-Waxu30
Reading package lists...
Building dependency tree...
Reading state information...
-The following package was automatically installed and is no longer required:
- libssl0.9.8
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- groff-base libpipeline1 libssl0.9.8 man-db
-Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
- cdbs* debhelper* file* gettext* gettext-base* html2text* intltool-debian*
- libcroco3* libglib2.0-0* libmagic1* libncurses5-dev* libunistring0* libxml2*
- po-debconf* zlib1g-dev*
-0 upgraded, 0 newly installed, 15 to remove and 20 not upgraded.
-After this operation, 21.2 MB disk space will be freed.
-(Reading database ... 12552 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
+ libncurses5-dev* libpipeline1* libunistring0* libxml2* man-db* po-debconf*
+ quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 20 to remove and 15 not upgraded.
+After this operation, 28.0 MB disk space will be freed.
+(Reading database ... 12647 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
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 ...
@@ -481,30 +498,31 @@ 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 ...
-Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 6220
-Build-Time: 252
+Build-Space: 6076
+Build-Time: 268
Distribution: sid
Fail-Stage: build
-Install-Time: 32
-Job: samtools_0.1.16-1
+Install-Time: 31
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 330
-Source-Version: 0.1.16-1
-Space: 6220
+Package-Time: 334
+Source-Version: 0.1.17-1
+Space: 6076
Status: attempted
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0448
-Build needed 00:05:30, 6220k disc space
+Finished at 20110712-1758
+Build needed 00:05:34, 6076k disc space
diff --git a/hurd-i386.log b/hurd-i386.log
index a0339f9..ba76113 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,68 +1,144 @@
-From buildd at mozart.debian.net Thu May 19 05:32:44 2011
-Return-path: <buildd at mozart.debian.net>
-Received: from callisto.debian.net ([80.87.129.151])
+From buildd at rossini.debian.net Mon Jul 11 13:19:00 2011
+Return-path: <buildd at rossini.debian.net>
+Received: from io.ethz.ch ([129.132.80.17] helo=io.debian.net)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
- id 1QMvql-0007PI-EM
- for logs at buildd.debian.org; Thu, 19 May 2011 05:32:44 +0000
-Received: from mozart.debian.net ([10.1.0.1])
- by callisto.debian.net with esmtp (Exim 4.69)
- (envelope-from <buildd at mozart.debian.net>)
- id 1QMvqj-0005St-SU; Thu, 19 May 2011 06:32:41 +0100
-Received: from buildd by mozart.debian.net with local (Exim 4.72)
- (envelope-from <buildd at mozart.debian.net>)
- id 1QMvr8-0002YF-Jh; Thu, 19 May 2011 05:33:06 +0000
-Date: Thu, 19 May 2011 05:33:06 +0000
-Message-Id: <E1QMvr8-0002YF-Jh at mozart.debian.net>
-From: Build Daemon <buildd at mozart.debian.net>
+ (Exim 4.72) (envelope-from <buildd at rossini.debian.net>)
+ id 1QgGO3-0002C6-U9
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 13:19:00 +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 1QgGO1-000Fmu-IX; Mon, 11 Jul 2011 15:18:57 +0200
+Received: from buildd by rossini.debian.net with local (Exim 4.72)
+ (envelope-from <buildd at rossini.debian.net>)
+ id 1QgGO0-0000zD-UB; Mon, 11 Jul 2011 13:18:56 +0000
+Message-Id: <E1QgGO0-0000zD-UB at rossini.debian.net>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.78; B3.08; Q3.08)
+Date: Mon, 11 Jul 2011 13:18:56 +0000
+From: Build Daemon <buildd at rossini.debian.net>
To: samuel.thibault at labri.fr, mbanck at gmx.net, logs at buildd.debian-ports.org,
logs at buildd.debian.org, debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on hurd-i386 (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
+Subject: Log for successful build of samtools_0.1.17-1 on hurd-i386 (dist=sid)
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.59.1 (31 Jan 2010) on mozart.debian.net
+sbuild (Debian sbuild) 0.62.3 (11 Jun 2011) on rossini.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (hurd-i386) 19 mai 2011 05:26 ║
+║ samtools 0.1.17-1 (hurd-i386) 11 Jul 2011 13:02 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
+Distribution: sid
Architecture: hurd-i386
-Chroot Build Dir: /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759
-Start Time: 20110519-0526
+
+I: NOTICE: Log filtering will replace 'build/samtools-Bjor1m/samtools-0.1.17' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-Bjor1m' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'home/buildd/build/chroot-sid' with '«CHROOT»'
+W: Stripped single quote from command for security:
+ use strict;
+ use warnings;
+ use POSIX;
+ use FileHandle;
+
+ my $lockfile="/var/lock/sbuild";
+ my $try = 0;
+
+ repeat:
+ if (!sysopen( F, $lockfile, O_WRONLY|O_CREAT|O_TRUNC|O_EXCL, 0644 )){
+ if ($! == EEXIST) {
+ # lock file exists, wait
+ goto repeat if !open( F, "<$lockfile" );
+ my $line = <F>;
+ my ($job, $pid, $user);
+ close( F );
+ if ($line !~ /^(\S+)\s+(\S+)\s+(\S+)/) {
+ print STDERR "Bad lock file contents ($lockfile) -- still trying\n";
+ } else {
+ ($job, $pid, $user) = ($1, $2, $3);
+ if (kill( 0, $pid ) == 0 && $! == ESRCH) {
+ # process doesn't exist anymore, remove stale lock
+ print STDERR "Removing stale lock file $lockfile ".
+ "(job $job, pid $pid, user $user)\n";
+ if (!unlink($lockfile)) {
+ if ($! != ENOENT) {
+ print STDERR "Cannot remove chroot lock file $lockfile: $!\n";
+ exit 1;
+ }
+ }
+ }
+ }
+ ++$try;
+ if ($try > 120) {
+ print STDERR "Lockfile $lockfile still present after " .
+ 120 * 5 . " seconds -- giving up\n";
+ exit 1;
+ }
+ print STDERR "Another sbuild process (job $job, pid $pid by user $user) is currently using the build chroot; waiting...\n"
+ if $try == 1;
+ sleep 5;
+ goto repeat;
+ } else {
+ print STDERR "Can't create lock file $lockfile: $!\n";
+ exit 1;
+ }
+ }
+
+ F->print("samtools_0.1.17-1 1424 buildd\n");
+ F->close();
+
+ exit 0;
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
Ign file: ./ InRelease
Ign file: ./ Release.gpg
Ign file: ./ Release
Ign file: ./ Translation-en
-Hit http://ftp.uk.debian.org sid InRelease
-Hit http://ftp.uk.debian.org sid/main Sources/DiffIndex
+Hit http://ftp.ch.debian.org unstable InRelease
+Hit http://ftp.ch.debian.org experimental InRelease
+Hit http://ftp.fr.debian.org unstable InRelease
+Hit http://ftp.ch.debian.org unstable/main Sources/DiffIndex
+Hit http://ftp.fr.debian.org experimental InRelease
Ign http://ftp.debian-ports.org unreleased InRelease
Ign http://incoming.debian.org InRelease
-Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
-Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
-Hit http://ftp.uk.debian.org sid/main TranslationIndex
-Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
+Hit http://ftp.ch.debian.org unstable/contrib Sources/DiffIndex
+Hit http://ftp.ch.debian.org unstable/non-free Sources/DiffIndex
+Hit http://ftp.ch.debian.org unstable/main hurd-i386 Packages/DiffIndex
Hit http://ftp.debian-ports.org unreleased Release.gpg
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Ign http://ftp.uk.debian.org sid/contrib Translation-en
-Ign http://ftp.uk.debian.org sid/non-free Translation-en
-Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://incoming.debian.org Release.gpg
+Hit http://ftp.ch.debian.org unstable/main TranslationIndex
+Hit http://ftp.ch.debian.org experimental/main Sources/DiffIndex
+Hit http://ftp.ch.debian.org experimental/contrib Sources/DiffIndex
+Hit http://ftp.ch.debian.org experimental/non-free Sources/DiffIndex
+Hit http://ftp.fr.debian.org unstable/main Sources/DiffIndex
+Get:1 http://incoming.debian.org Release [1604 B]
Hit http://ftp.debian-ports.org unreleased Release
-Get:3 http://incoming.debian.org Sources [26.4 kB]
+Ign 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
+Ign http://incoming.debian.org Sources/DiffIndex
+Hit http://ftp.fr.debian.org unstable/main hurd-i386 Packages/DiffIndex
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
-Get:4 http://incoming.debian.org Packages [244 kB]
+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
+Ign http://incoming.debian.org Packages/DiffIndex
+Hit http://incoming.debian.org Sources
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
+Get:2 http://incoming.debian.org Packages [451 kB]
Ign http://ftp.debian-ports.org unreleased/main Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 273 kB in 60s (4539 B/s)
+Fetched 453 kB in 2min 54s (2588 B/s)
Reading package lists...
+W: GPG error: http://incoming.debian.org Release: The following signatures were invalid: BADSIG 9AA38DCD55BE302B Debian Archive Automatic Signing Key (5.0/lenny) <ftpmaster at debian.org>
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -82,61 +158,158 @@ 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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (234 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 3s (128 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
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-WI3X4y/apt_archive/sbuild-build-depends-core-dummy.deb'.
+gpg: WARNING: using insecure memory!
+gpg: please see http://www.gnupg.org/faq.html for more information
+OK
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
+Need to get 0 B/712 B of archives.
+After this operation, 0 B of additional disk space will be used.
+WARNING: The following packages cannot be authenticated!
+ sbuild-build-depends-core-dummy
+Authentication warning overridden.
+Selecting previously deselected package sbuild-build-depends-core-dummy.
+(Reading database ... 12536 files and directories currently installed.)
+Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
+Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-lwozOr/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+gpg: WARNING: using insecure memory!
+gpg: please see http://www.gnupg.org/faq.html for more information
+OK
+Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install build dependencies (internal resolver) │
+│ Install samtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Checking for already installed source dependencies...
-debhelper: already installed (8.1.3 >= 8 is satisfied)
-cdbs: missing
-libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
-Checking for source dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev
+Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libboost-iostreams1.46.1 libsysfs2
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
Use 'apt-get autoremove' to remove them.
+The following extra packages will be installed:
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0
+ libxml2 po-debconf quilt zlib1g-dev
Suggested packages:
- devscripts ncurses-doc
+ devscripts dh-make gettext-doc ncurses-doc libmail-box-perl procmail
+ graphviz
Recommended packages:
- autotools-dev
+ autotools-dev autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev
-0 upgraded, 2 newly installed, 0 to remove and 72 not upgraded.
-Need to get 0 B/541 kB of archives.
-After this operation, 1712 kB of additional disk space will be used.
+ cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
+ libcroco3 libexpat1 libglib2.0-0 libmagic1 libncurses5-dev libunistring0
+ libxml2 po-debconf quilt sbuild-build-depends-samtools-dummy zlib1g-dev
+0 upgraded, 19 newly installed, 0 to remove and 1 not upgraded.
+Need to get 0 B/7611 kB of archives.
+After this operation, 23.3 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
- cdbs libncurses5-dev
+ libmagic1 file gettext-base libxml2 html2text libglib2.0-0 libcroco3
+ libexpat1 libunistring0 gettext intltool-debian po-debconf debhelper cdbs
+ diffstat libncurses5-dev quilt zlib1g-dev
+ sbuild-build-depends-samtools-dummy
Authentication warning overridden.
+Selecting previously deselected package libmagic1.
+(Reading database ... 12536 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-3_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_2.28.6-1_hurd-i386.deb) ...
+Selecting previously deselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-1_hurd-i386.deb) ...
+Selecting previously deselected package libexpat1.
+Unpacking libexpat1 (from .../libexpat1_2.0.1-7_hurd-i386.deb) ...
+Selecting previously deselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-4_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_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 16660 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_hurd-i386.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_hurd-i386.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
+Selecting previously deselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
+Selecting previously deselected package sbuild-build-depends-samtools-dummy.
+Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
Processing triggers for man-db ...
-Setting up cdbs (0.4.93) ...
+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-3) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libexpat1 (2.0.1-7) ...
+Setting up libunistring0 (0.9.3-4) ...
+Setting up gettext (0.18.1.1-3) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
-Removing negative dependencies:
-Checking correctness of source dependencies...
+Setting up quilt (0.48-7) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: libc0.3-dev_2.11.2-13 dpkg-dev_1.16.0.2 hurd-dev_20110303-1~1 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gcc-4.6_4.6.0-7 g++-4.6_4.6.0-7 binutils_2.21.51.20110419-2 libstdc++6-4.6-dev_4.6.0-7 libstdc++6_4.6.0-7
-Package versions: adduser_3.112+nmu1 apt_0.8.11.5+b1 apt-utils_0.8.11.5+b1 base-files_5.9 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.51.20110419-2 bsdmainutils_8.0.13 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.4_4.4.5-10 cpp-4.5_4.5.3-1 cpp-4.6_4.6.0-7 cron_3.0pl1-115 dash_0.5.5.1-7 debconf_1.5.35 debconf-english_1.5.35 debfoster_2.6-2 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_3.4.1 deborphan_1.7.28 dialog_1.1-20100428-1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.03-5+b1 findutils_4.4.2-1 fontconfig_2.8.0-2.2 fontconfig-config_2.8.0-2.2 g++_4:4.4.4-2 g++-4.4_4.4.5-10 g++-4.5_4.5.3-1 g++-4.6_4.6.0-7 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-5 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 gcc-4.5_4.5.3-1 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran-4.4_4.4.5-10 gnumach-dev_2:1.3.99.dfsg.git20100732-1 gnupg_1.4.10-4 gobjc-4.4_4.4.5-10 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15+b1 hurd_20110319-2 hurd-dev_20110303-1~1 initscripts_2.88dsf-12 insserv_1.14.0-2 install-info_4.13a.dfsg.1-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libapt-pkg-dev_0.8.11.5+b1 libattr1_1:2.4.44-2 libblkid1_2.16.2-0 libboost-iostreams1.46.1_1.46.1-5 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-13 libc-dev-bin_2.11.2-13 libc0.3_2.11.2-13 libc0.3-dev_2.11.2-13 libc0.3-xen_2.11.2-13 libcloog-ppl0_0.15.9-2 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.8_4.8.30-5 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libelfg0_0.8.13-1 libept-dev_1.0.3+b2 libept1_1.0.3+b2 libexpat1_2.0.1-7 libfontconfig1_2.8.0-2.2 libfreetype6_2.4.4-1 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgfortran3_4.6.0-7 libglib2.0-0_2.28.6-1 libglib2.0-data_2.28.0-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-1+b1 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.4-2 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libidn11_1.20-1 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.03-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libobjc2_4.4.5-10 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.2-3 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpng12-0_1.2.44-2 libpopt0_1.16-1 libppl-c2_0.10.2-9 libppl7_0.10.2-9 libpthread-stubs0_0.3-2 libpthread-stubs0-dev_0.3-2 libquadmath0_4.6.0-7 libreadline6_6.2-1 libsasl2-2_2.1.23.dfsg1-8 libsasl2-modules_2.1.23.dfsg1-8 libslang2_2.2.4-2 libss2_1.41.12-2 libssl0.9.8_0.9.8o-5 libssl1.0.0_1.0.0d-2 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.5-10 libstdc++6-4.5-dev_4.5.3-1 libstdc++6-4.6-dev_4.6.0-7 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.11-1.1 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libuuid1_2.16.2-0 libwibble-dev_0.1.26-1 libwrap0_7.6.dbs-14+hurd.2 libxapian-dev_1.2.3-2 libxapian22_1.2.3-2 libxml2_2.7.8.dfsg-2+b1 lsb-base_3.2-25 lynx-cur_2.8.8dev.8-1 make_3.81-8 man-db_2.5.7-4 mawk_1.3.3-15 mime-support_3.48-1 ncurses-base_5.7+20100313-4 ncurses-bin_5.9-1 netbase_4.42 netcat-traditional_1.10-38 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 pkg-config_0.25-1.1 po-debconf_1.0.16 procps_1:3.2.7-11 psmisc_22.3-1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sgml-base_1.26+nmu1 shared-mime-info_0.71-3 sudo_1.7.2p7-1 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 ttf-freefont_20100919-1 type-handling_0.2.23 tzdata_2010m-1 ucf_3.0025+nmu1 util-linux_2.16.2-0 xml-core_0.13 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.5_4.5.3-3 g++-4.6_4.6.1-1+hurd.1 gcc-4.4_4.4.6-6 gcc-4.5_4.5.3-3 gcc-4.6_4.6.1-1+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 hurd-dev_20110519-3 libc0.3-dev_2.13-10 libstdc++6_4.6.1-1+hurd.1 libstdc++6-4.5-dev_4.5.3-3 libstdc++6-4.6-dev_4.6.1-1+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.1 apt-utils_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-6 cpp-4.4_4.4.6-6 cpp-4.5_4.5.3-3 cpp-4.6_4.6.1-1+hurd.1 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.6-2 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.15.1-1 file_5.03-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.5_4.5.3-3 g++-4.6_4.6.1-1+hurd.1 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.0-6 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-6 gcc-4.4-base_4.4.6-6 gcc-4.5_4.5.3-3 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-1+hurd.1 gcc-4.6-base_4.6.1-1+hurd.1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran_4:4.6.0-6 gfortran-4.4_4.4.6-6 gfortran-4.6_4.6.1-1+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-6 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20110519-3 hurd-dev_20110519-3 ifupdown_0.6.9+hurd.1 inetutils-tools_2:1.8-3 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.47-3 libattr1_1:2.4.46-2 libblkid1_2.16.2-0 libboost-iostreams1.42.0_1.42.0-4+b2 libboost-iostreams1.46.1_1.46.1-6 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc0.3_2.13-10 libc0.3-dev_2.13-10 libc0.3-xen_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdigest-sha1-perl_2.13-2 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libexpat1_2.0.1-7 libfribidi0_0.19.2-1 libgcc1_1:4.6.1-1+hurd.1 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libgfortran3_4.6.1-1+hurd.1 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.4-2 libgomp1_4.6.1-1+hurd.1 libgpg-error0_1.10-0.3 libident_0.22-3 libldap-2.4-2_2.4.25-1 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 liblzo2-2_2.05-1 libmagic1_5.03-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libnewt0.52_0.52.11-2.1 libobjc2_4.5.3-3 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-3+b1 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libpopt0_1.16-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libpwl5_0.11.2-3 libquadmath0_4.6.1-1+hurd.1 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-1+hurd.1 libstdc++6-4.5-dev_4.5.3-3 libstdc++6-4.6-dev_4.6.1-1+hurd.1 libsysfs2_2.1.0+repack-1 libtasn1-3_2.9-4 libtext-charwidth-perl_0.04-6+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.16.2-0 libxml2_2.7.8.dfsg-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 netcat-traditional_1.10-39 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 quilt_0.48-7 random-egd_0.5-0+hurd.1 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-2 tzdata_2011h-3 util-linux_2.16.2-0 wget_1.11.4-4 whiptail_0.52.11-2.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -146,18 +319,23 @@ Package versions: adduser_3.112+nmu1 apt_0.8.11.5+b1 apt-utils_0.8.11.5+b1 base-
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 Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
+Sufficient free space for build
+
+User Environment
+────────────────
+
dpkg-buildpackage
─────────────────
@@ -168,35 +346,62 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»/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_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Entering directory `/«PKGBUILDDIR»/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_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
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
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/«PKGBUILDDIR»'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
debian/rules build
+rm -f debian/stamp-patch*
+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 -f debian/rules reverse-config
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/«PKGBUILDDIR»'
+cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/«PKGBUILDDIR»'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -217,7 +422,6 @@ bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-se
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -231,28 +435,28 @@ kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Entering directory `/«PKGBUILDDIR»/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -271,25 +475,25 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/«PKGBUILDDIR»'
+make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/«PKGBUILDDIR»'
+make[3]: Entering directory `/«PKGBUILDDIR»/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+make[3]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[3]: Entering directory `/«PKGBUILDDIR»/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/«PKGBUILDDIR»/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Entering directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -299,45 +503,42 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
[sam_header_read2] 2 sequences loaded.
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/examples'
+make[1]: Entering directory `/«PKGBUILDDIR»/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
+[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
+[bam_rmdup_core] processing reference seq1...
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-[bam_rmdup_core] processing reference seq1...
../samtools rmdup ex1f.bam ex1f-rmduppe.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
[mpileup] 1 samples in 1 input files
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
+../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
<mpileup> Set max per-file depth to 8000
gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
- /usr/bin/fakeroot debian/rules binary-arch
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/examples'
+make[1]: Leaving directory `/«PKGBUILDDIR»/examples'
touch debian/stamp-makefile-check
+ /usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
@@ -362,7 +563,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -370,7 +570,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /«PKGBUILDDIR»/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /«PKGBUILDDIR»/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -384,7 +586,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -392,11 +593,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-hurd-i386-FFB759/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«PKGBUILDDIR»/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -411,69 +613,82 @@ 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_0.1.16-1_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org> >../samtools_0.1.16-1_hurd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0532
+Build finished at 20110711-1317
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_0.1.17-1_hurd-i386.changes:
+────────────────────────────────────
-samtools_0.1.16-1_hurd-i386.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-mozart at buildd.debian.org>
+Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-rossini at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- d729804464743d8cdb2b2f29b09e24eec96af24d 612866 samtools_0.1.16-1_hurd-i386.deb
- c6ce3ca18986ece8279e1e17d6ac950c871b89ab 179160 libbam-dev_0.1.16-1_hurd-i386.deb
+ 81aa66efc48ab71fcbd27710134c99b43932cbd8 600368 samtools_0.1.17-1_hurd-i386.deb
+ dac894d0dfbb21af4dcd72dcd3ad1d28e30f81b6 178560 libbam-dev_0.1.17-1_hurd-i386.deb
Checksums-Sha256:
- 8e1af7bdf6f972f75f95f7c97d1761f3121257e755c9d74a771d491864e61dd1 612866 samtools_0.1.16-1_hurd-i386.deb
- 2b03cc8eb4670590d70c6df8868dd576e725db8ef7cc10905126e1886441f960 179160 libbam-dev_0.1.16-1_hurd-i386.deb
+ b24b32eb3aa40ec743903cb4a8c1ce0bf900a546e6ddea7019bc404711a706c2 600368 samtools_0.1.17-1_hurd-i386.deb
+ adfac0d7cc9eb4094f2258235e4404b69ba2819d57b9825249b73cd60b05240e 178560 libbam-dev_0.1.17-1_hurd-i386.deb
Files:
- 833087a78b1a0426fbd9275c72f435ed 612866 science optional samtools_0.1.16-1_hurd-i386.deb
- b5db8957d16153bcb45cc9478cbff162 179160 libdevel optional libbam-dev_0.1.16-1_hurd-i386.deb
+ aed65c6d5b46b486309246e007868e05 600368 science optional samtools_0.1.17-1_hurd-i386.deb
+ b0623a8eea9498b01c46921569d5827c 178560 libdevel optional libbam-dev_0.1.17-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_hurd-i386.deb
+samtools_0.1.17-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 612866 bytes: control archive= 1793 bytes.
+ size 600368 bytes: control archive= 1767 bytes.
793 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1140
- Depends: libc0.3 (>= 2.11), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1116
+ Depends: libc0.3 (>= 2.13), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
Priority: optional
@@ -485,33 +700,32 @@ samtools_0.1.16-1_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 2011-05-19 05:31 ./
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 05:30 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-07-11 13:14 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-05-19 05:31 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-05-19 05:31 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8438 2011-05-19 05:31 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2101 2011-05-19 05:31 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 05:32 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rw-r--r-- root/root 1966 2011-07-11 13:15 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-11 13:15 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-11 13:15 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-11 13:16 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./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 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
@@ -523,33 +737,34 @@ drwxr-xr-x root/root 0 2011-05-19 05:32 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-05-19 05:32 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/bin/
--rwxr-xr-x root/root 129252 2011-05-19 05:31 ./usr/bin/bcftools
--rwxr-xr-x root/root 25836 2011-05-19 05:31 ./usr/bin/razip
--rwxr-xr-x root/root 412296 2011-05-19 05:31 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/lib/samtools/
--rwxr-xr-x root/root 18208 2011-05-19 05:31 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6696 2011-05-19 05:31 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6696 2011-05-19 05:31 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10556 2011-05-19 05:31 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7384 2011-05-19 05:31 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.16-1_hurd-i386.deb
+-rwxr-xr-x root/root 5778 2011-07-11 13:16 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/bin/
+-rwxr-xr-x root/root 133464 2011-07-11 13:15 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25764 2011-07-11 13:15 ./usr/bin/razip
+-rwxr-xr-x root/root 385032 2011-07-11 13:15 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18224 2011-07-11 13:15 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6736 2011-07-11 13:15 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6736 2011-07-11 13:15 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10596 2011-07-11 13:15 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7424 2011-07-11 13:15 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 179160 bytes: control archive= 934 bytes.
+ size 178560 bytes: control archive= 927 bytes.
678 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 456
+ Installed-Size: 448
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -560,21 +775,21 @@ libbam-dev_0.1.16-1_hurd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 05:32 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 13:16 ./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 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 05:32 ./usr/lib/
--rw-r--r-- root/root 296362 2011-05-19 05:32 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 13:16 ./usr/lib/
+-rw-r--r-- root/root 290368 2011-07-11 13:16 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 13:15 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
@@ -582,17 +797,85 @@ drwxr-xr-x root/root 0 2011-05-19 05:31 ./usr/include/samtools/
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
+│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.16-1-hurd-i386-FFB759
-(Reading database ... 16760 files and directories currently installed.)
-Removing libncurses5-dev ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following package was automatically installed and is no longer required:
+ libboost-iostreams1.42.0
+Use 'apt-get autoremove' to remove them.
+The following packages will be REMOVED:
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
+ intltool-debian* libcroco3* libexpat1* libglib2.0-0* libmagic1*
+ libncurses5-dev* libunistring0* libxml2* po-debconf* quilt*
+ sbuild-build-depends-core-dummy* sbuild-build-depends-samtools-dummy*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 20 to remove and 1 not upgraded.
+After this operation, 23.3 MB disk space will be freed.
+(Reading database ... 13554 files and directories currently installed.)
+Removing sbuild-build-depends-samtools-dummy ...
Removing cdbs ...
+Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing file ...
+Purging configuration files for file ...
+Removing po-debconf ...
+Removing intltool-debian ...
+Removing gettext ...
+Removing gettext-base ...
+Removing html2text ...
+Purging configuration files for html2text ...
+Removing libcroco3 ...
+Purging configuration files for libcroco3 ...
+Removing libexpat1 ...
+Purging configuration files for libexpat1 ...
+Removing libglib2.0-0 ...
+Purging configuration files for libglib2.0-0 ...
+Removing libmagic1 ...
+Purging configuration files for libmagic1 ...
+Removing libncurses5-dev ...
+Removing libunistring0 ...
+Purging configuration files for libunistring0 ...
+Removing libxml2 ...
+Purging configuration files for libxml2 ...
+Removing sbuild-build-depends-core-dummy ...
+Removing zlib1g-dev ...
Processing triggers for man-db ...
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0532
-Build needed 00:06:51, 10420k disc space
+Processing triggers for install-info ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+Architecture: hurd-i386
+Build-Space: 10120
+Build-Time: 448
+Distribution: sid
+Install-Time: 235
+Job: samtools_0.1.17-1
+Package: samtools
+Package-Time: 917
+Source-Version: 0.1.17-1
+Space: 10120
+Status: successful
+Version: 0.1.17-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20110711-1317
+Build needed 00:15:17, 10120k disc space
diff --git a/i386.log b/i386.log
index 15f18a7..a30f726 100644
--- a/i386.log
+++ b/i386.log
@@ -1,68 +1,68 @@
-From buildd at biber.debian.org Thu May 19 04:45:52 2011
+From buildd at biber.debian.org Mon Jul 11 12:39:57 2011
Return-path: <buildd at biber.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1QMv7Q-0007TP-DC
- for logs at buildd.debian.org; Thu, 19 May 2011 04:45:52 +0000
+ id 1QgFmH-0003fS-Hh
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 12:39:57 +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 merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1QMv7P-0003OT-8l; Thu, 19 May 2011 04:45:51 +0000
+ id 1QgFmG-00081m-GK; Mon, 11 Jul 2011 12:39:56 +0000
Received: from buildd by biber.debian.org with local (Exim 4.72)
(envelope-from <buildd at biber.debian.org>)
- id 1QMv7N-0003bK-Cn; Thu, 19 May 2011 04:45:49 +0000
-Message-Id: <E1QMv7N-0003bK-Cn at biber.debian.org>
+ id 1QgFmF-0004YX-KI; Mon, 11 Jul 2011 12:39:55 +0000
+Message-Id: <E1QgFmF-0004YX-KI 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: Thu, 19 May 2011 04:45:49 +0000
+Date: Mon, 11 Jul 2011 12:39:55 +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_0.1.16-1 on i386 (dist=sid)
+Subject: Log for successful build of samtools_0.1.17-1 on i386 (dist=sid)
Key-Id: 44C3EAC7
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (i386) 19 May 2011 04:43 ║
+║ samtools 0.1.17-1 (i386) 11 Jul 2011 12:37 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: i386
Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5221 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
-Get:4 http://ftp.gr.debian.org unstable/contrib Sources [49.8 kB]
-Get:5 http://ftp.gr.debian.org unstable/non-free Sources [91.7 kB]
-Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7295 kB]
-Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [64.8 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [5379 kB]
+Get:3 http://ftp.gr.debian.org unstable/contrib Sources [52.4 kB]
+Get:4 http://ftp.gr.debian.org unstable/non-free Sources [95.0 kB]
+Get:5 http://incoming.debian.org unstable InRelease [146 kB]
+Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [7492 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [67.3 kB]
Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
-Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2264 B]
+Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.gr.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
Get:9 http://incoming.debian.org Release.gpg [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5221 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7295 kB]
-Get:14 http://incoming.debian.org unstable/contrib i386 Packages [64.8 kB]
+Get:10 http://incoming.debian.org unstable/main Sources [5379 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [7492 kB]
+Get:14 http://incoming.debian.org unstable/contrib i386 Packages [67.3 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [26.8 kB]
-Get:18 http://incoming.debian.org Packages [270 kB]
+Get:17 http://incoming.debian.org Sources [36.1 kB]
+Get:18 http://incoming.debian.org Packages [457 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 26.0 MB in 13s (1870 kB/s)
+Fetched 27.0 MB in 19s (1367 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (260 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 1s (214 kB/s)
Download complete and in download only mode
Check arch
@@ -101,91 +101,93 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 12 not upgraded.
+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 12 not upgraded.
+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-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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-2)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-2)
+mount: already installed (2.19.1-2)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-10)
+gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 12 not upgraded.
-Need to get 9515 kB of archives.
-After this operation, 28.5 MB of additional disk space will be used.
-Get:1 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.2 [200 kB]
-Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-5 [1125 kB]
-Get:3 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-1 [35.6 kB]
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 16 not upgraded.
+Need to get 9957 kB of archives.
+After this operation, 29.6 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-3 [37.6 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 8.2.3 [203 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-6 [1127 kB]
Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.0.2-1 [991 kB]
Get:5 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.04-5+b1 [233 kB]
Get:6 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.04-5+b1 [49.4 kB]
Get:7 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-3 [130 kB]
Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 8.12-3 [255 kB]
-Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-2+b1 [831 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.7.8.dfsg-3 [881 kB]
Get:10 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.28.6-1 [1503 kB]
Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.2-1 [116 kB]
@@ -193,19 +195,21 @@ Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-4
Get:14 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-3 [1973 kB]
Get:15 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
-Get:19 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-1 [467 kB]
-Get:20 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.54-1 [27.7 kB]
+Get:20 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-1 [467 kB]
+Get:21 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 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 9515 kB in 1s (5827 kB/s)
+Fetched 9957 kB in 1s (6547 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10694 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10641 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_i386.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_i386.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_i386.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_i386.deb) ...
Selecting previously deselected package libmagic1.
@@ -217,7 +221,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_i386.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_i386.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -233,25 +237,29 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_i386.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_i386.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.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) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -260,19 +268,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
-Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-5
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-7 libreadline6_6.2-1 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110703-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110703-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.1-2 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -283,12 +293,13 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -303,35 +314,62 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/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_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/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_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -352,7 +390,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -366,28 +403,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -406,25 +443,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -434,19 +471,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -462,7 +497,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtool
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -470,7 +504,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -497,7 +531,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -505,7 +538,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -519,7 +554,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -527,11 +561,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-i386-q2Ku0q/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-i386-Ir29Dn/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -546,27 +581,27 @@ 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_0.1.16-1_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.16-1_i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0445
+Build finished at 20110711-1239
-samtools_0.1.16-1_i386.changes:
+samtools_0.1.17-1_i386.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
@@ -574,40 +609,41 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- d30726d6d0eab2144afe1c486ac9574cde4b27c1 604418 samtools_0.1.16-1_i386.deb
- 07c2bc69c52e74960291daf88718d81f6f4a2bf5 178562 libbam-dev_0.1.16-1_i386.deb
+ 567a815b439ddc12d7411c2556d66fbcc7dd0ed7 594134 samtools_0.1.17-1_i386.deb
+ bfd91c2d792c346f99956b65dc0a8f4329ffa2a6 178086 libbam-dev_0.1.17-1_i386.deb
Checksums-Sha256:
- d408cd2b3f00081e83594e3e491575243cd0fee75bd38f2b1d5323f61bb429b7 604418 samtools_0.1.16-1_i386.deb
- 798f80d407f0a9f598896e0a5a232ef4ae1bfb4c51fa8b0b7a65a479e14fe07b 178562 libbam-dev_0.1.16-1_i386.deb
+ d4ca234ddab796eeebcbefa449beceeaedbe72d703d286951bb1408f0af48160 594134 samtools_0.1.17-1_i386.deb
+ e1f454875e1bb651926b8599f319da4d8ec127d3a41307691ab437a4347ac9ec 178086 libbam-dev_0.1.17-1_i386.deb
Files:
- e5847dc9e0609f4a1ccd20d7fe89d931 604418 science optional samtools_0.1.16-1_i386.deb
- cc391c4fcbb8c92cb7cd9aec540fcdec 178562 libdevel optional libbam-dev_0.1.16-1_i386.deb
+ dfd58b32a3cec1856847d0061288f2d4 594134 science optional samtools_0.1.17-1_i386.deb
+ e7ecf56a73e46be1d6a5cbefa3bf4fa8 178086 libdevel optional libbam-dev_0.1.17-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_i386.deb
+samtools_0.1.17-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 604418 bytes: control archive= 1785 bytes.
+ size 594134 bytes: control archive= 1762 bytes.
785 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1140
+ Installed-Size: 1112
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -620,71 +656,71 @@ samtools_0.1.16-1_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 2011-05-19 04:45 ./
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/lib/samtools/
--rwxr-xr-x root/root 7144 2011-05-19 04:45 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6536 2011-05-19 04:45 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6536 2011-05-19 04:45 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10380 2011-05-19 04:45 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17680 2011-05-19 04:45 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/bin/
--rwxr-xr-x root/root 129252 2011-05-19 04:45 ./usr/bin/bcftools
--rwxr-xr-x root/root 24748 2011-05-19 04:45 ./usr/bin/razip
--rwxr-xr-x root/root 411368 2011-05-19 04:45 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7184 2011-07-11 12:39 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6576 2011-07-11 12:39 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6576 2011-07-11 12:39 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10420 2011-07-11 12:39 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 18184 2011-07-11 12:39 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/bin/
+-rwxr-xr-x root/root 133368 2011-07-11 12:39 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24660 2011-07-11 12:39 ./usr/bin/razip
+-rwxr-xr-x root/root 384136 2011-07-11 12:39 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./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 2011-05-19 04:20 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./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 2011-05-19 04:45 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-07-11 12:39 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1966 2011-05-19 04:45 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/man/man1/
--rw-r--r-- root/root 2101 2011-05-19 04:45 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8438 2011-05-19 04:45 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-05-19 04:45 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-07-11 12:39 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2011-07-11 12:39 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-07-11 12:39 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-05-19 04:45 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-07-11 12:39 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+lrwxrwxrwx root/root 0 2011-07-11 12:39 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.16-1_i386.deb
+libbam-dev_0.1.17-1_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 178562 bytes: control archive= 926 bytes.
+ size 178086 bytes: control archive= 925 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 456
+ Installed-Size: 448
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -695,23 +731,23 @@ libbam-dev_0.1.16-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/lib/
--rw-r--r-- root/root 295422 2011-05-19 04:45 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/lib/
+-rw-r--r-- root/root 289336 2011-07-11 12:39 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./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 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:45 ./usr/include/samtools/
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 12:39 ./usr/include/samtools/
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
@@ -727,7 +763,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-a8a9eaac-dae5-4b1a-9d7b-aa07cd3b0949/build/buildd-samtools_0.1.16-1-i386-q2Ku0q
+Purging /var/lib/schroot/mount/sid-i386-sbuild-973056c3-5002-4a94-b56a-a4a10ceda557/build/buildd-samtools_0.1.17-1-i386-Ir29Dn
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -735,18 +771,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 10396
-Build-Time: 48
+Build-Space: 10108
+Build-Time: 47
Distribution: sid
-Install-Time: 38
-Job: samtools_0.1.16-1
+Install-Time: 41
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 112
-Source-Version: 0.1.16-1
-Space: 10396
+Package-Time: 121
+Source-Version: 0.1.17-1
+Space: 10108
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0445
-Build needed 00:01:52, 10396k disc space
+Finished at 20110711-1239
+Build needed 00:02:01, 10108k disc space
Signature with key '44C3EAC7' requested:
diff --git a/ia64.log b/ia64.log
index 09aedea..489530f 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,65 +1,67 @@
-From buildd at caballero.debian.org Thu May 19 11:26:08 2011
-Return-path: <buildd at caballero.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at alkman.debian.org Mon Jul 11 12:43:15 2011
+Return-path: <buildd at alkman.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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 4.72) (envelope-from <buildd at caballero.debian.org>)
- id 1QN1Ml-00054I-LN
- for logs at buildd.debian.org; Thu, 19 May 2011 11:26:08 +0000
-Received: from caballero.debian.org ([193.201.200.200])
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1QgFpT-0004J9-EX
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 12:43:15 +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=caballero.debian.org,
- EMAIL=hostmaster at caballero.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
- id 1QN1Mk-0005lq-Cf; Thu, 19 May 2011 11:26:06 +0000
-Received: from buildd by caballero.debian.org with local (Exim 4.69)
- (envelope-from <buildd at caballero.debian.org>) id 1QN1Mj-0006JC-J2
- for buildd-porters at caballero.debian.org; Thu, 19 May 2011 11:26:05 +0000
-From: buildd on caballero <buildd at caballero.debian.org>
-To: buildd-porters at caballero.debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on ia64 (dist=sid)
+ CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1QgFpS-00089h-4P
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 12:43:14 +0000
+Received: from buildd by alkman.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at alkman.debian.org>)
+ id 1QgFpP-0001ff-MY; Mon, 11 Jul 2011 12:43:11 +0000
+Date: Mon, 11 Jul 2011 12:43:11 +0000
+Message-Id: <E1QgFpP-0001ff-MY 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_0.1.17-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QN1Mj-0006JC-J2 at caballero.debian.org>
-Date: Thu, 19 May 2011 11:26:05 +0000
-Delivered-To: buildd-porters at caballero.debian.org
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on caballero.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (ia64) 19 May 2011 11:23 ║
+║ samtools 0.1.17-1 (ia64) 11 Jul 2011 12:39 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: ia64
-Hit http://mirror.positive-internet.com sid InRelease
-Hit http://mirror.positive-internet.com sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://spohr.debian.org unstable InRelease [146 kB]
+Get:2 http://spohr.debian.org unstable/main Sources [5379 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:4 http://spohr.debian.org unstable/contrib Sources [52.4 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [95.0 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [7242 kB]
Ign http://incoming.debian.org InRelease
-Hit http://mirror.positive-internet.com sid/contrib Sources/DiffIndex
-Hit http://mirror.positive-internet.com sid/main ia64 Packages/DiffIndex
-Hit http://mirror.positive-internet.com sid/contrib ia64 Packages/DiffIndex
-Ign http://mirror.positive-internet.com sid/contrib TranslationIndex
-Hit http://mirror.positive-internet.com sid/main TranslationIndex
-Hit http://incoming.debian.org Release.gpg
-Ign http://mirror.positive-internet.com sid/contrib Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main ia64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org unstable/main Sources [5379 kB]
+Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [54.5 kB]
+Ign http://spohr.debian.org unstable/contrib TranslationIndex
+Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://spohr.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
+Get:13 http://incoming.debian.org unstable/main ia64 Packages [7242 kB]
+Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [54.5 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [36.1 kB]
+Get:18 http://incoming.debian.org Packages [457 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
+Fetched 26.4 MB in 23s (1134 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 389 kB of source archives.
-Get:1 http://mirror.positive-internet.com/debian/ sid/main samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://mirror.positive-internet.com/debian/ sid/main samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://mirror.positive-internet.com/debian/ sid/main samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 0s (1261 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 0s (449 kB/s)
Download complete and in download only mode
Check arch
@@ -98,90 +100,124 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 10 not upgraded.
+The following package was automatically installed and is no longer required:
+ libdb4.8
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+The following package was automatically installed and is no longer required:
+ libdb4.8
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 36 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.3-7+b1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-2)
+libc6.1-dev: already installed (2.13-7)
gcc: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following package was automatically installed and is no longer required:
+ libdb4.8
+Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 36 not upgraded.
+Need to get 12.1 MB of archives.
+After this operation, 42.3 MB of additional disk space will be used.
+Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-3 [47.8 kB]
+Get:2 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
+Get:3 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
+Get:4 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-1 [1122 kB]
+Get:5 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.04-5+b1 [263 kB]
+Get:6 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5+b1 [52.0 kB]
+Get:7 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-3 [174 kB]
+Get:8 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-3 [316 kB]
+Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-3 [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 2.28.6-1 [1973 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 0.9.3-4 [467 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 8.9.0 [559 kB]
+Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9 kB]
+Get:20 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.9-1 [614 kB]
+Get:21 http://spohr.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 20 newly installed, 0 to remove and 10 not upgraded.
-Need to get 0 B/11.7 MB of archives.
-After this operation, 41.4 MB of additional disk space will be used.
+Fetched 12.1 MB in 1s (10.7 MB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10485 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_ia64.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10484 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_ia64.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_ia64.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_ia64.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_ia64.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_ia64.deb) ...
Selecting previously deselected package libmagic1.
@@ -193,7 +229,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_ia64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_ia64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_ia64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_ia64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -209,25 +245,29 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_ia64.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_ia64.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.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) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -236,19 +276,24 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
+The following package was automatically installed and is no longer required:
+ libdb4.8
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-3 gcc-4.4_4.4.6-3 libc6.1-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 linux-libc-dev_2.6.38-5
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-9 g++-4.4_4.4.6-3 gcc_4:4.4.5-9 gcc-4.4_4.4.6-3 gcc-4.4-base_4.4.6-3 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6.1_2.13-2 libc6.1-dev_2.13-2 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.2-1 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
+Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-6 gcc-4.4_4.4.6-6 libc6.1-dev_2.13-7 libstdc++6_4.6.0-13 libstdc++6-4.4-dev_4.4.6-6 linux-libc-dev_2.6.39-2
+Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.4.5-9 g++-4.4_4.4.6-6 gcc_4:4.4.5-9 gcc-4.4_4.4.6-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6-base_4.6.0-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6.1_2.13-7 libc6.1-dev_2.13-7 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.7_4.7.25-20 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-13 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-13 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-13 libstdc++6-4.4-dev_4.4.6-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.2 libunwind7-dev_0.99-0.2 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7+b1 perl-base_5.12.3-7+b1 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -258,14 +303,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -274,50 +319,68 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/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_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/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_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
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 -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -328,7 +391,6 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -338,9 +400,9 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -350,14 +412,14 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -374,25 +436,25 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -402,19 +464,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -430,7 +490,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtool
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -438,13 +497,9 @@ 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_0.1.16-1-ia64-WI6whj/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -469,7 +524,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -477,7 +531,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -491,7 +547,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -499,11 +554,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-ia64-WI6whj/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-ia64-I37Jnr/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -518,68 +574,69 @@ 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_0.1.16-1_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../samtools_0.1.16-1_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-1125
+Build finished at 20110711-1243
-samtools_0.1.16-1_ia64.changes:
+samtools_0.1.17-1_ia64.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org>
+Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- 2d814117eb6228b4f746ad9580f9b2855d93ccf6 763130 samtools_0.1.16-1_ia64.deb
- a3ae4eda51357142e0bbb2c3d570c477165df47a 225830 libbam-dev_0.1.16-1_ia64.deb
+ 53724ca4450953f26bb333732dd7bbc1e3e4f24e 736796 samtools_0.1.17-1_ia64.deb
+ 27d38e521bd412d533c275bcfec6c6af09f2ddef 224840 libbam-dev_0.1.17-1_ia64.deb
Checksums-Sha256:
- 24fda0427420cd875626e586841c679a89da1ff764e7b3682b8a75380f4c54e4 763130 samtools_0.1.16-1_ia64.deb
- 2f2e39507ac6e18c60b376c746c873084b20be7f37b116370c3e30c01f01142b 225830 libbam-dev_0.1.16-1_ia64.deb
+ ac412a98f8bf0f39f72e79fc3c0f4017a5ccbfc0a782fc982f18b9dc30418823 736796 samtools_0.1.17-1_ia64.deb
+ c4b4e46a0759362dae0f5f2b53284fa99e1264578e303f083e8e5858d0d3c3b0 224840 libbam-dev_0.1.17-1_ia64.deb
Files:
- 5a9924fdc7c72111c1a693608f34e91b 763130 science optional samtools_0.1.16-1_ia64.deb
- fd54a55ad6e186dca773abdd40c5fb29 225830 libdevel optional libbam-dev_0.1.16-1_ia64.deb
+ 524ee77879c61357d2eb06beaca76d49 736796 science optional samtools_0.1.17-1_ia64.deb
+ fac3f60640a89682510996d03ade0939 224840 libdevel optional libbam-dev_0.1.17-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_ia64.deb
+samtools_0.1.17-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 763130 bytes: control archive= 1782 bytes.
+ size 736796 bytes: control archive= 1760 bytes.
787 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1784
+ Installed-Size: 2032
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -592,71 +649,71 @@ samtools_0.1.16-1_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 2011-05-19 11:25 ./
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 11:25 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-05-19 11:25 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-05-19 11:25 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8438 2011-05-19 11:25 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2101 2011-05-19 11:25 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30712 2011-07-11 12:42 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13360 2011-07-11 12:42 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13296 2011-07-11 12:42 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 22384 2011-07-11 12:42 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2011-07-11 12:42 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/bin/
+-rwxr-xr-x root/root 298104 2011-07-11 12:42 ./usr/bin/bcftools
+-rwxr-xr-x root/root 52520 2011-07-11 12:42 ./usr/bin/razip
+-rwxr-xr-x root/root 777880 2011-07-11 12:42 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-07-11 12:42 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-05-19 11:25 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/bin/
--rwxr-xr-x root/root 287712 2011-05-19 11:25 ./usr/bin/bcftools
--rwxr-xr-x root/root 52520 2011-05-19 11:25 ./usr/bin/razip
--rwxr-xr-x root/root 832184 2011-05-19 11:25 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/lib/samtools/
--rwxr-xr-x root/root 30712 2011-05-19 11:25 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13360 2011-05-19 11:25 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13296 2011-05-19 11:25 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 22384 2011-05-19 11:25 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2011-05-19 11:25 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.16-1_ia64.deb
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 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 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-11 12:42 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-11 12:42 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./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 2011-07-11 12:42 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2011-07-11 12:42 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 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 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+lrwxrwxrwx root/root 0 2011-07-11 12:42 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 225830 bytes: control archive= 926 bytes.
+ size 224840 bytes: control archive= 922 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 716
+ Installed-Size: 800
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -667,25 +724,25 @@ libbam-dev_0.1.16-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/lib/
--rw-r--r-- root/root 565154 2011-05-19 11:25 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 11:25 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/include/samtools/
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/lib/
+-rw-r--r-- root/root 556858 2011-07-11 12:42 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:42 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./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 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -699,71 +756,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-6a35d064-ee4f-4030-a03e-85b48da87405/build/buildd-samtools_0.1.16-1-ia64-WI6whj
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- bsdmainutils* cdbs* debhelper* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
- libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
- po-debconf* zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 10 not upgraded.
-After this operation, 41.4 MB disk space will be freed.
-(Reading database ... 11917 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-4179d541-5a60-42d5-83dc-43fa767e5f24/build/buildd-samtools_0.1.17-1-ia64-I37Jnr
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 14204
-Build-Time: 111
+Build-Space: 16068
+Build-Time: 120
Distribution: sid
-Install-Time: 21
-Job: samtools_0.1.16-1
+Install-Time: 64
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 142
-Source-Version: 0.1.16-1
-Space: 14204
+Package-Time: 235
+Source-Version: 0.1.17-1
+Space: 16068
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-1125
-Build needed 00:02:22, 14204k disc space
+Finished at 20110711-1243
+Build needed 00:03:55, 16068k disc space
+Signature with key '591AB71E' requested:
diff --git a/info b/info
index ed09071..e06e6cb 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-powerpc~1305780308~sid~successful
-i386~1305780353~sid~successful
-armel~1305780503~sid~failed
-s390~1305780519~sid~successful
-sparc~1305780540~sid~failed
-kfreebsd-amd64~1305780549~sid~successful
-kfreebsd-i386~1305780607~sid~successful
-mips~1305780671~sid~successful
-mipsel~1305780676~sid~successful
-hurd-i386~1305783164~sid~successful
-ia64~1305804368~sid~successful
+i386~1310388004~sid~successful
+powerpc~1310388092~sid~successful
+ia64~1310388196~sid~successful
+kfreebsd-i386~1310388443~sid~successful
+sparc~1310388463~sid~failed
+mips~1310389257~sid~successful
+hurd-i386~1310390340~sid~successful
+kfreebsd-amd64~1310395607~sid~successful
+s390~1310412477~sid~successful
+mipsel~1310455676~sid~successful
+armel~1310493558~sid~failed
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index aeeb745..1e7c15b 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,85 +1,81 @@
-From buildd at fano.debian.org Thu May 19 04:49:08 2011
-Return-path: <buildd at fano.debian.org>
+From buildd at fasch.debian.org Mon Jul 11 14:46:46 2011
+Return-path: <buildd at fasch.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 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1QMvAa-0007sT-EP
- for logs at buildd.debian.org; Thu, 19 May 2011 04:49:08 +0000
-Received: from fano.debian.org ([206.12.19.110])
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1QgHl0-0007Jz-7N
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 14:46:46 +0000
+Received: from fasch.debian.org ([194.177.211.201])
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)
+ CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1QMvAY-0003Xp-FX; Thu, 19 May 2011 04:49:07 +0000
-Received: from buildd by fano.debian.org with local (Exim 4.72)
- (envelope-from <buildd at fano.debian.org>)
- id 1QMvAV-000B4m-PJ; Thu, 19 May 2011 04:49:03 +0000
-Message-Id: <E1QMvAV-000B4m-PJ at fano.debian.org>
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1QgHky-0002td-Os; Mon, 11 Jul 2011 14:46:45 +0000
+Received: from buildd by fasch.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fasch.debian.org>)
+ id 1QgHkx-0004bK-Mx; Mon, 11 Jul 2011 14:46:43 +0000
+Message-Id: <E1QgHkx-0004bK-Mx at fasch.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 19 May 2011 04:49:03 +0000
-From: buildd on fano <buildd at fano.debian.org>
+Date: Mon, 11 Jul 2011 14:46:43 +0000
+From: buildd on fasch <buildd at fasch.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on kfreebsd-amd64
+Subject: Log for successful build of samtools_0.1.17-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 91116966
+Key-Id: 516A3A7B
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (kfreebsd-amd64) 19 May 2011 04:46 ║
+║ samtools 0.1.17-1 (kfreebsd-amd64) 11 Jul 2011 14:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: kfreebsd-amd64
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
Get:1 http://incoming.debian.org sid InRelease [146 kB]
-Get:2 http://mirror-ubc.debian.org sid InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
+Ign http://ftp.gr.debian.org sid/contrib Translation-en
+Ign http://ftp.gr.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org InRelease
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Get:4 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Get:5 http://mirror-ubc.debian.org sid/main TranslationIndex [2264 B]
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://mirror-ubc.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Get:8 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
-Get:9 http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages [81.2 kB]
-Get:10 http://mirror-ubc.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Get:11 http://incoming.debian.org Release [1604 B]
-Get:12 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:13 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Get:4 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:14 http://incoming.debian.org sid/main TranslationIndex [2264 B]
+Get:5 http://incoming.debian.org sid/main TranslationIndex [2045 B]
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:15 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
-Get:16 http://incoming.debian.org Sources [26.8 kB]
-Get:17 http://incoming.debian.org Packages [270 kB]
-Get:18 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Get:19 http://incoming.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
-Get:20 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [81.2 kB]
-Get:21 http://incoming.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Ign http://incoming.debian.org Translation-en
+Get:6 http://incoming.debian.org Release [1604 B]
+Get:7 http://incoming.debian.org sid/main 2011-07-11-1412.48.pdiff [8897 B]
+Get:8 http://incoming.debian.org sid/main kfreebsd-amd64 2011-07-11-1412.48.pdiff [14.6 kB]
+Get:9 http://incoming.debian.org sid/main 2011-07-11-1412.48.pdiff [8897 B]
+Get:10 http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages [82.8 kB]
+Hit http://incoming.debian.org Sources
+Get:11 http://incoming.debian.org Packages [435 kB]
+Get:12 http://incoming.debian.org sid/main kfreebsd-amd64 2011-07-11-1412.48.pdiff [14.6 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
-Get:22 http://incoming.debian.org sid/main kfreebsd-amd64 2011-05-19-0211.17.pdiff [9758 B]
-Fetched 796 kB in 13s (57.1 kB/s)
+Ign http://incoming.debian.org Translation-en
+Fetched 696 kB in 5s (121 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -100,11 +96,11 @@ 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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (291 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/debian/ sid/main samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/debian/ sid/main samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/debian/ sid/main samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 2s (187 kB/s)
Download complete and in download only mode
Check arch
@@ -118,88 +114,89 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 7 not upgraded.
+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 7 not upgraded.
+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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
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 (3.4.5)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.1-4+b1)
-grep: already installed (2.6.3-3)
+freebsd-utils: already installed (8.2+ds2-1)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt 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 libpcre3 libpipeline1 libunistring0 libxml2 man-db
- po-debconf
+ diffstat 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 dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl
+ libmail-box-perl procmail graphviz
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
+ cdbs debhelper diffstat 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
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 7 not upgraded.
-Need to get 0 B/9714 kB of archives.
-After this operation, 27.5 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 12278 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-5_kfreebsd-amd64.deb) ...
+0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/10.1 MB of archives.
+After this operation, 28.4 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-amd64.deb) ...
+(Reading database ... 12157 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-amd64.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libmagic1.
@@ -211,7 +208,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_kfreebsd-amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_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.
@@ -227,22 +224,26 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-amd64.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_kfreebsd-amd64.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.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 (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -251,19 +252,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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 7 not upgraded.
+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: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.13-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.5 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.1-4+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc0.1_2.13-4 libc0.1-dev_2.13-4 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-7 libreadline6_6.2-2 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 type-handling_0.2.23 tzdata_2011g-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-3 gcc-4.6_4.6.1-3 kfreebsd-kernel-headers_0.56 libc0.1-dev_2.13-10 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.1-1 cpp-4.6_4.6.1-3 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-1 g++_4:4.6.1-1 g++-4.6_4.6.1-3 gcc_4:4.6.1-1 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-3 gcc-4.6-base_4.6.1-3 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.56 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.17.2-9.1 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc0.1_2.13-10 libc0.1-dev_2.13-10 libcam0_8.2+ds1-3 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-3 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-3 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-2 libgomp1_4.6.1-3 libgpg-error0_1.10-0.3 libkiconv4_8.2+ds1-3 libkvm0_8.2+ds1-3 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.1-3 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libsbuf0_8.2+ds1-3 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 libtasn1-3_2.9-4 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 type-handling_0.2.23 tzdata_2011h-3 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 │
@@ -274,12 +277,13 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -294,35 +298,62 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/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_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/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_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -337,7 +368,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -351,28 +381,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -391,25 +421,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -419,19 +449,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -447,7 +475,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUy
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -455,7 +482,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -482,7 +509,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -490,7 +516,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -504,7 +532,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -512,11 +539,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -531,68 +559,69 @@ 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_0.1.16-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.16-1_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0448
+Build finished at 20110711-1445
-samtools_0.1.16-1_kfreebsd-amd64.changes:
+samtools_0.1.17-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- dc4d27fdb1baf8a28e0158f1c06acc5492b10687 606552 samtools_0.1.16-1_kfreebsd-amd64.deb
- 5c0dff2ccbc0b725d6c34168482700e25f7b4b54 171268 libbam-dev_0.1.16-1_kfreebsd-amd64.deb
+ 0f8061d716d9b73d056557e924f44b11f4188b3f 594980 samtools_0.1.17-1_kfreebsd-amd64.deb
+ 928599643e76e0ceb2dada8d4b6609dbe19309e4 170180 libbam-dev_0.1.17-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 981670e02108f5079d5b5ca5ef0d07a2d7312cf7f4ce3a0535e7d35cc2006c9c 606552 samtools_0.1.16-1_kfreebsd-amd64.deb
- 3e898dca30f23b4b26f5411f3f3a8644165aa19c92d99b19389f23921afea56d 171268 libbam-dev_0.1.16-1_kfreebsd-amd64.deb
+ 40b708b18d43aa4217b69c2355f074ea657aa953fdccbb453da134ba2ef9b350 594980 samtools_0.1.17-1_kfreebsd-amd64.deb
+ 5b3d670c56f99a8bdd5f1b246c846fae99ca16652f6a390eb7ca1a2a8dfb0736 170180 libbam-dev_0.1.17-1_kfreebsd-amd64.deb
Files:
- 7f2c8c1b5d563906c3e7c00057383137 606552 science optional samtools_0.1.16-1_kfreebsd-amd64.deb
- c0bbfd9d86e432571ce304d66a8e9f63 171268 libdevel optional libbam-dev_0.1.16-1_kfreebsd-amd64.deb
+ 7183a76d762a07a74723ea4061a87a6d 594980 science optional samtools_0.1.17-1_kfreebsd-amd64.deb
+ da8422ad9630e4d5abfaaeb0091bc0e0 170180 libdevel optional libbam-dev_0.1.17-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_kfreebsd-amd64.deb
+samtools_0.1.17-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 606552 bytes: control archive= 1789 bytes.
+ size 594980 bytes: control archive= 1764 bytes.
797 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1052
+ Installed-Size: 1022
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -605,33 +634,32 @@ samtools_0.1.16-1_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 2011-05-19 04:48 ./
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./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 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 04:48 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-07-11 14:45 ./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 2011-05-19 04:48 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-05-19 04:48 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8438 2011-05-19 04:48 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2101 2011-05-19 04:48 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rw-r--r-- root/root 1966 2011-07-11 14:45 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-11 14:45 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-11 14:45 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./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 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
@@ -643,33 +671,34 @@ drwxr-xr-x root/root 0 2011-05-19 04:48 ./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 2011-05-19 04:48 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/bin/
--rwxr-xr-x root/root 126376 2011-05-19 04:48 ./usr/bin/bcftools
--rwxr-xr-x root/root 24544 2011-05-19 04:48 ./usr/bin/razip
--rwxr-xr-x root/root 384280 2011-05-19 04:48 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/samtools/
--rwxr-xr-x root/root 19272 2011-05-19 04:48 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8160 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8096 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11952 2011-05-19 04:48 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8696 2011-05-19 04:48 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.16-1_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2011-07-11 14:45 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/bin/
+-rwxr-xr-x root/root 130528 2011-07-11 14:45 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24448 2011-07-11 14:45 ./usr/bin/razip
+-rwxr-xr-x root/root 356920 2011-07-11 14:45 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19288 2011-07-11 14:45 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8208 2011-07-11 14:45 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8144 2011-07-11 14:45 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11992 2011-07-11 14:45 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8736 2011-07-11 14:45 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 171268 bytes: control archive= 932 bytes.
+ size 170180 bytes: control archive= 932 bytes.
683 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 480
+ Installed-Size: 464
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -680,21 +709,21 @@ libbam-dev_0.1.16-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
--rw-r--r-- root/root 328218 2011-05-19 04:48 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/lib/
+-rw-r--r-- root/root 320058 2011-07-11 14:45 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 14:45 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
@@ -712,24 +741,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1305780415-40848/build/buildd-samtools_0.1.16-1-kfreebsd-amd64-bSUyWA
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1310395393-15518/build/buildd-samtools_0.1.17-1-kfreebsd-amd64-Jo8qZd
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+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 7 not upgraded.
-After this operation, 27.5 MB disk space will be freed.
-(Reading database ... 13603 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
+ libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
+ po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 21 to remove and 0 not upgraded.
+After this operation, 28.4 MB disk space will be freed.
+(Reading database ... 13567 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
@@ -763,18 +795,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 12066
-Build-Time: 50
+Build-Space: 11694
+Build-Time: 57
Distribution: sid
-Install-Time: 36
-Job: samtools_0.1.16-1
+Install-Time: 81
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 110
-Source-Version: 0.1.16-1
-Space: 12066
+Package-Time: 161
+Source-Version: 0.1.17-1
+Space: 11694
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0448
-Build needed 00:01:50, 12066k disc space
-Signature with key '91116966' requested:
+Finished at 20110711-1445
+Build needed 00:02:41, 11694k disc space
+Signature with key '516A3A7B' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 9b98db1..512c33b 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,4 +1,4 @@
-From buildd at field.debian.org Thu May 19 04:50:07 2011
+From buildd at field.debian.org Mon Jul 11 12:47:23 2011
Return-path: <buildd at field.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,
@@ -6,25 +6,25 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1QMvBW-0008EJ-Pl
- for logs at buildd.debian.org; Thu, 19 May 2011 04:50:06 +0000
+ id 1QgFtS-0004mp-Nx
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 12:47:22 +0000
Received: from field.debian.org ([194.177.211.210])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at field.debian.org>)
- id 1QMvBV-0003Y2-Hx; Thu, 19 May 2011 04:50:05 +0000
+ id 1QgFtQ-0000DQ-Mp; Mon, 11 Jul 2011 12:47:20 +0000
Received: from buildd by field.debian.org with local (Exim 4.72)
(envelope-from <buildd at field.debian.org>)
- id 1QMvBU-000DTE-9K; Thu, 19 May 2011 04:50:04 +0000
-Message-Id: <E1QMvBU-000DTE-9K at field.debian.org>
+ id 1QgFtO-0000VJ-Vd; Mon, 11 Jul 2011 12:47:19 +0000
+Message-Id: <E1QgFtO-0000VJ-Vd at field.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Thu, 19 May 2011 04:50:04 +0000
+Date: Mon, 11 Jul 2011 12:47:18 +0000
From: buildd on field <buildd at field.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on kfreebsd-i386
+Subject: Log for successful build of samtools_0.1.17-1 on kfreebsd-i386
(dist=sid)
Key-Id: 22C61858
Delivered-To: logs at buildd.debian.org
@@ -32,28 +32,26 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (kfreebsd-i386) 19 May 2011 04:46 ║
+║ samtools 0.1.17-1 (kfreebsd-i386) 11 Jul 2011 12:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: kfreebsd-i386
-Get:1 http://ftp.gr.debian.org sid InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Get:3 http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages [6663 kB]
-Get:4 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.gr.debian.org sid/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:5 http://ftp.gr.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
-Get:6 http://ftp.gr.debian.org sid/main 2011-05-19-0211.17.pdiff [5075 B]
+Get:1 http://incoming.debian.org Release.gpg [836 B]
Ign http://ftp.gr.debian.org sid/contrib Translation-en
Ign http://ftp.gr.debian.org sid/non-free Translation-en
Hit http://incoming.debian.org sid/main Sources/DiffIndex
@@ -65,13 +63,13 @@ 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:7 http://incoming.debian.org Release [1604 B]
-Get:8 http://incoming.debian.org Sources [26.8 kB]
-Get:9 http://incoming.debian.org Packages [270 kB]
+Get:2 http://incoming.debian.org Release [1604 B]
+Get:3 http://incoming.debian.org Sources [36.1 kB]
+Get:4 http://incoming.debian.org Packages [457 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 7116 kB in 5s (1388 kB/s)
+Fetched 496 kB in 5s (85.1 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -92,11 +90,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (205 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 1s (213 kB/s)
Download complete and in download only mode
Check arch
@@ -110,88 +108,89 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 7 not upgraded.
+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 7 not upgraded.
+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, 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
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 (3.4.5)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.1-4)
-grep: already installed (2.6.3-3)
+freebsd-utils: already installed (8.2+ds1-2)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt 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 libpcre3 libpipeline1 libunistring0 libxml2 man-db
- po-debconf
+ diffstat 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 dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl
+ libmail-box-perl procmail graphviz
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
+ cdbs debhelper diffstat 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
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 7 not upgraded.
-Need to get 0 B/9244 kB of archives.
-After this operation, 25.9 MB of additional disk space will be used.
-Selecting previously deselected package groff-base.
-(Reading database ... 12220 files and directories currently installed.)
-Unpacking groff-base (from .../groff-base_1.21-5_kfreebsd-i386.deb) ...
+0 upgraded, 21 newly installed, 0 to remove and 16 not upgraded.
+Need to get 0 B/9683 kB of archives.
+After this operation, 27.0 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_kfreebsd-i386.deb) ...
+(Reading database ... 12215 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-i386.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libmagic1.
@@ -203,7 +202,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_kfreebsd-i386.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_kfreebsd-i386.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_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.
@@ -219,22 +218,26 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_kfreebsd-i386.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_kfreebsd-i386.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
-Setting up groff-base (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -243,19 +246,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 kfreebsd-kernel-headers_0.53 libc0.1-dev_2.13-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.5 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.1-4 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.53 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbsd0_0.2.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc0.1_2.13-4 libc0.1-dev_2.13-4 libcam0_8.1-5 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libedit2_2.11-20080614-2 libexpat1_2.0.1-7 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgcrypt11_1.4.6-5 libgdbm3_1.8.3-9 libgeom0_8.1-5 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-1+b1 libgomp1_4.6.0-7 libgpg-error0_1.10-0.3 libkiconv4_8.1-5 libkvm0_8.1-5 libldap-2.4-2_2.4.25-1+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpng12-0_1.2.44-2 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-7 libreadline6_6.2-2 libsasl2-2_2.1.23.dfsg1-8 libsbuf0_8.1-5 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtasn1-3_2.9-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.45 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 type-handling_0.2.23 tzdata_2011g-1 ufsutils_7.3-1+b1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 kfreebsd-kernel-headers_0.56 libc0.1-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.2+ds1-2 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kfreebsd-kernel-headers_0.56 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.17.2-9.1 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc0.1_2.13-10 libc0.1-dev_2.13-10 libcam0_8.2+ds1-3 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgcrypt11_1.4.6-7 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-3 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgnutls26_2.10.5-2 libgomp1_4.6.1-2 libgpg-error0_1.10-0.3 libkiconv4_8.2+ds1-3 libkvm0_8.2+ds1-3 libldap-2.4-2_2.4.25-1.1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.1-2 libreadline6_6.2-2 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-4 libsbuf0_8.2+ds1-3 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtasn1-3_2.9-4 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 type-handling_0.2.23 tzdata_2011h-3 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 │
@@ -266,12 +271,13 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -286,35 +292,62 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/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_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/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_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -335,7 +368,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -349,28 +381,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -389,25 +421,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -417,19 +449,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -445,7 +475,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -453,7 +482,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -480,7 +509,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -488,7 +516,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -502,7 +532,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -510,11 +539,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -529,27 +559,27 @@ 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_0.1.16-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.16-1_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0449
+Build finished at 20110711-1246
-samtools_0.1.16-1_kfreebsd-i386.changes:
+samtools_0.1.17-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (field) <buildd_kfreebsd-i386-field at buildd.debian.org>
@@ -557,40 +587,41 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- 59c2ca026bef8ab1fe5a5b04614331f80be21dee 612828 samtools_0.1.16-1_kfreebsd-i386.deb
- f093e93bf617d98712f11167a439aa884d24b18b 179098 libbam-dev_0.1.16-1_kfreebsd-i386.deb
+ 079b9aad31db2a2c636198f0eb90bb2b49f51e66 599780 samtools_0.1.17-1_kfreebsd-i386.deb
+ 9f4e107f6de963aaef4e5dbe500cdda6336d8324 178550 libbam-dev_0.1.17-1_kfreebsd-i386.deb
Checksums-Sha256:
- eb40119fa981b7a38f1616cb2b671c24fce1ac10db6acb5882d9543787335e05 612828 samtools_0.1.16-1_kfreebsd-i386.deb
- 4fb2209112d595e22cf283c8dfaffc2bcb68b44ceaad90f34efcdb8ad4e3e318 179098 libbam-dev_0.1.16-1_kfreebsd-i386.deb
+ 62064c9bc162cb6aa58400a5b8564e6f12002468ba9d69e5ec20e64c948f45a3 599780 samtools_0.1.17-1_kfreebsd-i386.deb
+ fe092366bc2af8f5a5ab9d7aa793ecb6d80eb7dc195a448cf908aa3126f59332 178550 libbam-dev_0.1.17-1_kfreebsd-i386.deb
Files:
- 4425dad329f2c01c745fc168a85d9bf0 612828 science optional samtools_0.1.16-1_kfreebsd-i386.deb
- 1e17c04130d252b8895b62095249a0c6 179098 libdevel optional libbam-dev_0.1.16-1_kfreebsd-i386.deb
+ 873c09ed27b4dc6158a49ac405bd5a1c 599780 science optional samtools_0.1.17-1_kfreebsd-i386.deb
+ 8389c9a0977c09e4de6c4af887f9bbba 178550 libdevel optional libbam-dev_0.1.17-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_kfreebsd-i386.deb
+samtools_0.1.17-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 612828 bytes: control archive= 1792 bytes.
+ size 599780 bytes: control archive= 1763 bytes.
796 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1086
+ Installed-Size: 1054
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -603,33 +634,32 @@ samtools_0.1.16-1_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 2011-05-19 04:49 ./
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 04:49 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-07-11 12:46 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-05-19 04:49 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-05-19 04:49 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8438 2011-05-19 04:49 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2101 2011-05-19 04:49 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rw-r--r-- root/root 1966 2011-07-11 12:46 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-11 12:46 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-11 12:46 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./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 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
@@ -641,33 +671,34 @@ drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-05-19 04:49 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/bin/
--rwxr-xr-x root/root 129252 2011-05-19 04:49 ./usr/bin/bcftools
--rwxr-xr-x root/root 25676 2011-05-19 04:49 ./usr/bin/razip
--rwxr-xr-x root/root 412264 2011-05-19 04:49 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/lib/samtools/
--rwxr-xr-x root/root 18184 2011-05-19 04:49 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6520 2011-05-19 04:49 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6520 2011-05-19 04:49 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10348 2011-05-19 04:49 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7096 2011-05-19 04:49 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.16-1_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2011-07-11 12:46 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/bin/
+-rwxr-xr-x root/root 133368 2011-07-11 12:46 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25588 2011-07-11 12:46 ./usr/bin/razip
+-rwxr-xr-x root/root 385000 2011-07-11 12:46 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18184 2011-07-11 12:46 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6560 2011-07-11 12:46 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6560 2011-07-11 12:46 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10388 2011-07-11 12:46 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7136 2011-07-11 12:46 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 179098 bytes: control archive= 934 bytes.
+ size 178550 bytes: control archive= 926 bytes.
682 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 448
+ Installed-Size: 432
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -678,21 +709,21 @@ libbam-dev_0.1.16-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/lib/
--rw-r--r-- root/root 296410 2011-05-19 04:49 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:49 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/lib/
+-rw-r--r-- root/root 290308 2011-07-11 12:46 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 12:46 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
@@ -710,24 +741,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1305780418-49932/build/buildd-samtools_0.1.16-1-kfreebsd-i386-92SZ9L
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1310388232-99437/build/buildd-samtools_0.1.17-1-kfreebsd-i386-Lhw5BB
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 16 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 7 not upgraded.
-After this operation, 25.9 MB disk space will be freed.
-(Reading database ... 13545 files and directories currently installed.)
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
+ html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
+ libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
+ po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 21 to remove and 16 not upgraded.
+After this operation, 27.0 MB disk space will be freed.
+(Reading database ... 13625 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
@@ -761,18 +795,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 10124
-Build-Time: 54
+Build-Space: 9806
+Build-Time: 56
Distribution: sid
-Install-Time: 73
-Job: samtools_0.1.16-1
+Install-Time: 78
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 148
-Source-Version: 0.1.16-1
-Space: 10124
+Package-Time: 156
+Source-Version: 0.1.17-1
+Space: 9806
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0449
-Build needed 00:02:28, 10124k disc space
+Finished at 20110711-1246
+Build needed 00:02:36, 9806k disc space
Signature with key '22C61858' requested:
diff --git a/mips.log b/mips.log
index 71be0d9..04aa6ac 100644
--- a/mips.log
+++ b/mips.log
@@ -1,67 +1,67 @@
-From buildd at ball.debian.org Thu May 19 04:51:06 2011
-Return-path: <buildd at ball.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd2 at corelli.debian.org Mon Jul 11 13:00:57 2011
+Return-path: <buildd2 at corelli.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 4.72) (envelope-from <buildd at ball.debian.org>)
- id 1QMvCT-00007D-Ul
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:06 +0000
-Received: from ball.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d09])
+ (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
+ id 1QgG6a-0007JP-Ng
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 13:00:57 +0000
+Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
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 kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ball.debian.org>)
- id 1QMvCT-0008RL-1c
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:05 +0000
-Received: from buildd by ball.debian.org with local (Exim 4.72)
- (envelope-from <buildd at ball.debian.org>)
- id 1QMvCS-0007R9-2b; Thu, 19 May 2011 04:51:04 +0000
-Date: Thu, 19 May 2011 04:51:04 +0000
-Message-Id: <E1QMvCS-0007R9-2b at ball.debian.org>
-From: buildd on ball <buildd at ball.debian.org>
-To: logs at buildd.debian.org,buildd-porters at ball.debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on mips (dist=sid)
+ CN=corelli.debian.org, EMAIL=hostmaster at corelli.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd2 at corelli.debian.org>)
+ id 1QgG6Y-0000ZY-Js
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 13:00:55 +0000
+Received: from buildd2 by corelli.debian.org with local (Exim 4.69)
+ (envelope-from <buildd2 at corelli.debian.org>) id 1QgG6V-0007c9-U4
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 13:00:52 +0000
+From: buildd on corelli <buildd2 at corelli.debian.org>
+To: logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.17-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1QgG6V-0007c9-U4 at corelli.debian.org>
+Date: Mon, 11 Jul 2011 13:00:51 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ball.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on corelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (mips) 19 May 2011 04:42 ║
+║ samtools 0.1.17-1 (mips) 11 Jul 2011 12:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: mips
-Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [5221 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5379 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 [5221 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [49.8 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [91.7 kB]
-Get:8 http://ftp.de.debian.org unstable/main mips Packages [7091 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib mips Packages [54.4 kB]
-Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2264 B]
-Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7091 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5379 kB]
+Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [52.4 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [95.0 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7297 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [54.4 kB]
+Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
+Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
+Get:13 http://incoming.debian.org unstable/main mips Packages [7297 kB]
Get:14 http://incoming.debian.org unstable/contrib mips Packages [54.4 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [26.8 kB]
-Get:18 http://incoming.debian.org Packages [270 kB]
+Get:17 http://incoming.debian.org Sources [36.1 kB]
+Get:18 http://incoming.debian.org Packages [457 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.6 MB in 1min 7s (382 kB/s)
+Fetched 26.5 MB in 1min 10s (375 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 0s (417 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 1s (285 kB/s)
Download complete and in download only mode
Check arch
@@ -100,111 +100,115 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.2)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-2)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-2)
+mount: already installed (2.19.1-2)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-8)
+gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 37 not upgraded.
-Need to get 9755 kB of archives.
-After this operation, 31.3 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips 8.2.2 [210 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base mips 1.21-5 [1203 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-1 [35.7 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db mips 2.6.0.2-1 [1005 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 mips 5.04-5+b1 [239 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main file mips 5.04-5+b1 [49.9 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-3 [153 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 mips 8.12-3 [262 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-2+b1 [837 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.6-1 [1509 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-4 [415 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext mips 0.18.1.1-3 [2037 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-1 [509 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 21 not upgraded.
+Need to get 10.1 MB of archives.
+After this operation, 31.8 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-3 [35.6 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-1 [1005 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5+b1 [239 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5+b1 [49.9 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-3 [859 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 2.28.6-1 [1509 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 0.9.3-4 [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 all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-1 [509 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 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 9755 kB in 1s (6702 kB/s)
+Fetched 10.1 MB in 1s (6138 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10644 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mips.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 11381 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_mips.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mips.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_mips.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_mips.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_mips.deb) ...
Selecting previously deselected package libmagic1.
@@ -216,7 +220,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_mips.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_mips.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_mips.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_mips.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -232,25 +236,29 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_mips.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mips.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.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) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -259,19 +267,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-sb1-bcm91250a mips (mips64)
-Toolchain package versions: binutils_2.21.51.20110421-3 dpkg-dev_1.16.0.2 g++-4.4_4.4.6-2 g++-4.6_4.6.0-6 gcc-4.4_4.4.6-2 gcc-4.6_4.6.0-6 libc6-dev_2.13-2 libstdc++6_4.6.0-6 libstdc++6-4.4-dev_4.4.6-2 libstdc++6-4.6-dev_4.6.0-6 linux-libc-dev_2.6.38-4
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.4_4.4.6-2 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.4_4.4.6-2 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4_4.4.6-2 gcc-4.4-base_4.4.6-2 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-18 libdb4.8_4.8.30-7 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-1 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.4-dev_4.4.6-2 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
+Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-1 gcc-4.6_4.6.1-1 libc6-dev_2.13-8 libstdc++6_4.6.1-1 libstdc++6-4.6-dev_4.6.1-1 linux-libc-dev_2.6.39-2
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-1 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-1 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-1 gcc-4.6-base_4.6.1-1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-1 libattr1_1:2.4.46-1 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-8 libc-dev-bin_2.13-8 libc6_2.13-8 libc6-dev_2.13-8 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-1 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-1 libstdc++6-4.6-dev_4.6.1-1 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-8 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-2 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -281,13 +291,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -302,35 +313,62 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture mips
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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/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_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/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_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -351,7 +389,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -365,28 +402,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -405,25 +442,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -433,19 +470,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -461,7 +496,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtool
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -469,7 +503,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -496,7 +530,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -504,7 +537,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -518,7 +553,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -526,11 +560,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-mips-2pLxAp/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -545,68 +580,69 @@ 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_0.1.16-1_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_mips.deb'.
- dpkg-genchanges -B -mDebian Build Daemon <buildd_mips-ball at buildd.debian.org> >../samtools_0.1.16-1_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0450
+Build finished at 20110711-1300
-samtools_0.1.16-1_mips.changes:
+samtools_0.1.17-1_mips.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
-Maintainer: Debian Build Daemon <buildd_mips-ball at buildd.debian.org>
+Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- 55c1a23a0d88c2ecad20124d60bf46afd7975690 642396 samtools_0.1.16-1_mips.deb
- 89378ff7eb087f4ca816d964dd9c9bdd9cf49391 200826 libbam-dev_0.1.16-1_mips.deb
+ 8a62b3bfaaa332229c07c073ec06ba0ef5a05b95 627090 samtools_0.1.17-1_mips.deb
+ cd135ea4f4380d05f4212639e5065f8cadc3711c 199160 libbam-dev_0.1.17-1_mips.deb
Checksums-Sha256:
- c9195e03fed7f253826074241ba79c18df53479cdf95c88484dce05513f032a7 642396 samtools_0.1.16-1_mips.deb
- 2baa61a4103179779b184b4ec70712ac736d928cff3b40879a7b2d0125f4a5bf 200826 libbam-dev_0.1.16-1_mips.deb
+ 0eea617858da545210ba046879e222886aae48b13c9dc5a230c74807a86c0186 627090 samtools_0.1.17-1_mips.deb
+ 12c2f5042c024a06a28272f137cae7ac3b949a6206d446306afc246000d7363e 199160 libbam-dev_0.1.17-1_mips.deb
Files:
- 7748d6133eb54120fabe64918ef733cc 642396 science optional samtools_0.1.16-1_mips.deb
- 14b030bb99223024b49cf8b9fbfcd7d1 200826 libdevel optional libbam-dev_0.1.16-1_mips.deb
+ 52bed6f44e522cd92d9d1ba9816a443a 627090 science optional samtools_0.1.17-1_mips.deb
+ 77be420c35e3c9ef7baeb5e5025d5bf2 199160 libdevel optional libbam-dev_0.1.17-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_mips.deb
+samtools_0.1.17-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 642396 bytes: control archive= 1783 bytes.
+ size 627090 bytes: control archive= 1767 bytes.
785 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1216
+ Installed-Size: 1188
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -619,71 +655,71 @@ samtools_0.1.16-1_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 2011-05-19 04:50 ./
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-05-19 04:50 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-05-19 04:49 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/man1/
--rw-r--r-- root/root 2101 2011-05-19 04:50 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8438 2011-05-19 04:50 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-05-19 04:50 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/samtools/
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-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 15707 2011-07-07 02:59 ./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 5778 2011-07-11 12:59 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 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 2011-05-19 04:50 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 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 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/bin/
--rwxr-xr-x root/root 29264 2011-05-19 04:50 ./usr/bin/razip
--rwxr-xr-x root/root 462772 2011-05-19 04:50 ./usr/bin/samtools
--rwxr-xr-x root/root 146724 2011-05-19 04:50 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/samtools/
--rwxr-xr-x root/root 18676 2011-05-19 04:50 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9252 2011-05-19 04:50 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 12512 2011-05-19 04:50 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-short
-
-
-libbam-dev_0.1.16-1_mips.deb
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-11 12:59 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-11 12:59 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./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 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 2011-07-11 12:48 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2011-07-11 12:59 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/lib/samtools/
+-rwxr-xr-x root/root 12512 2011-07-11 12:59 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2011-07-11 12:59 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2011-07-11 12:59 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9252 2011-07-11 12:59 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18660 2011-07-11 12:59 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/bin/
+-rwxr-xr-x root/root 151072 2011-07-11 12:59 ./usr/bin/bcftools
+-rwxr-xr-x root/root 432004 2011-07-11 12:59 ./usr/bin/samtools
+-rwxr-xr-x root/root 29296 2011-07-11 12:59 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2011-07-11 12:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 200826 bytes: control archive= 931 bytes.
+ size 199160 bytes: control archive= 924 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 500
+ Installed-Size: 492
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -694,25 +730,25 @@ libbam-dev_0.1.16-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/include/samtools/
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
--rw-r--r-- root/root 340398 2011-05-19 04:50 ./usr/lib/libbam.a
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-07-11 12:59 ./usr/lib/
+-rw-r--r-- root/root 332126 2011-07-11 12:59 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -726,92 +762,96 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-3aef4ba4-a3b8-4919-a5ff-30ef7e006e4f/build/buildd-samtools_0.1.16-1-mips-2pLxAp
+Purging /var/lib/schroot/mount/sid-mips-sbuild-60a27d1f-4720-45f9-a7e3-7e3bfa63d2a9/build/buildd2-samtools_0.1.17-1-mips-CHIJ5Z
Not cleaning session: cloned chroot in use
+Can't open average time db /var/lib/sbuild/avg-build-times
+Can't open average space db /var/lib/sbuild/avg-build-space
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 10976
-Build-Time: 284
+Build-Space: 10672
+Build-Time: 1157
Distribution: sid
-Install-Time: 115
-Job: samtools_0.1.16-1
+Install-Time: 78
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 522
-Source-Version: 0.1.16-1
-Space: 10976
+Package-Time: 1351
+Source-Version: 0.1.17-1
+Space: 10672
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0450
-Build needed 00:08:42, 10976k disc space
-Signature with key '40E097C5' requested:
+Finished at 20110711-1300
+Build needed 00:22:31, 10672k disc space
+Signature with key '865BEAD2' requested:
-From buildd at mayer.debian.org Thu May 19 04:51:16 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at rem.debian.org Tue Jul 12 07:27:55 2011
+Return-path: <buildd at rem.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1QMvCd-00009N-CD
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:16 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1QgXNq-0002WS-GT
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:55 +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)
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1QMvCb-0008RR-Qe
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:14 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1QMvCY-00052Y-48
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:10 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1QgXNp-0003oU-KU
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:53 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>) id 1QgXNo-0004sl-AG
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:52 +0000
+Date: Tue, 12 Jul 2011 07:27:52 +0000
+Message-Id: <E1QgXNo-0004sl-AG at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.17-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QMvCY-00052Y-48 at mayer.debian.org>
-Date: Thu, 19 May 2011 04:51:10 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (mipsel) 19 May 2011 04:44 ║
+║ samtools 0.1.17-1 (mipsel) 12 Jul 2011 07:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
-Get:2 http://incoming.debian.org sid InRelease [146 kB]
-Get:3 http://debian.oregonstate.edu sid/main Sources [5221 kB]
+Get:1 http://mirror.ayous.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [5385 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org sid/main Sources [5221 kB]
-Get:6 http://debian.oregonstate.edu sid/contrib Sources [49.8 kB]
-Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [7108 kB]
-Get:8 http://debian.oregonstate.edu sid/contrib mipsel Packages [54.7 kB]
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Get:9 http://debian.oregonstate.edu sid/main TranslationIndex [2264 B]
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Get:10 http://incoming.debian.org sid/contrib Sources [49.8 kB]
-Get:11 http://incoming.debian.org sid/main mipsel Packages [7108 kB]
-Get:12 http://incoming.debian.org sid/contrib mipsel Packages [54.7 kB]
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:13 http://incoming.debian.org sid/main TranslationIndex [2264 B]
-Get:14 http://incoming.debian.org Release [1604 B]
-Get:15 http://incoming.debian.org Sources [26.8 kB]
-Get:16 http://incoming.debian.org Packages [270 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:5 http://incoming.debian.org Release [1604 B]
+Get:6 http://incoming.debian.org unstable/main Sources [5385 kB]
+Get:7 http://mirror.ayous.org unstable/contrib Sources [52.4 kB]
+Get:8 http://mirror.ayous.org unstable/non-free Sources [96.0 kB]
+Get:9 http://mirror.ayous.org unstable/main mipsel Packages [7308 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:11 http://mirror.ayous.org unstable/contrib mipsel Packages [54.7 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:12 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Get:13 http://incoming.debian.org unstable/non-free Sources [96.0 kB]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:14 http://incoming.debian.org unstable/main mipsel Packages [7308 kB]
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [54.7 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [40.4 kB]
+Get:18 http://incoming.debian.org Packages [530 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 25.5 MB in 55s (457 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 26.7 MB in 1min 1s (436 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -832,11 +872,11 @@ 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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 0s (426 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 0s (1256 kB/s)
Download complete and in download only mode
Check arch
@@ -850,94 +890,188 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.2)
-e2fsprogs: already installed (1.41.12-3)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.3-7+b1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-2)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-2)
+mount: already installed (2.19.1-2)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-7)
+gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
-debhelper: already installed (8.1.6 >= 8 is satisfied)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+debhelper: missing
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following extra packages will be installed:
+ bsdmainutils diffstat 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 ncurses-doc
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev zlib1g-dev
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 40 not upgraded.
+Need to get 10.1 MB of archives.
+After this operation, 31.8 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-1 [1008 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5+b1 [238 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5+b1 [49.9 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-3 [858 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.9-1 [506 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-7 [354 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, 3 newly installed, 0 to remove and 20 not upgraded.
-Need to get 0 B/774 kB of archives.
-After this operation, 2384 kB of additional disk space will be used.
+Fetched 10.1 MB in 1s (5938 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10621 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-1_mipsel.deb) ...
+Selecting previously deselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../file_5.04-5+b1_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-3_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_2.28.6-1_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_0.9.3-4_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_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 12237 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mipsel.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Processing triggers for man-db ...
-Setting up cdbs (0.4.93) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
+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 (1.21-6) ...
+Setting up man-db (2.6.0.2-1) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libunistring0 (0.9.3-4) ...
+Setting up gettext (0.18.1.1-3) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-4
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-3 e2fsprogs_1.41.12-3 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtimedate-perl_1.2000-1 libudev0_168-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 module-init-tools_3.12-1 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 udev_168-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-13 gcc-4.6_4.6.0-13 libc6-dev_2.13-7 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 linux-libc-dev_2.6.39-2
+Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.0-13 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.0-13 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.6_4.6.0-13 gcc-4.6-base_4.6.0-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6_2.13-7 libc6-dev_2.13-7 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-13 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-13 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7+b1 perl-base_5.12.3-7+b1 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011g-1 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -947,14 +1081,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -963,50 +1097,68 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/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_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/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_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
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 -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -1027,7 +1179,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -1041,28 +1192,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -1081,25 +1232,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -1109,19 +1260,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -1137,7 +1286,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samto
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -1145,13 +1293,9 @@ 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_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -1176,7 +1320,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -1184,7 +1327,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1198,7 +1343,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -1206,11 +1350,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -1225,68 +1370,69 @@ 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_0.1.16-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.16-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0450
+Build finished at 20110712-0727
-samtools_0.1.16-1_mipsel.changes:
+samtools_0.1.17-1_mipsel.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.16-1
+Version: 0.1.17-1
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: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- b2148541e752f5aaccabada3bb2717e861d896cc 642924 samtools_0.1.16-1_mipsel.deb
- fb651f8517cf3a151030cdfd03283bdf040f419c 200948 libbam-dev_0.1.16-1_mipsel.deb
+ 9d262fdb8603b5ad735afc967cc4f3e313727d9f 638486 samtools_0.1.17-1_mipsel.deb
+ f0c56bb4a5193d8f00d91a43d1e914427a168929 200426 libbam-dev_0.1.17-1_mipsel.deb
Checksums-Sha256:
- d14e7b7580a68da2f14a393e715ca8d3bab81830265b4052d3a59616be5843af 642924 samtools_0.1.16-1_mipsel.deb
- 15428af9658f7601a743250beddf9012b150ade02b2339dbb53c6404dd51cae9 200948 libbam-dev_0.1.16-1_mipsel.deb
+ 2339081f1fd713f4c6740bdf17a6f1a74fbd9765c8f6d7e75189652acac650e9 638486 samtools_0.1.17-1_mipsel.deb
+ 2d9f9ef295f21fe7412a7b54c6e25a25e342ce9dc794f51c795a121d4f78aede 200426 libbam-dev_0.1.17-1_mipsel.deb
Files:
- e7c7374c687aefca57d1ffdfc3e81f04 642924 science optional samtools_0.1.16-1_mipsel.deb
- 2d7fe9dff0e0dc49ae911564a9a5a9cf 200948 libdevel optional libbam-dev_0.1.16-1_mipsel.deb
+ d84eee56a2dafb7caa64ab0ed036e223 638486 science optional samtools_0.1.17-1_mipsel.deb
+ 21ee4145a9ac304c18c1ab47f54b1d22 200426 libdevel optional libbam-dev_0.1.17-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_mipsel.deb
+samtools_0.1.17-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 642924 bytes: control archive= 1786 bytes.
+ size 638486 bytes: control archive= 1761 bytes.
787 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1216
+ Installed-Size: 1188
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -1299,71 +1445,71 @@ samtools_0.1.16-1_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 2011-05-19 04:50 ./
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 04:49 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-05-19 04:50 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-05-19 04:50 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8438 2011-05-19 04:50 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2101 2011-05-19 04:50 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9252 2011-07-12 07:27 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 18660 2011-07-12 07:27 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 12512 2011-07-12 07:27 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-12 07:27 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-12 07:27 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-07-12 07:27 ./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 15707 2011-07-07 02:59 ./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 2011-05-19 04:50 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/bin/
--rwxr-xr-x root/root 146724 2011-05-19 04:50 ./usr/bin/bcftools
--rwxr-xr-x root/root 29136 2011-05-19 04:50 ./usr/bin/razip
--rwxr-xr-x root/root 462692 2011-05-19 04:50 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/samtools/
--rwxr-xr-x root/root 18676 2011-05-19 04:50 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12512 2011-05-19 04:50 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9252 2011-05-19 04:50 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.16-1_mipsel.deb
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2011-07-12 07:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2011-07-12 07:27 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./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 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/bin/
+-rwxr-xr-x root/root 432788 2011-07-12 07:27 ./usr/bin/samtools
+-rwxr-xr-x root/root 151072 2011-07-12 07:27 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29152 2011-07-12 07:27 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2011-07-12 07:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 200948 bytes: control archive= 927 bytes.
+ size 200426 bytes: control archive= 926 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 500
+ Installed-Size: 492
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -1374,25 +1520,25 @@ libbam-dev_0.1.16-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
--rw-r--r-- root/root 340310 2011-05-19 04:50 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/samtools/
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
+-rw-r--r-- root/root 334126 2011-07-12 07:27 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./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 5371 2011-07-11 11:19 ./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 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1406,42 +1552,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-6a84821d-880a-40fd-b190-007198c56346/build/buildd-samtools_0.1.16-1-mipsel-fZSyln
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- cdbs* libncurses5-dev* zlib1g-dev*
-0 upgraded, 0 newly installed, 3 to remove and 20 not upgraded.
-After this operation, 2384 kB disk space will be freed.
-(Reading database ... 12361 files and directories currently installed.)
-Removing cdbs ...
-Removing libncurses5-dev ...
-Removing zlib1g-dev ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-9e208add-8fa5-4149-8d78-337bd94eed0f/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10972
-Build-Time: 283
+Build-Space: 10676
+Build-Time: 274
Distribution: sid
-Install-Time: 34
-Job: samtools_0.1.16-1
+Install-Time: 77
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 409
-Source-Version: 0.1.16-1
-Space: 10972
+Package-Time: 452
+Source-Version: 0.1.17-1
+Space: 10676
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0450
-Build needed 00:06:49, 10972k disc space
-Signature with key '68D1B022' requested:
+Finished at 20110712-0727
+Build needed 00:07:32, 10676k disc space
+Signature with key '21BDEC11' requested:
diff --git a/mipsel.log b/mipsel.log
index 1db7756..c113b50 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,65 +1,67 @@
-From buildd at mayer.debian.org Thu May 19 04:51:16 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at rem.debian.org Tue Jul 12 07:27:55 2011
+Return-path: <buildd at rem.debian.org>
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1QMvCd-00009N-CD
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:16 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1QgXNq-0002WS-GT
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:55 +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)
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1QMvCb-0008RR-Qe
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:14 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1QMvCY-00052Y-48
- for logs at buildd.debian.org; Thu, 19 May 2011 04:51:10 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1QgXNp-0003oU-KU
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:53 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>) id 1QgXNo-0004sl-AG
+ for logs at buildd.debian.org; Tue, 12 Jul 2011 07:27:52 +0000
+Date: Tue, 12 Jul 2011 07:27:52 +0000
+Message-Id: <E1QgXNo-0004sl-AG at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.17-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1QMvCY-00052Y-48 at mayer.debian.org>
-Date: Thu, 19 May 2011 04:51:10 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (mipsel) 19 May 2011 04:44 ║
+║ samtools 0.1.17-1 (mipsel) 12 Jul 2011 07:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
-Get:2 http://incoming.debian.org sid InRelease [146 kB]
-Get:3 http://debian.oregonstate.edu sid/main Sources [5221 kB]
+Get:1 http://mirror.ayous.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [5385 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org sid/main Sources [5221 kB]
-Get:6 http://debian.oregonstate.edu sid/contrib Sources [49.8 kB]
-Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [7108 kB]
-Get:8 http://debian.oregonstate.edu sid/contrib mipsel Packages [54.7 kB]
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Get:9 http://debian.oregonstate.edu sid/main TranslationIndex [2264 B]
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Get:10 http://incoming.debian.org sid/contrib Sources [49.8 kB]
-Get:11 http://incoming.debian.org sid/main mipsel Packages [7108 kB]
-Get:12 http://incoming.debian.org sid/contrib mipsel Packages [54.7 kB]
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:13 http://incoming.debian.org sid/main TranslationIndex [2264 B]
-Get:14 http://incoming.debian.org Release [1604 B]
-Get:15 http://incoming.debian.org Sources [26.8 kB]
-Get:16 http://incoming.debian.org Packages [270 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:5 http://incoming.debian.org Release [1604 B]
+Get:6 http://incoming.debian.org unstable/main Sources [5385 kB]
+Get:7 http://mirror.ayous.org unstable/contrib Sources [52.4 kB]
+Get:8 http://mirror.ayous.org unstable/non-free Sources [96.0 kB]
+Get:9 http://mirror.ayous.org unstable/main mipsel Packages [7308 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:11 http://mirror.ayous.org unstable/contrib mipsel Packages [54.7 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:12 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Get:13 http://incoming.debian.org unstable/non-free Sources [96.0 kB]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:14 http://incoming.debian.org unstable/main mipsel Packages [7308 kB]
+Get:15 http://incoming.debian.org unstable/contrib mipsel Packages [54.7 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [40.4 kB]
+Get:18 http://incoming.debian.org Packages [530 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 25.5 MB in 55s (457 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 26.7 MB in 1min 1s (436 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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 0s (426 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 0s (1256 kB/s)
Download complete and in download only mode
Check arch
@@ -98,94 +100,188 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.2)
-e2fsprogs: already installed (1.41.12-3)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.41.12-4)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.3-7+b1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-2)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-2)
+mount: already installed (2.19.1-2)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-7)
+gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
-debhelper: already installed (8.1.6 >= 8 is satisfied)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+debhelper: missing
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following extra packages will be installed:
+ bsdmainutils diffstat 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 ncurses-doc
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
- autotools-dev
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs libncurses5-dev zlib1g-dev
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 40 not upgraded.
+Need to get 10.1 MB of archives.
+After this operation, 31.8 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-3 [35.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-1 [1008 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.04-5+b1 [238 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.04-5+b1 [49.9 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-3 [152 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-3 [262 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-3 [858 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.6-1 [1503 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-1 [110 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-4 [411 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-3 [2023 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.54-1 [28.7 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.9-1 [506 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main quilt all 0.48-7 [354 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, 3 newly installed, 0 to remove and 20 not upgraded.
-Need to get 0 B/774 kB of archives.
-After this operation, 2384 kB of additional disk space will be used.
+Fetched 10.1 MB in 1s (5938 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10621 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
+Selecting previously deselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Selecting previously deselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-1_mipsel.deb) ...
+Selecting previously deselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
+Selecting previously deselected package file.
+Unpacking file (from .../file_5.04-5+b1_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-3_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_2.28.6-1_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_0.9.3-4_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_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-(Reading database ... 12237 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_mipsel.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mipsel.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Processing triggers for man-db ...
-Setting up cdbs (0.4.93) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
+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 (1.21-6) ...
+Setting up man-db (2.6.0.2-1) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.04-5+b1) ...
+Setting up file (5.04-5+b1) ...
+Setting up gettext-base (0.18.1.1-3) ...
+Setting up libpcre3 (8.12-3) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libglib2.0-0 (2.28.6-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3 (0.6.2-1) ...
+Setting up libunistring0 (0.9.3-4) ...
+Setting up gettext (0.18.1.1-3) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-4
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dmsetup_2:1.02.63-3 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-3 e2fsprogs_1.41.12-3 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-3 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdevmapper1.02.1_2:1.02.63-3 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libtimedate-perl_1.2000-1 libudev0_168-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 module-init-tools_3.12-1 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 udev_168-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-13 gcc-4.6_4.6.0-13 libc6-dev_2.13-7 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 linux-libc-dev_2.6.39-2
+Package versions: apt_0.8.14.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.0-13 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.0-13 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.6_4.6.0-13 gcc-4.6-base_4.6.0-13 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-5 libattr1_1:2.4.44-3 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-7 libc-dev-bin_2.13-7 libc6_2.13-7 libc6-dev_2.13-7 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.0-13 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmp3c2_2:4.3.2+dfsg-2 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-13 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-1 libpam-runtime_1.1.3-1 libpam0g_1.1.3-1 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-13 libstdc++6-4.6-dev_4.6.0-13 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-7 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.3-7+b1 perl-base_5.12.3-7+b1 perl-modules_5.12.3-7 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011g-1 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -195,14 +291,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -211,50 +307,68 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/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_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/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_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
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 -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -275,7 +389,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -289,28 +402,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -329,25 +442,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -357,19 +470,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -385,7 +496,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samto
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -393,13 +503,9 @@ 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_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -424,7 +530,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -432,7 +537,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -446,7 +553,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -454,11 +560,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-mipsel-fZSyln/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-mipsel-0JWvrG/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -473,68 +580,69 @@ 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_0.1.16-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.16-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0450
+Build finished at 20110712-0727
-samtools_0.1.16-1_mipsel.changes:
+samtools_0.1.17-1_mipsel.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.16-1
+Version: 0.1.17-1
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: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- b2148541e752f5aaccabada3bb2717e861d896cc 642924 samtools_0.1.16-1_mipsel.deb
- fb651f8517cf3a151030cdfd03283bdf040f419c 200948 libbam-dev_0.1.16-1_mipsel.deb
+ 9d262fdb8603b5ad735afc967cc4f3e313727d9f 638486 samtools_0.1.17-1_mipsel.deb
+ f0c56bb4a5193d8f00d91a43d1e914427a168929 200426 libbam-dev_0.1.17-1_mipsel.deb
Checksums-Sha256:
- d14e7b7580a68da2f14a393e715ca8d3bab81830265b4052d3a59616be5843af 642924 samtools_0.1.16-1_mipsel.deb
- 15428af9658f7601a743250beddf9012b150ade02b2339dbb53c6404dd51cae9 200948 libbam-dev_0.1.16-1_mipsel.deb
+ 2339081f1fd713f4c6740bdf17a6f1a74fbd9765c8f6d7e75189652acac650e9 638486 samtools_0.1.17-1_mipsel.deb
+ 2d9f9ef295f21fe7412a7b54c6e25a25e342ce9dc794f51c795a121d4f78aede 200426 libbam-dev_0.1.17-1_mipsel.deb
Files:
- e7c7374c687aefca57d1ffdfc3e81f04 642924 science optional samtools_0.1.16-1_mipsel.deb
- 2d7fe9dff0e0dc49ae911564a9a5a9cf 200948 libdevel optional libbam-dev_0.1.16-1_mipsel.deb
+ d84eee56a2dafb7caa64ab0ed036e223 638486 science optional samtools_0.1.17-1_mipsel.deb
+ 21ee4145a9ac304c18c1ab47f54b1d22 200426 libdevel optional libbam-dev_0.1.17-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_mipsel.deb
+samtools_0.1.17-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 642924 bytes: control archive= 1786 bytes.
+ size 638486 bytes: control archive= 1761 bytes.
787 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1216
+ Installed-Size: 1188
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -547,71 +655,71 @@ samtools_0.1.16-1_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 2011-05-19 04:50 ./
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 04:49 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-05-19 04:50 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-05-19 04:50 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8438 2011-05-19 04:50 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 2101 2011-05-19 04:50 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/samtools/
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9252 2011-07-12 07:27 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 18660 2011-07-12 07:27 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 12512 2011-07-12 07:27 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2011-07-12 07:27 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-12 07:27 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-12 07:27 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2011-07-12 07:27 ./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 15707 2011-07-07 02:59 ./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 2011-05-19 04:50 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/bin/
--rwxr-xr-x root/root 146724 2011-05-19 04:50 ./usr/bin/bcftools
--rwxr-xr-x root/root 29136 2011-05-19 04:50 ./usr/bin/razip
--rwxr-xr-x root/root 462692 2011-05-19 04:50 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/samtools/
--rwxr-xr-x root/root 18676 2011-05-19 04:50 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2011-05-19 04:50 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12512 2011-05-19 04:50 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9252 2011-05-19 04:50 ./usr/lib/samtools/md5sum-lite
-
-
-libbam-dev_0.1.16-1_mipsel.deb
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2011-07-12 07:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2011-07-12 07:27 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./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 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/bin/
+-rwxr-xr-x root/root 432788 2011-07-12 07:27 ./usr/bin/samtools
+-rwxr-xr-x root/root 151072 2011-07-12 07:27 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29152 2011-07-12 07:27 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2011-07-12 07:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 200948 bytes: control archive= 927 bytes.
+ size 200426 bytes: control archive= 926 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 500
+ Installed-Size: 492
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -622,25 +730,25 @@ libbam-dev_0.1.16-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/lib/
--rw-r--r-- root/root 340310 2011-05-19 04:50 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:50 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/include/samtools/
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/lib/
+-rw-r--r-- root/root 334126 2011-07-12 07:27 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-12 07:27 ./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 5371 2011-07-11 11:19 ./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 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -654,42 +762,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-6a84821d-880a-40fd-b190-007198c56346/build/buildd-samtools_0.1.16-1-mipsel-fZSyln
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- cdbs* libncurses5-dev* zlib1g-dev*
-0 upgraded, 0 newly installed, 3 to remove and 20 not upgraded.
-After this operation, 2384 kB disk space will be freed.
-(Reading database ... 12361 files and directories currently installed.)
-Removing cdbs ...
-Removing libncurses5-dev ...
-Removing zlib1g-dev ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-9e208add-8fa5-4149-8d78-337bd94eed0f/build/buildd-samtools_0.1.17-1-mipsel-0JWvrG
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10972
-Build-Time: 283
+Build-Space: 10676
+Build-Time: 274
Distribution: sid
-Install-Time: 34
-Job: samtools_0.1.16-1
+Install-Time: 77
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 409
-Source-Version: 0.1.16-1
-Space: 10972
+Package-Time: 452
+Source-Version: 0.1.17-1
+Space: 10676
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0450
-Build needed 00:06:49, 10972k disc space
-Signature with key '68D1B022' requested:
+Finished at 20110712-0727
+Build needed 00:07:32, 10676k disc space
+Signature with key '21BDEC11' requested:
diff --git a/powerpc.log b/powerpc.log
index 07ad9a4..0aeec27 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,69 @@
-From buildd at porpora.debian.org Thu May 19 04:45:08 2011
+From buildd at porpora.debian.org Mon Jul 11 12:41:31 2011
Return-path: <buildd at porpora.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1QMv6i-0007Ia-2K
- for logs at buildd.debian.org; Thu, 19 May 2011 04:45:08 +0000
+ id 1QgFnn-0003zI-7F
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 12:41:31 +0000
Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
helo=porpora.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1QMv6g-0003Gx-T0; Thu, 19 May 2011 04:45:07 +0000
-Received: from buildd by porpora.debian.org with local (Exim 4.69)
+ id 1QgFnm-00087a-F0; Mon, 11 Jul 2011 12:41:30 +0000
+Received: from buildd by porpora.debian.org with local (Exim 4.72)
(envelope-from <buildd at porpora.debian.org>)
- id 1QMv6f-00031W-QB; Thu, 19 May 2011 04:45:05 +0000
+ id 1QgFnl-0006tU-VM; Mon, 11 Jul 2011 12:41:30 +0000
+Message-Id: <E1QgFnl-0006tU-VM at porpora.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Thu, 19 May 2011 04:45:05 +0000
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Mon, 11 Jul 2011 12:41:29 +0000
From: buildd on porpora <buildd at porpora.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.16-1 on powerpc (dist=sid)
+Subject: Log for successful build of samtools_0.1.17-1 on powerpc (dist=sid)
Key-Id: CDFA0A89
-Message-Id: <E1QMv6f-00031W-QB at porpora.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (powerpc) 19 May 2011 04:41 ║
+║ samtools 0.1.17-1 (powerpc) 11 Jul 2011 12:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: powerpc
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5221 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [5379 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 [5221 kB]
-Get:6 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
-Get:7 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
-Get:8 http://incoming.debian.org unstable/main powerpc Packages [7196 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib Sources [49.8 kB]
-Get:10 http://ftp.uk.debian.org unstable/non-free Sources [91.7 kB]
-Get:11 http://ftp.uk.debian.org unstable/main powerpc Packages [7196 kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [54.0 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5379 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [52.4 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [95.0 kB]
+Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7392 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [54.0 kB]
Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2264 B]
+Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7392 kB]
Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [54.0 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [26.8 kB]
-Get:18 http://incoming.debian.org Packages [270 kB]
+Get:17 http://incoming.debian.org Sources [36.1 kB]
+Get:18 http://incoming.debian.org Packages [457 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.8 MB in 30s (836 kB/s)
+Fetched 26.7 MB in 24s (1077 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (254 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 1s (351 kB/s)
Download complete and in download only mode
Check arch
@@ -102,91 +102,93 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.2)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-2)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-2)
+mount: already installed (2.19.1-2)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-10)
+gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 30 not upgraded.
-Need to get 9874 kB of archives.
-After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.2 [209 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-5 [1189 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-1 [37.2 kB]
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 12 not upgraded.
+Need to get 10.2 MB of archives.
+After this operation, 31.0 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-3 [37.2 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-1 [1020 kB]
Get:5 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5+b1 [240 kB]
Get:6 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5+b1 [49.9 kB]
Get:7 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-3 [141 kB]
Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-3 [258 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-2+b1 [853 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-3 [837 kB]
Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.6-1 [1611 kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
@@ -194,19 +196,21 @@ Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.
Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-3 [2046 kB]
Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-1 [489 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-1 [489 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 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 9874 kB in 4s (2236 kB/s)
+Fetched 10.2 MB in 2s (3787 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10789 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_powerpc.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10599 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_powerpc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_powerpc.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_powerpc.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_powerpc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_powerpc.deb) ...
Selecting previously deselected package libmagic1.
@@ -218,7 +222,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_powerpc.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_powerpc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_powerpc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_powerpc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -234,25 +238,29 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_powerpc.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_powerpc.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.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) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -261,19 +269,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.26-2-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.51.20110421-3 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-6 gcc-4.6_4.6.0-6 libc6-dev_2.13-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 linux-libc-dev_2.6.38-4
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-2 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-2 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
+Toolchain package versions: binutils_2.21.52.20110703-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110703-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-i18n_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblocale-gettext-perl_1.05-6+b2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtext-charwidth-perl_0.04-6+b3 libtext-iconv-perl_1.7-2+b2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -283,14 +293,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -299,50 +309,68 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/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_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/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_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
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 -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -363,7 +391,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -377,28 +404,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -417,25 +444,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -445,19 +472,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -465,15 +490,14 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-powerpc-stuaIj/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'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -481,13 +505,9 @@ 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_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -512,7 +532,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -520,7 +539,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -534,7 +555,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -542,11 +562,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-powerpc-stuaIj/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-powerpc-oStMKO/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -561,27 +582,27 @@ 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_0.1.16-1_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.16-1_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0445
+Build finished at 20110711-1241
-samtools_0.1.16-1_powerpc.changes:
+samtools_0.1.17-1_powerpc.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
@@ -589,40 +610,41 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- 1c7d432fb60c24c6443c3718c2b0e6d77b4ad398 613252 samtools_0.1.16-1_powerpc.deb
- aacbba612655c0b569ddb33742ddbb8d3a5f2e38 177132 libbam-dev_0.1.16-1_powerpc.deb
+ 26bfabbc96a9796352ad07507c503099668dff55 601652 samtools_0.1.17-1_powerpc.deb
+ ae1d4ef1b47efbf57d8071146ce74c74da50d996 176310 libbam-dev_0.1.17-1_powerpc.deb
Checksums-Sha256:
- c16194d78bcd8e296cd82d9832c8b4ffdeaba33b977084aaf078be1ba8d4b6e9 613252 samtools_0.1.16-1_powerpc.deb
- a91c00bca09d0d6d8ea3be5887fa73c8ca684305b9efa54d5a8394b1642f9492 177132 libbam-dev_0.1.16-1_powerpc.deb
+ 8a6be5d436e0eac96f8a674c30c23645bbf66f2188739bd9286e1f9ec751b95a 601652 samtools_0.1.17-1_powerpc.deb
+ 0f39f874f69623b9879ceb16a1768459a3c8c6d25874bf63c37ce88b00132574 176310 libbam-dev_0.1.17-1_powerpc.deb
Files:
- f25d0ed9745876880cca6f83ac5cea13 613252 science optional samtools_0.1.16-1_powerpc.deb
- 9e59cee60d51ce7c7dd8482c76164734 177132 libdevel optional libbam-dev_0.1.16-1_powerpc.deb
+ 3ab0ca69226f2b6c7e8cb7914a700742 601652 science optional samtools_0.1.17-1_powerpc.deb
+ 63edbea9ae7e3c6e550ca0148bbae691 176310 libdevel optional libbam-dev_0.1.17-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_powerpc.deb
+samtools_0.1.17-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 613252 bytes: control archive= 1786 bytes.
+ size 601652 bytes: control archive= 1759 bytes.
788 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1116
+ Installed-Size: 1092
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -635,71 +657,71 @@ samtools_0.1.16-1_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 2011-05-19 04:44 ./
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/bin/
--rwxr-xr-x root/root 123916 2011-05-19 04:44 ./usr/bin/bcftools
--rwxr-xr-x root/root 392588 2011-05-19 04:44 ./usr/bin/samtools
--rwxr-xr-x root/root 25280 2011-05-19 04:44 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/bin/
+-rwxr-xr-x root/root 129480 2011-07-11 12:41 ./usr/bin/bcftools
+-rwxr-xr-x root/root 366980 2011-07-11 12:41 ./usr/bin/samtools
+-rwxr-xr-x root/root 25296 2011-07-11 12:41 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/samtools/
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-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 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5778 2011-05-19 04:44 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-07-11 12:41 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/man/man1/
--rw-r--r-- root/root 2101 2011-05-19 04:44 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 8438 2011-05-19 04:44 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-05-19 04:44 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2011-07-11 12:41 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-07-11 12:41 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/samtools/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 04:44 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-07-11 12:41 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2011-05-19 04:44 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/lib/samtools/
--rwxr-xr-x root/root 18908 2011-05-19 04:44 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7832 2011-05-19 04:44 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7112 2011-05-19 04:44 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7128 2011-05-19 04:44 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10956 2011-05-19 04:44 ./usr/lib/samtools/md5fa
-
-
-libbam-dev_0.1.16-1_powerpc.deb
+-rw-r--r-- root/root 1966 2011-07-11 12:41 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18892 2011-07-11 12:41 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7832 2011-07-11 12:41 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7112 2011-07-11 12:41 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7128 2011-07-11 12:41 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10956 2011-07-11 12:41 ./usr/lib/samtools/md5fa
+lrwxrwxrwx root/root 0 2011-07-11 12:41 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.17-1_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 177132 bytes: control archive= 928 bytes.
+ size 176310 bytes: control archive= 925 bytes.
676 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 436
+ Installed-Size: 432
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -710,25 +732,25 @@ libbam-dev_0.1.16-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./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 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/include/samtools/
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/include/samtools/
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2011-05-19 04:44 ./usr/lib/
--rw-r--r-- root/root 278090 2011-05-19 04:44 ./usr/lib/libbam.a
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-07-11 12:41 ./usr/lib/
+-rw-r--r-- root/root 272578 2011-07-11 12:41 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -742,7 +764,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-a9ae3202-a878-453f-a305-b429f5998cfe/build/buildd-samtools_0.1.16-1-powerpc-stuaIj
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-048f7e08-ffb0-4f12-82a5-b134ec7f4b61/build/buildd-samtools_0.1.17-1-powerpc-oStMKO
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -750,18 +772,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 10464
-Build-Time: 91
+Build-Space: 10180
+Build-Time: 85
Distribution: sid
-Install-Time: 65
-Job: samtools_0.1.16-1
+Install-Time: 45
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 204
-Source-Version: 0.1.16-1
-Space: 10464
+Package-Time: 169
+Source-Version: 0.1.17-1
+Space: 10180
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0445
-Build needed 00:03:24, 10464k disc space
+Finished at 20110711-1241
+Build needed 00:02:49, 10180k disc space
Signature with key 'CDFA0A89' requested:
diff --git a/s390.log b/s390.log
index 781b402..970da2d 100644
--- a/s390.log
+++ b/s390.log
@@ -1,69 +1,69 @@
-From buildd at zandonai.debian.org Thu May 19 04:48:39 2011
+From buildd at zandonai.debian.org Mon Jul 11 19:27:56 2011
Return-path: <buildd at zandonai.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1QMvA7-0007lC-Cc
- for logs at buildd.debian.org; Thu, 19 May 2011 04:48:39 +0000
+ id 1QgM96-0004WV-Ly
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 19:27:56 +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)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1QMvA6-0008L4-F6; Thu, 19 May 2011 04:48:38 +0000
-Received: from buildd by zandonai.debian.org with local (Exim 4.69)
+ id 1QgM95-0001Jo-GA; Mon, 11 Jul 2011 19:27:55 +0000
+Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1QMvA6-0000cf-1Z; Thu, 19 May 2011 04:48:38 +0000
+ id 1QgM95-0002SX-1c; Mon, 11 Jul 2011 19:27:55 +0000
+Message-Id: <E1QgM95-0002SX-1c at zandonai.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Thu, 19 May 2011 04:48:38 +0000
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Mon, 11 Jul 2011 19:27:55 +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_0.1.16-1 on s390 (dist=sid)
+Subject: Log for successful build of samtools_0.1.17-1 on s390 (dist=sid)
Key-Id: 9BD94C88
-Message-Id: <E1QMvA6-0000cf-1Z at zandonai.debian.org>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (s390) 19 May 2011 04:46 ║
+║ samtools 0.1.17-1 (s390) 11 Jul 2011 19:26 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: s390
Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [5221 kB]
+Get:2 http://ftp.de.debian.org unstable/main Sources [5381 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 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 [5221 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [49.8 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [91.7 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7104 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [53.0 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5381 kB]
+Get:6 http://ftp.de.debian.org unstable/contrib Sources [52.4 kB]
+Get:7 http://ftp.de.debian.org unstable/non-free Sources [95.0 kB]
+Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7306 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [53.1 kB]
Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2264 B]
+Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7104 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [53.0 kB]
+Get:11 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
+Get:13 http://incoming.debian.org unstable/main s390 Packages [7306 kB]
+Get:14 http://incoming.debian.org unstable/contrib s390 Packages [53.1 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [26.8 kB]
-Get:18 http://incoming.debian.org Packages [270 kB]
+Get:17 http://incoming.debian.org Sources [34.7 kB]
+Get:18 http://incoming.debian.org Packages [337 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.6 MB in 28s (894 kB/s)
+Fetched 26.4 MB in 30s (867 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (309 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 0s (1651 kB/s)
Download complete and in download only mode
Check arch
@@ -102,91 +102,93 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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 31 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 31 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (3.4.4)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.2)
-e2fsprogs: already installed (1.41.12-2)
+dpkg: already installed (1.16.0.3)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-2)
-gcc: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-5 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-2)
+mount: already installed (2.19.1-2)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-10)
+gcc: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.2 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 31 not upgraded.
-Need to get 9943 kB of archives.
-After this operation, 29.8 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.2 [208 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-5 [1158 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-1 [38.7 kB]
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 15 not upgraded.
+Need to get 10.3 MB of archives.
+After this operation, 30.8 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-3 [39.0 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-1 [1017 kB]
Get:5 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5+b1 [243 kB]
Get:6 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5+b1 [50.1 kB]
Get:7 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-3 [142 kB]
Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-3 [262 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-2+b1 [873 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-3 [881 kB]
Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.6-1 [1639 kB]
Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
@@ -194,19 +196,21 @@ Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-4
Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-3 [2068 kB]
Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-1 [504 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.0 [559 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-1 [504 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 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 9943 kB in 2s (3408 kB/s)
+Fetched 10.3 MB in 2s (3494 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10570 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_s390.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10521 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_s390.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_s390.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_s390.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_s390.deb) ...
Selecting previously deselected package libmagic1.
@@ -218,7 +222,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_s390.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_s390.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_s390.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_s390.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -234,25 +238,29 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_s390.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_s390.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.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) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -261,19 +269,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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 31 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 15 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-bpo.5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.51.20110421-3 dpkg-dev_1.16.0.2 g++-4.6_4.6.0-6 gcc-4.6_4.6.0-6 libc6-dev_2.13-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 linux-libc-dev_2.6.38-4
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-6 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.2 dpkg-dev_1.16.0.2 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-6 gcc_4:4.6.0-5 gcc-4.4-base_4.4.6-2 gcc-4.5-base_4.5.3-1 gcc-4.6_4.6.0-6 gcc-4.6-base_4.6.0-6 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-2 libc-dev-bin_2.13-2 libc6_2.13-2 libc6-dev_2.13-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.2 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-6 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-1 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-1 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-2 libstdc++6_4.6.0-6 libstdc++6-4.6-dev_4.6.0-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-4 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-s390x s390 (s390x)
+Toolchain package versions: binutils_2.21.52.20110703-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110703-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.0-6 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-6 g++-4.6_4.6.1-2 gcc_4:4.6.0-6 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -283,14 +293,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -299,50 +309,68 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/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_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/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_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
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 -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -357,7 +385,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -371,28 +398,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -411,25 +438,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -439,19 +466,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -467,7 +492,6 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-s390-i66oQB/samtool
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -475,13 +499,9 @@ 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_0.1.16-1-s390-i66oQB/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
test -x debian/rules
dh_testroot
dh_prep
@@ -506,7 +526,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -514,7 +533,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -528,7 +549,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -536,11 +556,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.16-1-s390-i66oQB/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.17-1-s390-A4DcW9/samtools-0.1.17/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -555,27 +576,27 @@ 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_0.1.16-1_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_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_0.1.16-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.16-1_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_s390.deb'.
+ dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.17-1_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-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0448
+Build finished at 20110711-1927
-samtools_0.1.16-1_s390.changes:
+samtools_0.1.17-1_s390.changes:
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: sid
Urgency: low
Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
@@ -583,40 +604,41 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- df8a424feb4767c8f8be139a5ef1cf45f6ecf9f1 613906 samtools_0.1.16-1_s390.deb
- a4e7768ad9256a7411bcd8bf108f157cf1f89e76 182110 libbam-dev_0.1.16-1_s390.deb
+ 967a23a0149ba52edd46b0d9a433e094c4137d5c 603632 samtools_0.1.17-1_s390.deb
+ fcb8f9dee9a1388fefd969f369fca88427be147e 180332 libbam-dev_0.1.17-1_s390.deb
Checksums-Sha256:
- 8f30d44d923f05f8fa429c2487c66f3be1534c438d8bd5a47c6b14d7dc70f4ed 613906 samtools_0.1.16-1_s390.deb
- 5f41a98c70792210f9f7dec900f912bbccf76b07285c6a0d950fe0689daf17f8 182110 libbam-dev_0.1.16-1_s390.deb
+ 645db24cae75df25daa1902c214feb9e210752820fd6fd0bd0616d37936c0e35 603632 samtools_0.1.17-1_s390.deb
+ 18a469606c7e0859291d03f4388f168655cdb24c02e7a67c7fdca1d0a2840be5 180332 libbam-dev_0.1.17-1_s390.deb
Files:
- 1b88ee56dd430f4819a74461705c3d0d 613906 science optional samtools_0.1.16-1_s390.deb
- 69fba3e4b57503aa5674e8421bf43bbb 182110 libdevel optional libbam-dev_0.1.16-1_s390.deb
+ 293df49ac670e99a49b826eb038a3329 603632 science optional samtools_0.1.17-1_s390.deb
+ f31a692d919fc0b2c58824670ca92621 180332 libdevel optional libbam-dev_0.1.17-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_s390.deb
+samtools_0.1.17-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 613906 bytes: control archive= 1785 bytes.
+ size 603632 bytes: control archive= 1753 bytes.
785 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1176
+ Installed-Size: 1148
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -629,71 +651,71 @@ samtools_0.1.16-1_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 2011-05-19 04:48 ./
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/bin/
--rwxr-xr-x root/root 133484 2011-05-19 04:48 ./usr/bin/bcftools
--rwxr-xr-x root/root 439612 2011-05-19 04:48 ./usr/bin/samtools
--rwxr-xr-x root/root 27484 2011-05-19 04:48 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/samtools/
--rwxr-xr-x root/root 11548 2011-05-19 04:48 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7428 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7428 2011-05-19 04:48 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8288 2011-05-19 04:48 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 18748 2011-05-19 04:48 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/man/man1/
--rw-r--r-- root/root 8438 2011-05-19 04:48 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-05-19 04:48 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 2101 2011-05-19 04:48 ./usr/share/man/man1/bcftools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/bin/
+-rwxr-xr-x root/root 141448 2011-07-11 19:27 ./usr/bin/bcftools
+-rwxr-xr-x root/root 409316 2011-07-11 19:27 ./usr/bin/samtools
+-rwxr-xr-x root/root 27452 2011-07-11 19:27 ./usr/bin/razip
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11536 2011-07-11 19:27 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7416 2011-07-11 19:27 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7416 2011-07-11 19:27 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8276 2011-07-11 19:27 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 18692 2011-07-11 19:27 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2011-07-11 19:27 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2011-07-11 19:27 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./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
--rwxr-xr-x root/root 15437 2011-03-01 19:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2011-05-19 04:48 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-07-11 19:27 ./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 2011-05-19 04:48 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/samtools/
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2011-05-19 04:20 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2011-05-20 09:55 ./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 2011-05-19 04:20 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2011-05-19 04:48 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2011-05-20 09:55 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2011-07-11 19:27 ./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 1462 2011-05-19 04:24 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-05-19 04:48 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-07-11 19:27 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+lrwxrwxrwx root/root 0 2011-07-11 19:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.16-1_s390.deb
+libbam-dev_0.1.17-1_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 182110 bytes: control archive= 926 bytes.
+ size 180332 bytes: control archive= 922 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 452
+ Installed-Size: 444
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -704,25 +726,25 @@ libbam-dev_0.1.16-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/include/samtools/
--rw-r--r-- root/root 24548 2011-04-22 03:16 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/include/samtools/
+-rw-r--r-- root/root 24548 2011-07-07 02:59 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/lib/
--rw-r--r-- root/root 292566 2011-05-19 04:48 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 04:48 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 9373 2011-04-22 03:16 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/lib/
+-rw-r--r-- root/root 285766 2011-07-11 19:27 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 19:27 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 9930 2011-07-07 02:59 ./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 1462 2011-05-19 04:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5392 2011-05-19 04:20 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1573 2011-07-11 12:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5371 2011-07-11 11:19 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -736,7 +758,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-5b08dd2a-81c8-46b3-a4d9-7dab745e15f5/build/buildd-samtools_0.1.16-1-s390-i66oQB
+Purging /var/lib/schroot/mount/sid-s390-sbuild-d38d2160-eff9-4944-8614-e527240226bd/build/buildd-samtools_0.1.17-1-s390-A4DcW9
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -744,18 +766,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 11204
-Build-Time: 51
+Build-Space: 10896
+Build-Time: 45
Distribution: sid
-Install-Time: 21
-Job: samtools_0.1.16-1
+Install-Time: 15
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 114
-Source-Version: 0.1.16-1
-Space: 11204
+Package-Time: 96
+Source-Version: 0.1.17-1
+Space: 10896
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0448
-Build needed 00:01:54, 11204k disc space
+Finished at 20110711-1927
+Build needed 00:01:36, 10896k disc space
Signature with key '9BD94C88' requested:
diff --git a/sparc.log b/sparc.log
index e719067..041b107 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,69 +1,70 @@
-From buildd at lebrun.debian.org Thu May 19 04:48:59 2011
-Return-path: <buildd at lebrun.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:216:35ff:fec4:6340])
+From buildd at schroeder.debian.org Mon Jul 11 12:47:43 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 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1QMvAR-0007oc-QR
- for logs at buildd.debian.org; Thu, 19 May 2011 04:48:59 +0000
-Received: from lebrun.debian.org ([193.198.184.10])
+ (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
+ id 1QgFtn-0004sF-9R
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 12:47:43 +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 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1QMvAR-0008LP-0U
- for logs at buildd.debian.org; Thu, 19 May 2011 04:48:59 +0000
-Received: from buildd by lebrun.debian.org with local (Exim 4.69)
- (envelope-from <buildd at lebrun.debian.org>)
- id 1QMvAQ-0007uq-78; Thu, 19 May 2011 04:48:58 +0000
+ 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 1QgFtl-0000Dc-Vr
+ for logs at buildd.debian.org; Mon, 11 Jul 2011 12:47:42 +0000
+Received: from buildd by schroeder.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at schroeder.debian.org>)
+ id 1QgFtj-0001WZ-Q7; Mon, 11 Jul 2011 12:47:39 +0000
+Message-Id: <E1QgFtj-0001WZ-Q7 at schroeder.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Thu, 19 May 2011 04:48:58 +0000
-From: buildd on lebrun <buildd at lebrun.debian.org>
-To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
-Subject: Log for attempted build of samtools_0.1.16-1 on sparc (dist=sid)
-Key-Id: 81587D01
-Message-Id: <E1QMvAQ-0007uq-78 at lebrun.debian.org>
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Mon, 11 Jul 2011 12:47:39 +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_0.1.17-1 on sparc (dist=sid)
+Key-Id: 9BBB678A
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (sparc) 19 May 2011 04:45 ║
+║ samtools 0.1.17-1 (sparc) 11 Jul 2011 12:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Architecture: sparc
-Get:1 http://debian.carnet.hr unstable InRelease [146 kB]
+Get:1 http://ftp.carnet.hr unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://debian.carnet.hr unstable/main Sources [5221 kB]
-Get:4 http://debian.carnet.hr unstable/contrib Sources [49.8 kB]
+Get:3 http://ftp.carnet.hr unstable/main Sources [5379 kB]
+Get:4 http://ftp.carnet.hr unstable/contrib Sources [52.4 kB]
Ign http://incoming.debian.org InRelease
-Get:5 http://incoming.debian.org Release.gpg [836 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5221 kB]
-Get:7 http://debian.carnet.hr unstable/non-free Sources [91.7 kB]
-Get:8 http://debian.carnet.hr unstable/main sparc Packages [7131 kB]
-Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [54.0 kB]
-Ign http://debian.carnet.hr unstable/contrib TranslationIndex
-Get:10 http://debian.carnet.hr unstable/main TranslationIndex [2264 B]
-Get:11 http://incoming.debian.org unstable/contrib Sources [49.8 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [91.7 kB]
-Get:13 http://incoming.debian.org unstable/main sparc Packages [7131 kB]
-Ign http://debian.carnet.hr unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib sparc Packages [54.0 kB]
+Get:5 http://ftp.carnet.hr unstable/non-free Sources [95.0 kB]
+Get:6 http://incoming.debian.org Release.gpg [836 B]
+Get:7 http://incoming.debian.org Release [1604 B]
+Get:8 http://incoming.debian.org unstable/main Sources [5379 kB]
+Get:9 http://ftp.carnet.hr unstable/main sparc Packages [7336 kB]
+Get:10 http://ftp.carnet.hr unstable/contrib sparc Packages [54.1 kB]
+Ign http://ftp.carnet.hr unstable/contrib TranslationIndex
+Get:11 http://ftp.carnet.hr unstable/main TranslationIndex [2045 B]
+Get:12 http://incoming.debian.org unstable/contrib Sources [52.4 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [95.0 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7336 kB]
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [54.1 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2264 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [26.8 kB]
-Get:18 http://incoming.debian.org Packages [270 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [36.1 kB]
+Get:18 http://incoming.debian.org Packages [457 kB]
+Ign http://ftp.carnet.hr unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 25.7 MB in 27s (923 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 26.6 MB in 27s (954 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +85,11 @@ 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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (dsc) [1939 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (tar) [380 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.16-1 (diff) [7161 B]
-Fetched 389 kB in 1s (282 kB/s)
+Need to get 384 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (dsc) [1946 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (tar) [374 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.17-1 (diff) [7643 B]
+Fetched 384 kB in 1s (305 kB/s)
Download complete and in download only mode
Check arch
@@ -102,112 +103,116 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.15.1-1)
+fakeroot: already installed (1.16-1)
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.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 11 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
+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, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.3)
+base-files: already installed (6.4)
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)
+debianutils: already installed (4.0.2)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.41.12-4)
+e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
findutils: already installed (4.4.2-1+b2)
-grep: already installed (2.6.3-3)
+grep: already installed (2.8-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-1)
ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.3-6)
+perl-base: already installed (5.12.4-1)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.2)
-sysvinit: already installed (2.88dsf-13.2)
+sysvinit-utils: already installed (2.88dsf-13.10)
+sysvinit: already installed (2.88dsf-13.10)
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 (2.13-4)
-libc6-dev-sparc64: already installed (2.13-4)
-gcc: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.4.5-9 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.19.1-2)
+mount: already installed (2.19.1-2)
+util-linux: already installed (2.19.1-2)
+libc6-dev: already installed (2.13-10)
+libc6-dev-sparc64: already installed (2.13-10)
+gcc: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.1.6
+Using default version 8.9.0
cdbs: missing
+quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 20 newly installed, 0 to remove and 8 not upgraded.
-Need to get 9701 kB of archives.
-After this operation, 29.6 MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.2 [205 kB]
-Get:2 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-5 [1152 kB]
-Get:3 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-1 [35.8 kB]
-Get:4 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-1 [1013 kB]
-Get:5 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5+b1 [239 kB]
-Get:6 http://debian.carnet.hr/debian/ unstable/main file sparc 5.04-5+b1 [49.6 kB]
-Get:7 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
-Get:8 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
-Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-2+b1 [840 kB]
-Get:10 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
-Get:12 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
-Get:14 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-3 [2006 kB]
-Get:15 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.1.6 [557 kB]
-Get:18 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.93 [75.5 kB]
-Get:19 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 kB]
-Get:20 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+ bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
+ libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 22 newly installed, 0 to remove and 11 not upgraded.
+Need to get 10.1 MB of archives.
+After this operation, 30.6 MB of additional disk space will be used.
+Get:1 http://ftp.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
+Get:2 http://ftp.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:3 http://ftp.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:4 http://ftp.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-1 [1013 kB]
+Get:5 http://ftp.carnet.hr/debian/ unstable/main libmagic1 sparc 5.04-5+b1 [239 kB]
+Get:6 http://ftp.carnet.hr/debian/ unstable/main file sparc 5.04-5+b1 [49.6 kB]
+Get:7 http://ftp.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-3 [140 kB]
+Get:8 http://ftp.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-3 [265 kB]
+Get:9 http://ftp.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-3 [841 kB]
+Get:10 http://ftp.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:11 http://ftp.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 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 0.9.3-4 [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 all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.carnet.hr/debian/ unstable/main debhelper all 8.9.0 [559 kB]
+Get:18 http://ftp.carnet.hr/debian/ unstable/main cdbs all 0.4.94 [75.5 kB]
+Get:19 http://ftp.carnet.hr/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
+Get:20 http://ftp.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 kB]
+Get:21 http://ftp.carnet.hr/debian/ unstable/main quilt all 0.48-7 [354 kB]
+Get:22 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 9701 kB in 7s (1231 kB/s)
+Fetched 10.1 MB in 8s (1189 kB/s)
+Selecting previously deselected package libpipeline1.
+(Reading database ... 10906 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_sparc.deb) ...
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10783 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_sparc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_sparc.deb) ...
Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_sparc.deb) ...
-Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_sparc.deb) ...
+Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_sparc.deb) ...
Selecting previously deselected package libmagic1.
@@ -219,7 +224,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_sparc.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_sparc.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_sparc.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_sparc.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -235,25 +240,29 @@ 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_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_sparc.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_sparc.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.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) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up bsdmainutils (8.2.3) ...
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 groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -262,19 +271,21 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
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.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-bpo.5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.51.20110421-4 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-3 gcc-4.4_4.4.6-3 libc6-dev_2.13-4 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 linux-libc-dev_2.6.38-5
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.51.20110421-4 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.4.5-9 cpp-4.4_4.4.6-3 dash_0.5.5.1-7.4 debconf_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b2 g++_4:4.4.5-9 g++-4.4_4.4.6-3 gcc_4:4.4.5-9 gcc-4.4_4.4.6-3 gcc-4.4-base_4.4.6-3 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.2 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc6_2.13-4 libc6-dev_2.13-4 libc6-dev-sparc64_2.13-4 libc6-sparc64_2.13-4 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9+b1 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libreadline6_6.2-1 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.4-dev_4.4.6-3 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15+b1 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-1 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.2 sysvinit_2.88dsf-13.2 sysvinit-utils_2.88dsf-13.2 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
+Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-2 gcc-4.6_4.6.1-2 libc6-dev_2.13-10 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 linux-libc-dev_2.6.39-3
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22+b1 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.1-1 cpp-4.6_4.6.1-2 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 fakeroot_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b2 g++_4:4.6.1-1 g++-4.6_4.6.1-2 gcc_4:4.6.1-1 gcc-4.6_4.6.1-2 gcc-4.6-base_4.6.1-2 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libc6-dev-sparc64_2.13-10 libc6-sparc64_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-2 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-2 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-3 libpipeline1_1.2.0-3 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-2 libstdc++6-4.6-dev_4.6.1-2 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15+b1 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -284,14 +295,14 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22+b1 bash_4.1-3 b
Unpack source
─────────────
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/Source/Package.pm line 258.
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu May 19 04:26:30 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Jul 11 12:10:24 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_0.1.16-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.17-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
@@ -300,67 +311,88 @@ 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 0.1.16-1
- dpkg-source --before-build samtools-0.1.16
+dpkg-buildpackage: source version 0.1.17-1
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
-Use of uninitialized value $ENV{"HOME"} in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 109.
-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 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/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_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/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_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
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 -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Now at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'bgzf_close':
+bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
bam_import.c: In function 'append_text':
-bam_import.c:179: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
-bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+bam_pileup.c: In function 'resolve_cigar2':
+bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -368,28 +400,34 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
+kprobaln.c: In function 'kpa_glocal':
+kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+ar -csru 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 razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -404,27 +442,29 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+cut_target.c: In function 'main_cut_target':
+cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -434,27 +474,27 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.16-1-sparc-psy34J/samtools-0.1.16/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/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_0.1.16-1-sparc-psy34J/samtools-0.1.16/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2/samtools-0.1.17/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-0448
+Build finished at 20110711-1247
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-94375e8b-7bbf-4396-aa26-31919c6c5d18/build/buildd-samtools_0.1.16-1-sparc-psy34J
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-761f2948-8f46-47c3-8963-ec2b01392c87/build/buildd-samtools_0.1.17-1-sparc-Z4n5s2
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -462,18 +502,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 5924
-Build-Time: 102
+Build-Space: 6412
+Build-Time: 125
Distribution: sid
Fail-Stage: build
-Install-Time: 66
-Job: samtools_0.1.16-1
+Install-Time: 53
+Job: samtools_0.1.17-1
Package: samtools
-Package-Time: 219
-Source-Version: 0.1.16-1
-Space: 5924
+Package-Time: 226
+Source-Version: 0.1.17-1
+Space: 6412
Status: attempted
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-0448
-Build needed 00:03:39, 5924k disc space
+Finished at 20110711-1247
+Build needed 00:03:46, 6412k disc space
--
Processing of sequence alignments in SAM and BAM formats.
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