[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.18-1-4-gb8d566c
Charles Plessy
plessy at debian.org
Sat Mar 30 08:54:49 UTC 2013
The following commit has been merged in the meta branch:
commit 409916495cb4f1777726185e6ee1e71c427ecf1f
Author: Charles Plessy <plessy at debian.org>
Date: Sat Mar 30 17:47:27 2013 +0900
Build logs for 0.1.18-4.
diff --git a/amd64.log b/amd64.log
index 0cd904e..7792dc1 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,171 +1,311 @@
-sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on anx191
+From buildd at barber.debian.org Sun Dec 23 04:55:14 2012
+Return-path: <buildd at barber.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 barber.debian.org>)
+ id 1Tmdak-00070E-8Y
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 04:55:14 +0000
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+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=barber.debian.org, EMAIL=hostmaster at barber.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at barber.debian.org>)
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+ (envelope-from <buildd at barber.debian.org>)
+ id 1Tmdag-0000mN-Rj; Sun, 23 Dec 2012 04:55:10 +0000
+Date: Sun, 23 Dec 2012 04:55:10 +0000
+Message-Id: <E1Tmdag-0000mN-Rj at barber.debian.org>
+From: buildd on barber <buildd at barber.debian.org>
+To: fs at lowpingbastards.de,kurt at roeckx.be,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.18-4 on amd64 (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on barber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (amd64) 06 Sep 2011 17:20 ║
+║ samtools 0.1.18-4 (amd64) 23 Dec 2012 04:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
-Distribution: unstable
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: amd64
-
-I: NOTICE: Log filtering will replace 'build/samtools-eg6khG/samtools-0.1.18' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-eg6khG' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-9b3324e0-1f62-47c6-8efe-a3cd5862fbbd' with '«CHROOT»'
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Update chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Hit http://ftp.jp.debian.org sid InRelease
-Hit http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
-Hit http://ftp.jp.debian.org sid/main TranslationIndex
-Reading package lists...
+Get:1 http://ftp.gr.debian.org unstable InRelease [227 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [6458 kB]
+Get:3 http://ftp.gr.debian.org unstable/contrib Sources [53.0 kB]
+Get:4 http://ftp.gr.debian.org unstable/non-free Sources [101 kB]
+Get:5 http://incoming.debian.org unstable InRelease [227 kB]
+Get:6 http://ftp.gr.debian.org unstable/main amd64 Packages [6244 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib amd64 Packages [45.2 kB]
+Ign http://incoming.debian.org InRelease
+Get:8 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main amd64 Packages [6244 kB]
+Get:12 http://incoming.debian.org unstable/contrib amd64 Packages [45.2 kB]
+Get:13 http://incoming.debian.org Release.gpg [836 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 26.4 MB in 13s (2008 kB/s)
Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
-Local sources
-─────────────
+Check APT
+─────────
+
+Checking available source versions...
-samtools_0.1.18-1.dsc exists in .; copying to chroot
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (238 kB/s)
+Download complete and in download only mode
Check arch
──────────
-Merged Build-Depends: build-essential, fakeroot
-Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-0YalQJ/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (apt-based resolver) │
+│ Install core build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Installing build dependencies
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5)
+fakeroot: already installed (1.18.4-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-sbuild-build-depends-core-dummy is already the newest version.
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Merged 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
-Filtered 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, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-5aucVI/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
-OK
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+Removing negative dependencies:
Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (apt-based resolver) │
+│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Installing build dependencies
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Checking for already installed dependencies...
+base-files: already installed (6.12)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
+coreutils: already installed (8.20-3)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-15)
+sed: already installed (4.2.1-10)
+login: already installed (1:4.1.5.1-1)
+sysvinit-utils: already installed (2.88dsf-34)
+sysvinit: already installed (2.88dsf-34)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-5.2)
+mount: already installed (2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
+libc6-dev: already installed (2.13-37)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+debhelper: missing
+Using default version 9.20120909
+bash-completion: missing
+cdbs: missing
+quilt: missing
+libncurses5-dev: missing
+zlib1g-dev: missing
+Checking for dependency conflicts...
+Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be 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
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl procmail graphviz
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
+ mail-transport-agent
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 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
- sbuild-build-depends-samtools-dummy zlib1g-dev
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 20 not upgraded.
+Need to get 10.8 MB of archives.
+After this operation, 29.9 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 amd64 1.2.2-1 [39.9 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base amd64 1.21-9 [1153 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils amd64 9.0.3 [209 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db amd64 2.6.3-3 [898 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-10 [27.2 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 amd64 5.11-2 [202 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 amd64 1:8.31-1 [247 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-7 [903 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 amd64 2.33.12+really2.32.4-3 [1838 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 amd64 0.6.6-2 [134 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-10 [145 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main file amd64 5.11-2 [51.8 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main gettext-base amd64 0.18.1.1-10 [154 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main libasprintf-dev amd64 0.18.1.1-10 [26.8 kB]
+Get:20 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo-dev amd64 0.18.1.1-10 [184 kB]
+Get:21 http://ftp.gr.debian.org/debian/ unstable/main gettext amd64 0.18.1.1-10 [1815 kB]
+Get:22 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp.gr.debian.org/debian/ unstable/main diffstat amd64 1.55-3 [30.0 kB]
+Get:26 http://ftp.gr.debian.org/debian/ unstable/main libtinfo-dev amd64 5.9-10 [105 kB]
+Get:27 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev amd64 5.9-10 [223 kB]
+Get:28 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/10.1 MB of archives.
-After this operation, 29.7 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 11007 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_amd64.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_amd64.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ...
-Selecting previously deselected package html2text.
+Fetched 10.8 MB in 0s (13.8 MB/s)
+Selecting previously unselected package libpipeline1:amd64.
+(Reading database ... 10843 files and directories currently installed.)
+Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.2-1_amd64.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_amd64.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_amd64.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_amd64.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
+Selecting previously unselected package libasprintf0c2:amd64.
+Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-10_amd64.deb) ...
+Selecting previously unselected package libmagic1:amd64.
+Unpacking libmagic1:amd64 (from .../libmagic1_5.11-2_amd64.deb) ...
+Selecting previously unselected package libpcre3:amd64.
+Unpacking libpcre3:amd64 (from .../libpcre3_1%3a8.31-1_amd64.deb) ...
+Selecting previously unselected package libxml2:amd64.
+Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-7_amd64.deb) ...
+Selecting previously unselected package libffi5:amd64.
+Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ...
+Selecting previously unselected package libglib2.0-0:amd64.
+Unpacking libglib2.0-0:amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-3_amd64.deb) ...
+Selecting previously unselected package libcroco3:amd64.
+Unpacking libcroco3:amd64 (from .../libcroco3_0.6.6-2_amd64.deb) ...
+Selecting previously unselected package libunistring0:amd64.
+Unpacking libunistring0:amd64 (from .../libunistring0_0.9.3-5_amd64.deb) ...
+Selecting previously unselected package libgettextpo0:amd64.
+Unpacking libgettextpo0:amd64 (from .../libgettextpo0_0.18.1.1-10_amd64.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.11-2_amd64.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_amd64.deb) ...
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package libasprintf-dev:amd64.
+Unpacking libasprintf-dev:amd64 (from .../libasprintf-dev_0.18.1.1-10_amd64.deb) ...
+Selecting previously unselected package libgettextpo-dev:amd64.
+Unpacking libgettextpo-dev:amd64 (from .../libgettextpo-dev_0.18.1.1-10_amd64.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-10_amd64.deb) ...
+Selecting previously unselected 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_8.9.6_all.deb) ...
-Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
-Selecting previously deselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_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_amd64.deb) ...
-Selecting previously deselected package sbuild-build-depends-samtools-dummy.
-Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_amd64.deb) ...
+Selecting previously unselected package libtinfo-dev:amd64.
+Unpacking libtinfo-dev:amd64 (from .../libtinfo-dev_5.9-10_amd64.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_amd64.deb) ...
+Selecting previously unselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev:amd64.
+Unpacking zlib1g-dev:amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_amd64.deb) ...
+Setting up libpipeline1:amd64 (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
+Setting up bsdmainutils (9.0.3) ...
+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 man-db (2.6.3-3) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.6-1) ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:amd64 (0.18.1.1-10) ...
+Setting up libmagic1:amd64 (5.11-2) ...
+Setting up libpcre3:amd64 (1:8.31-1) ...
+Setting up libxml2:amd64 (2.8.0+dfsg1-7) ...
+Setting up libffi5:amd64 (3.0.10-3) ...
+Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up libcroco3:amd64 (0.6.6-2) ...
+Setting up libunistring0:amd64 (0.9.3-5) ...
+Setting up libgettextpo0:amd64 (0.18.1.1-10) ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libasprintf-dev:amd64 (0.18.1.1-10) ...
+Setting up libgettextpo-dev:amd64 (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.6) ...
-Setting up cdbs (0.4.96) ...
-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) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build environment │
-└──────────────────────────────────────────────────────────────────────────────┘
-
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:amd64 (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ...
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
-Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 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_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libclass-isa-perl_0.36-2 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_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 libgpm2_1.20.4-4 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 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_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpod-plainer-perl_1.03-1 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-9 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 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-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.20-3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-34 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libitm1_4.7.2-4 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -175,73 +315,63 @@ Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (samtools_0.1.18-1.dsc)
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
-Sufficient free space for build
-
-User Environment
-────────────────
-
-HOME=/sbuild-nonexistent
-LOGNAME=charles
-PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_CHROOT_NAME=sid-amd64-sbuild
-SCHROOT_COMMAND=env
-SCHROOT_GID=1000
-SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-9b3324e0-1f62-47c6-8efe-a3cd5862fbbd
-SCHROOT_UID=31051
-SCHROOT_USER=charles
-SHELL=/bin/sh
-TERM=xterm
-USER=charles
-USERNAME=charles
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
-dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture 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 `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/«PKGBUILDDIR»'
-make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/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 `/«PKGBUILDDIR»/bcftools'
-make[2]: Entering directory `/«PKGBUILDDIR»/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
+Removing patch fix_coverage_cap.patch
+Restoring bam2depth.c
+
+Removing patch fix_segfault_with_small_ref.patch
+Restoring bam_plcmd.c
+
Removing patch no-pileup-tests.patch
Restoring examples/Makefile
@@ -249,138 +379,150 @@ 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
- dpkg-source -b samtools-0.1.18
-dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: warning: patches have not been applied, applying them now (use --no-preparation to override)
-dpkg-source: info: applying no-pileup-tests.patch
-dpkg-source: info: building samtools using existing ./samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: building samtools in samtools_0.1.18-1.debian.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.18-1.dsc
- debian/rules build
+ debian/rules build-arch
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
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
-File series fully applied, ends at patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Applying patch fix_segfault_with_small_ref.patch
+patching file bam_plcmd.c
+
+Applying patch fix_coverage_cap.patch
+patching file bam2depth.c
+
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
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 `/«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
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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. razf.c -o razf.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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
-gcc -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. 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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-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_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_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»'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»'
-make[3]: Entering directory `/«PKGBUILDDIR»/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«PKGBUILDDIR»/bcftools'
-make[3]: Entering directory `/«PKGBUILDDIR»/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-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 `/«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
-gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+md5.c: In function 'MD5Final':
+md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+md5.c: In function 'MD5Final':
+md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
-gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-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
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18'
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 `/«PKGBUILDDIR»/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -406,15 +548,16 @@ 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 `/«PKGBUILDDIR»/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
- fakeroot debian/rules binary
+ fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -441,8 +584,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
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
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -465,12 +610,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«PKGBUILDDIR»/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-amd64-3Qw6rz/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -480,92 +625,85 @@ dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_amd64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.18-1_amd64.changes
-dpkg-genchanges: including full source code in upload
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_amd64.deb'.
+ dpkg-genchanges -B -mamd64 Builddd Daemon (barber) <buildd_amd64-barber at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
-dpkg-buildpackage: full upload (original source is included)
+dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110906-1721
-
-Finished
-────────
-
-I: Built successfully
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.18-1_amd64.changes:
-────────────────────────────────
+Build finished at 20121223-0455
+samtools_0.1.18-4_amd64.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
-Architecture: source amd64
-Version: 0.1.18-1
-Distribution: unstable
+Architecture: amd64
+Version: 0.1.18-4
+Distribution: sid
Urgency: low
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: amd64 Builddd Daemon (barber) <buildd_amd64-barber at buildd.debian.org>
+Changed-By: Dominique Belhachemi <domibel at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
+ .
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
.
- [b990d9d3] New upstream release.
- [d59366b9] Updated copyright statements.
- [aa08abe5] Compress binary packages with xz.
- [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
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- 58bdc966e27240dd40f3360217c61da6c1aec7a68de9ab5ad5142211c5d03a26 528100 samtools_0.1.18-1_amd64.deb
- 8b93deaa8e3ca489689405598f1bbdfc209f57ae306e1d614468c3df74d906bd 154072 libbam-dev_0.1.18-1_amd64.deb
+ bda934eff386609c599e971f8eacfa2f764832880e50362a87cc2408bca2ed02 533424 samtools_0.1.18-4_amd64.deb
+ 3cb5f3a33ec713a96876b77f7b0666044e7924d535436610ab0e227842955ee2 156458 libbam-dev_0.1.18-4_amd64.deb
Files:
- 9e57a71fdfa8ee2942acb84456d347a1 1060 science optional samtools_0.1.18-1.dsc
- 71dab132e21c0766f0de84c2371a9157 379306 science optional samtools_0.1.18.orig.tar.bz2
- c129651f68209b9cd88c84637fdba478 7593 science optional samtools_0.1.18-1.debian.tar.gz
- 3ff72808597c8549d9646c92b27e761a 528100 science optional samtools_0.1.18-1_amd64.deb
- 50297b7d71115ba69ba85ce8cac86497 154072 libdevel optional libbam-dev_0.1.18-1_amd64.deb
+ b959e9792dc2e967313de46f76f5cc8f 533424 science optional samtools_0.1.18-4_amd64.deb
+ 17326a4357880a46b529b52ac2acbe6c 156458 libdevel optional libbam-dev_0.1.18-4_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_amd64.deb
+samtools_0.1.18-4_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 528100 bytes: control archive= 1760 bytes.
- 786 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ size 533424 bytes: control archive= 1807 bytes.
+ 32 bytes, 1 lines conffiles
+ 792 bytes, 16 lines control
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-4
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1072
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1021
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -577,71 +715,74 @@ samtools_0.1.18-1_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 2011-09-06 17:21 ./
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/lib/samtools/
--rwxr-xr-x root/root 11832 2011-09-06 17:21 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17968 2011-09-06 17:21 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8688 2011-09-06 17:21 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 8080 2011-09-06 17:21 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8144 2011-09-06 17:21 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/bin/
--rwxr-xr-x root/root 363832 2011-09-06 17:21 ./usr/bin/samtools
--rwxr-xr-x root/root 24488 2011-09-06 17:21 ./usr/bin/razip
--rwxr-xr-x root/root 130528 2011-09-06 17:21 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/samtools/
--rwxr-xr-x root/root 18572 2011-03-22 12:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-09-06 17:21 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 4996 2010-11-17 13:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 13:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 13:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 13:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 13:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 13:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 13:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 15707 2011-07-07 11:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 13:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 13:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5989 2010-11-17 13:16 ./usr/share/samtools/novo2sam.pl
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-09-06 17:21 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-09-06 17:21 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 786 2011-04-22 12:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-09-06 17:21 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-11-17 13:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 13:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 33578 2011-03-02 04:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 10122 2011-09-03 01:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 16:01 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1966 2011-09-06 17:21 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1676 2011-09-06 16:52 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 1031 2011-09-06 16:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-09-06 16:01 ./usr/share/doc/samtools/reference
-lrwxrwxrwx root/root 0 2011-09-06 17:21 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-1_amd64.deb
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/bin/
+-rwxr-xr-x root/root 24768 2012-12-23 04:55 ./usr/bin/razip
+-rwxr-xr-x root/root 130600 2012-12-23 04:55 ./usr/bin/bcftools
+-rwxr-xr-x root/root 372448 2012-12-23 04:55 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:54 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./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 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1966 2012-12-23 04:55 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2012-12-23 04:54 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 126583 2012-12-23 04:54 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-12-23 04:54 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2012-12-23 04:54 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2012-12-23 04:54 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/share/samtools/
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.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 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 5778 2012-12-23 04:55 ./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 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 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17984 2012-12-23 04:55 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8200 2012-12-23 04:55 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8280 2012-12-23 04:55 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11976 2012-12-23 04:55 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8848 2012-12-23 04:55 ./usr/lib/samtools/md5sum-lite
+lrwxrwxrwx root/root 0 2012-12-23 04:55 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_amd64.deb
─────────────────────────────
new debian package, version 2.0.
- size 154072 bytes: control archive= 924 bytes.
- 674 bytes, 15 lines control
+ size 156458 bytes: control archive= 941 bytes.
+ 712 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-4
Architecture: 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
@@ -651,125 +792,62 @@ libbam-dev_0.1.18-1_amd64.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/lib/
--rw-r--r-- root/root 323274 2011-09-06 17:21 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/include/samtools/
--rw-r--r-- root/root 17815 2011-03-02 04:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 13:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 4617 2011-04-11 07:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 2625 2010-11-17 13:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 24720 2011-09-03 01:58 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 33578 2011-03-02 04:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-03 01:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 16:01 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1676 2011-09-06 16:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./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 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./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 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 24732 2012-12-23 04:54 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2012-12-23 04:55 ./usr/lib/
+-rw-r--r-- root/root 332346 2012-12-23 04:55 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
+│ Finished │
└──────────────────────────────────────────────────────────────────────────────┘
-
-lintian
-───────
-
-P: samtools source: unneeded-build-dep-on-quilt
-W: samtools source: debian-watch-file-should-use-sf-redirector line 4
-W: samtools: manpage-has-errors-from-man usr/share/man/man1/samtools.1.gz around line 725: table wider than line width
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:9
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:23
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:25
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:33
-I: samtools: spelling-error-in-manpage usr/share/man/man1/samtools.1.gz allows to allows one to
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:58
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:59
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:317
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:327
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:334
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:351
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz 26 more occurrences not shown
-
-I: Lintian run was successful.
+Built successfully
+────────────────────────────────────────────────────────────────────────────────
┌──────────────────────────────────────────────────────────────────────────────┐
-│ Cleanup │
+│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /«BUILDDIR»
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- cdbs* debhelper* 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* sbuild-build-depends-samtools-dummy* zlib1g-dev*
-0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded.
-After this operation, 29.7 MB disk space will be freed.
-(Reading database ... 12421 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 ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-amd64-sbuild-b464f04b-aaf2-480e-8e87-26d7ea8d45d7/build/buildd-samtools_0.1.18-4-amd64-3Qw6rz
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 12700
-Build-Time: 23
-Distribution: unstable
-Install-Time: 27
-Job: samtools_0.1.18-1.dsc
-Lintian: pass
+Build-Space: 13868
+Build-Time: 53
+Distribution: sid
+Install-Time: 54
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 51
-Source-Version: 0.1.18-1
-Space: 12700
+Package-Time: 136
+Source-Version: 0.1.18-4
+Space: 13868
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-1721
-Build needed 00:00:51, 12700k disc space
+Finished at 20121223-0455
+Build needed 00:02:16, 13868k disc space
+Signature with key '4E07683D' requested:
+
diff --git a/armel.log b/armel.log
index 9e0130a..7e8e21e 100644
--- a/armel.log
+++ b/armel.log
@@ -1,61 +1,60 @@
-From buildd at antheil.debian.org Fri Jul 27 15:49:07 2012
-Return-path: <buildd at antheil.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at alain.debian.org Sun Dec 23 05:02:49 2012
+Return-path: <buildd at alain.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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-Date: Fri, 27 Jul 2012 15:49:05 +0000
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-From: buildd on antheil <buildd at antheil.debian.org>
-To: buildd-porters at antheil.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-3 on armel (dist=sid)
+ CN=alain.debian.org, EMAIL=hostmaster at alain.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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+Date: Sun, 23 Dec 2012 05:02:46 +0000
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+From: buildd on alain <buildd at alain.debian.org>
+To: buildd-porters at alain.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.18-4 on armel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on antheil.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alain.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (armel) 27 Jul 2012 15:39 ║
+║ samtools 0.1.18-4 (armel) 23 Dec 2012 04:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: armel
-Get:1 http://incoming.debian.org unstable InRelease [249 kB]
-Get:2 http://ftp.uk.debian.org unstable InRelease [249 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
+Get:1 http://incoming.debian.org unstable InRelease [227 kB]
+Get:2 http://ftp.uk.debian.org unstable InRelease [227 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 [6315 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armel Packages [5978 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main armel Packages [5978 kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [37.6 kB]
-Get:13 http://incoming.debian.org unstable/contrib armel Packages [37.6 kB]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.6 MB in 1min 41s (252 kB/s)
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1141 B]
+Get:5 http://ftp.uk.debian.org unstable/main Sources [6458 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:7 http://ftp.uk.debian.org unstable/contrib Sources [53.0 kB]
+Get:8 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
+Get:9 http://ftp.uk.debian.org unstable/main armel Packages [6097 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:12 http://incoming.debian.org unstable/main armel Packages [6097 kB]
+Get:13 http://ftp.uk.debian.org unstable/contrib armel Packages [36.7 kB]
+Get:14 http://incoming.debian.org unstable/contrib armel Packages [36.7 kB]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 26.1 MB in 1min 39s (261 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,11 +75,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (298 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (311 kB/s)
Download complete and in download only mode
Check arch
@@ -100,65 +99,66 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (6.12)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-4)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.8)
-e2fsprogs: already installed (1.42.4-3)
-findutils: already installed (4.4.2-4)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
grep: already installed (2.12-2)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-15)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-29)
-sysvinit: already installed (2.88dsf-29)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-mount: already installed (2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-35)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.20.1-5.2)
+mount: already installed (2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
+libc6-dev: already installed (2.13-36)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
@@ -167,84 +167,94 @@ 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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 1 not upgraded.
-Need to get 10.4 MB of archives.
-After this operation, 27.3 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.1-1 [34.9 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armel 0.18.1.1-9 [26.4 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.11-2 [200 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 1:8.30-5 [241 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.8.0+dfsg1-5 [825 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.32.3-1 [1962 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.5-1 [142 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armel 0.18.1.1-9 [132 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.3 [208 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-9 [1079 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.2-1 [1025 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.11-2 [51.4 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-9 [138 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-9 [1888 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-3 [28.6 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armel 5.9-10 [90.3 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-10 [205 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.7.dfsg-13 [211 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 37 not upgraded.
+Need to get 10.2 MB of archives.
+After this operation, 28.2 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.2-1 [35.1 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-9 [1079 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.3 [208 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.3-3 [868 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armel 0.18.1.1-10 [26.6 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.11-2 [200 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 1:8.31-1 [247 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.8.0+dfsg1-7 [825 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.33.12+really2.32.4-3 [1694 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.6-2 [120 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armel 0.18.1.1-10 [132 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.11-2 [51.4 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-10 [138 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev armel 0.18.1.1-10 [26.5 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev armel 0.18.1.1-10 [163 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-10 [1749 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-3 [28.6 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armel 5.9-10 [90.3 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-10 [205 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 5s (1798 kB/s)
+Fetched 10.2 MB in 5s (1995 kB/s)
Selecting previously unselected package libpipeline1:armel.
-(Reading database ... 10640 files and directories currently installed.)
-Unpacking libpipeline1:armel (from .../libpipeline1_1.2.1-1_armel.deb) ...
+(Reading database ... 10693 files and directories currently installed.)
+Unpacking libpipeline1:armel (from .../libpipeline1_1.2.2-1_armel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_armel.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_armel.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:armel.
-Unpacking libasprintf0c2:armel (from .../libasprintf0c2_0.18.1.1-9_armel.deb) ...
+Unpacking libasprintf0c2:armel (from .../libasprintf0c2_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package libmagic1:armel.
Unpacking libmagic1:armel (from .../libmagic1_5.11-2_armel.deb) ...
Selecting previously unselected package libpcre3:armel.
-Unpacking libpcre3:armel (from .../libpcre3_1%3a8.30-5_armel.deb) ...
+Unpacking libpcre3:armel (from .../libpcre3_1%3a8.31-1_armel.deb) ...
Selecting previously unselected package libxml2:armel.
-Unpacking libxml2:armel (from .../libxml2_2.8.0+dfsg1-5_armel.deb) ...
+Unpacking libxml2:armel (from .../libxml2_2.8.0+dfsg1-7_armel.deb) ...
Selecting previously unselected package libffi5:armel.
Unpacking libffi5:armel (from .../libffi5_3.0.10-3_armel.deb) ...
Selecting previously unselected package libglib2.0-0:armel.
-Unpacking libglib2.0-0:armel (from .../libglib2.0-0_2.32.3-1_armel.deb) ...
+Unpacking libglib2.0-0:armel (from .../libglib2.0-0_2.33.12+really2.32.4-3_armel.deb) ...
Selecting previously unselected package libcroco3:armel.
-Unpacking libcroco3:armel (from .../libcroco3_0.6.5-1_armel.deb) ...
+Unpacking libcroco3:armel (from .../libcroco3_0.6.6-2_armel.deb) ...
Selecting previously unselected package libunistring0:armel.
Unpacking libunistring0:armel (from .../libunistring0_0.9.3-5_armel.deb) ...
Selecting previously unselected package libgettextpo0:armel.
-Unpacking libgettextpo0:armel (from .../libgettextpo0_0.18.1.1-9_armel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armel.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_armel.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_armel.deb) ...
+Unpacking libgettextpo0:armel (from .../libgettextpo0_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.11-2_armel.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_armel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
+Selecting previously unselected package libasprintf-dev:armel.
+Unpacking libasprintf-dev:armel (from .../libasprintf-dev_0.18.1.1-10_armel.deb) ...
+Selecting previously unselected package libgettextpo-dev:armel.
+Unpacking libgettextpo-dev:armel (from .../libgettextpo-dev_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_armel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_armel.deb) ...
Selecting previously unselected package libtinfo-dev:armel.
@@ -255,31 +265,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:armel.
Unpacking zlib1g-dev:armel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_armel.deb) ...
-Setting up libpipeline1:armel (1.2.1-1) ...
-Setting up libasprintf0c2:armel (0.18.1.1-9) ...
-Setting up libmagic1:armel (5.11-2) ...
-Setting up libpcre3:armel (1:8.30-5) ...
-Setting up libxml2:armel (2.8.0+dfsg1-5) ...
-Setting up libffi5:armel (3.0.10-3) ...
-Setting up libglib2.0-0:armel (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:armel (0.6.5-1) ...
-Setting up libunistring0:armel (0.9.3-5) ...
-Setting up libgettextpo0:armel (0.18.1.1-9) ...
+Setting up libpipeline1:armel (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
Setting up bsdmainutils (9.0.3) ...
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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
+Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:armel (0.18.1.1-10) ...
+Setting up libmagic1:armel (5.11-2) ...
+Setting up libpcre3:armel (1:8.31-1) ...
+Setting up libxml2:armel (2.8.0+dfsg1-7) ...
+Setting up libffi5:armel (3.0.10-3) ...
+Setting up libglib2.0-0:armel (2.33.12+really2.32.4-3) ...
+No schema files found: doing nothing.
+Setting up libcroco3:armel (0.6.6-2) ...
+Setting up libunistring0:armel (0.9.3-5) ...
+Setting up libgettextpo0:armel (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:armel (0.18.1.1-10) ...
+Setting up libgettextpo-dev:armel (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:armel (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -289,11 +302,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-35 libstdc++6_4.7.1-5 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.2 base-files_6.11 base-passwd_3.5.26 bash_4.2-4 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-1 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-29 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.2 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-5 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-5 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-29 sysvinit_2.88dsf-29 sysvinit-utils_2.88dsf-29 tar_1.26-4 tzdata_2012d-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-4 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -304,15 +317,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -322,7 +336,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
@@ -330,26 +344,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/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_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -367,11 +384,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -381,15 +399,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -424,8 +445,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -440,10 +461,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -464,24 +485,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armel-zkuM87/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armel-zkuM87/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -503,14 +524,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armel-zkuM87/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armel-zkuM87/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -518,14 +539,14 @@ Line 2, sequence length 35 vs 8960 from CIGAR
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_0.1.18-3-armel-zkuM87/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1549
+Build finished at 20121223-0502
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-6b9b83f9-bc18-46e0-945b-39cd8ecff13a/build/buildd-samtools_0.1.18-3-armel-zkuM87
+Purging /var/lib/schroot/mount/sid-armel-sbuild-eb1bd0de-67fc-4971-b540-486b400c689e/build/buildd-samtools_0.1.18-4-armel-E7vUyT
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -533,19 +554,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 6464
-Build-Time: 318
+Build-Space: 6504
+Build-Time: 316
Distribution: sid
Fail-Stage: build
-Install-Time: 103
-Job: samtools_0.1.18-3
+Install-Time: 113
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 560
-Source-Version: 0.1.18-3
-Space: 6464
+Package-Time: 565
+Source-Version: 0.1.18-4
+Space: 6504
Status: attempted
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1549
-Build needed 00:09:20, 6464k disc space
+Finished at 20121223-0502
+Build needed 00:09:25, 6504k disc space
diff --git a/armhf.log b/armhf.log
index 15a59bd..14b380f 100644
--- a/armhf.log
+++ b/armhf.log
@@ -1,60 +1,60 @@
-From buildd at henze.debian.org Fri Jul 27 15:47:24 2012
-Return-path: <buildd at henze.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at hasse.debian.org Sun Dec 23 05:02:50 2012
+Return-path: <buildd at hasse.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 henze.debian.org>)
- id 1Suml9-0006EV-Nl
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:47:24 +0000
-Received: from [217.140.96.70] (helo=henze.debian.org)
+ (Exim 4.72) (envelope-from <buildd at hasse.debian.org>)
+ id 1Tmdi6-0008Kt-9D
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:02:50 +0000
+Received: from [217.140.96.68] (helo=hasse.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=henze.debian.org, EMAIL=hostmaster at henze.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at henze.debian.org>)
- id 1Suml8-000208-L2
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:47:22 +0000
-Received: from buildd by henze.debian.org with local (Exim 4.80)
- (envelope-from <buildd at henze.debian.org>)
- id 1Suml1-0002dV-07; Fri, 27 Jul 2012 15:47:15 +0000
-From: buildd on henze <buildd at henze.debian.org>
-To: logs at buildd.debian.org,buildd-porters at henze.debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on armhf (dist=sid)
+ CN=hasse.debian.org, EMAIL=hostmaster at hasse.debian.org (verified)
+ by merikanto.debian.org with esmtps
+ (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.72)
+ (envelope-from <buildd at hasse.debian.org>) id 1Tmdi5-0008Is-6X
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:02:49 +0000
+Received: from buildd by hasse.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at hasse.debian.org>)
+ id 1Tmdhz-0000jb-Pj; Sun, 23 Dec 2012 05:02:43 +0000
+From: buildd on hasse <buildd at hasse.debian.org>
+To: logs at buildd.debian.org,buildd-porters at hasse.debian.org
+Subject: Log for successful build of samtools_0.1.18-4 on armhf (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Suml1-0002dV-07 at henze.debian.org>
-Date: Fri, 27 Jul 2012 15:47:15 +0000
+Message-Id: <E1Tmdhz-0000jb-Pj at hasse.debian.org>
+Date: Sun, 23 Dec 2012 05:02:43 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on henze.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hasse.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (armhf) 27 Jul 2012 15:38 ║
+║ samtools 0.1.18-4 (armhf) 23 Dec 2012 04:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: armhf
-Get:1 http://incoming.debian.org unstable InRelease [249 kB]
-Get:2 http://ftp.uk.debian.org unstable InRelease [249 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [227 kB]
+Get:2 http://incoming.debian.org unstable InRelease [227 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6458 kB]
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:5 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
-Get:6 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
-Get:7 http://ftp.uk.debian.org unstable/main armhf Packages [5950 kB]
-Get:8 http://ftp.uk.debian.org unstable/contrib armhf Packages [36.1 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main armhf Packages [5950 kB]
-Get:12 http://incoming.debian.org unstable/contrib armhf Packages [36.1 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.5 MB in 1min 28s (289 kB/s)
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.0 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [6061 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main armhf Packages [6061 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib armhf Packages [35.8 kB]
+Get:13 http://incoming.debian.org unstable/contrib armhf Packages [35.8 kB]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 26.0 MB in 1min 27s (297 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -75,11 +75,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (326 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (286 kB/s)
Download complete and in download only mode
Check arch
@@ -99,41 +99,42 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 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 23 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: 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
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-36)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
@@ -142,84 +143,94 @@ 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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 23 not upgraded.
-Need to get 10.1 MB of archives.
-After this operation, 25.3 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.1-1 [33.2 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-9 [26.4 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.11-2 [199 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.30-5 [240 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-5 [785 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.32.3-1 [1896 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.5-1 [134 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-9 [122 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.3 [204 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-9 [1031 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.2-1 [1014 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.11-2 [51.5 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-9 [130 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-9 [1828 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-3 [27.5 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armhf 5.9-10 [83.9 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armhf 5.9-10 [194 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.7.dfsg-13 [209 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 40 not upgraded.
+Need to get 10.0 MB of archives.
+After this operation, 26.2 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.2-1 [33.7 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-9 [1031 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.3 [204 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.3-3 [870 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-10 [26.8 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.11-2 [199 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.31-1 [246 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-7 [786 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.33.12+really2.32.4-3 [1708 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.6-2 [120 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-10 [123 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.11-2 [51.5 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-10 [129 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev armhf 0.18.1.1-10 [27.1 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev armhf 0.18.1.1-10 [143 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-10 [1706 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-3 [27.5 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armhf 5.9-10 [83.9 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armhf 5.9-10 [194 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.7.dfsg-13 [209 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.1 MB in 4s (2033 kB/s)
+Fetched 10.0 MB in 4s (2408 kB/s)
Selecting previously unselected package libpipeline1:armhf.
-(Reading database ... 10766 files and directories currently installed.)
-Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ...
+(Reading database ... 12862 files and directories currently installed.)
+Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.2-1_armhf.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_armhf.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armhf.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_armhf.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
-Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_armhf.deb) ...
+Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_5.11-2_armhf.deb) ...
Selecting previously unselected package libpcre3:armhf.
-Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ...
+Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.31-1_armhf.deb) ...
Selecting previously unselected package libxml2:armhf.
-Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-5_armhf.deb) ...
+Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-7_armhf.deb) ...
Selecting previously unselected package libffi5:armhf.
Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b1_armhf.deb) ...
Selecting previously unselected package libglib2.0-0:armhf.
-Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.3-1_armhf.deb) ...
+Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.33.12+really2.32.4-3_armhf.deb) ...
Selecting previously unselected package libcroco3:armhf.
-Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ...
+Unpacking libcroco3:armhf (from .../libcroco3_0.6.6-2_armhf.deb) ...
Selecting previously unselected package libunistring0:armhf.
Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5+b1_armhf.deb) ...
Selecting previously unselected package libgettextpo0:armhf.
-Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-9_armhf.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armhf.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_armhf.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_armhf.deb) ...
+Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.11-2_armhf.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_armhf.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_armhf.deb) ...
+Selecting previously unselected package libasprintf-dev:armhf.
+Unpacking libasprintf-dev:armhf (from .../libasprintf-dev_0.18.1.1-10_armhf.deb) ...
+Selecting previously unselected package libgettextpo-dev:armhf.
+Unpacking libgettextpo-dev:armhf (from .../libgettextpo-dev_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_armhf.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_armhf.deb) ...
Selecting previously unselected package libtinfo-dev:armhf.
@@ -230,31 +241,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:armhf.
Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_armhf.deb) ...
-Setting up libpipeline1:armhf (1.2.1-1) ...
-Setting up libasprintf0c2:armhf (0.18.1.1-9) ...
-Setting up libmagic1:armhf (5.11-2) ...
-Setting up libpcre3:armhf (1:8.30-5) ...
-Setting up libxml2:armhf (2.8.0+dfsg1-5) ...
-Setting up libffi5:armhf (3.0.10-3+b1) ...
-Setting up libglib2.0-0:armhf (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:armhf (0.6.5-1) ...
-Setting up libunistring0:armhf (0.9.3-5+b1) ...
-Setting up libgettextpo0:armhf (0.18.1.1-9) ...
+Setting up libpipeline1:armhf (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
Setting up bsdmainutils (9.0.3) ...
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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
+Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:armhf (0.18.1.1-10) ...
+Setting up libmagic1:armhf (5.11-2) ...
+Setting up libpcre3:armhf (1:8.31-1) ...
+Setting up libxml2:armhf (2.8.0+dfsg1-7) ...
+Setting up libffi5:armhf (3.0.10-3+b1) ...
+Setting up libglib2.0-0:armhf (2.33.12+really2.32.4-3) ...
+No schema files found: doing nothing.
+Setting up libcroco3:armhf (0.6.6-2) ...
+Setting up libunistring0:armhf (0.9.3-5+b1) ...
+Setting up libgettextpo0:armhf (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15+b1) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:armhf (0.18.1.1-10) ...
+Setting up libgettextpo-dev:armhf (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:armhf (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -264,11 +278,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 3.2.0-2-mx5 armhf (armv7l)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Kernel: Linux 3.2.0-4-mx5 armhf (armv7l)
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.01.08 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libalgorithm-diff-perl_1.19.02-3 libalgorithm-merge-perl_0.08-2 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-4 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8 make_3.81-8.2 man-db_2.6.3-3 manpages_3.42-1 manpages-dev_3.42-1 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -279,15 +293,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -297,7 +312,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
@@ -305,26 +320,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -342,11 +360,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -356,15 +375,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -399,8 +421,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -415,10 +437,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -439,24 +461,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -478,14 +500,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -511,7 +533,7 @@ 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_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -520,6 +542,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -546,8 +569,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -570,12 +595,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-armhf-XcQV5o/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -588,68 +613,79 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_armhf.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_armhf.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_armhf.deb'.
- dpkg-genchanges -B -marmhf Build Daemon (henze) <buildd_armhf-henze at buildd.debian.org> >../samtools_0.1.18-3_armhf.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org> >../samtools_0.1.18-4_armhf.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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1547
+Build finished at 20121223-0502
-samtools_0.1.18-3_armhf.changes:
+samtools_0.1.18-4_armhf.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: armhf
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
-Maintainer: armhf Build Daemon (henze) <buildd_armhf-henze at buildd.debian.org>
+Maintainer: armhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- 98301b0be383c90d436c8fe8c35ca44f5b598918 508386 samtools_0.1.18-3_armhf.deb
- 1ccd5f495a33014e0be19b668338c46bd458bac4 144934 libbam-dev_0.1.18-3_armhf.deb
+ ea1fbb66f93218a136ebd1be2a9ef4f27d3b1b18 509328 samtools_0.1.18-4_armhf.deb
+ df42fb0fd5de5c3da45b3e272d28f44242cbe470 145006 libbam-dev_0.1.18-4_armhf.deb
Checksums-Sha256:
- b6163dfe429a6fe61c3be508f7314e8cf69da69c047fc3c4ac1ebfa2fbc4dc8a 508386 samtools_0.1.18-3_armhf.deb
- cbdcfe98ebd9891164efbfffaa156f18e9554f8939c0b7680bb568bb95fd679e 144934 libbam-dev_0.1.18-3_armhf.deb
+ e72a183123fdb6ce8bb30cac6d100eec433dc1422f4a486cdccf6573fb3172e2 509328 samtools_0.1.18-4_armhf.deb
+ 1d0bc38fcc3935555aa5290629b5a454c8988c401e6c224da256dcf7bf8a11bb 145006 libbam-dev_0.1.18-4_armhf.deb
Files:
- 047b370d947bd6141610ebebe7582b48 508386 science optional samtools_0.1.18-3_armhf.deb
- b940a08a4f0aaaca8428bc51cacd420b 144934 libdevel optional libbam-dev_0.1.18-3_armhf.deb
+ e930890b5de1b5d0ea580195913a3e61 509328 science optional samtools_0.1.18-4_armhf.deb
+ 2e6f18b585bc19c181b45bf0df1d3e7c 145006 libdevel optional libbam-dev_0.1.18-4_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_armhf.deb
+samtools_0.1.18-4_armhf.deb
───────────────────────────
new debian package, version 2.0.
- size 508386 bytes: control archive=1778 bytes.
+ size 509328 bytes: control archive=1819 bytes.
+ 32 bytes, 1 lines conffiles
817 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 828
+ Installed-Size: 837
Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -662,71 +698,74 @@ samtools_0.1.18-3_armhf.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/lib/samtools/
--rwxr-xr-x root/root 12900 2012-07-27 15:46 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6484 2012-07-27 15:46 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 5892 2012-07-27 15:46 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8480 2012-07-27 15:46 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 5892 2012-07-27 15:46 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/bin/
--rwxr-xr-x root/root 17620 2012-07-27 15:46 ./usr/bin/razip
--rwxr-xr-x root/root 248724 2012-07-27 15:46 ./usr/bin/samtools
--rwxr-xr-x root/root 88388 2012-07-27 15:46 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/bin/
+-rwxr-xr-x root/root 17620 2012-12-23 05:02 ./usr/bin/razip
+-rwxr-xr-x root/root 88388 2012-12-23 05:02 ./usr/bin/bcftools
+-rwxr-xr-x root/root 248876 2012-12-23 05:02 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:01 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-12-23 05:01 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2012-07-27 15:46 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 1966 2012-07-27 15:46 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 126583 2012-12-23 05:01 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1966 2012-12-23 05:02 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:46 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:46 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 05:01 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 05:01 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 05:01 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/samtools/
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 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 5778 2012-07-27 15:46 ./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 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 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-lrwxrwxrwx root/root 0 2012-07-27 15:46 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_armhf.deb
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 5778 2012-12-23 05:02 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/lib/samtools/
+-rwxr-xr-x root/root 5892 2012-12-23 05:02 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 6484 2012-12-23 05:02 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 12900 2012-12-23 05:02 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 5892 2012-12-23 05:02 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8480 2012-12-23 05:02 ./usr/lib/samtools/md5fa
+lrwxrwxrwx root/root 0 2012-12-23 05:02 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_armhf.deb
─────────────────────────────
new debian package, version 2.0.
- size 144934 bytes: control archive=925 bytes.
- 674 bytes, 15 lines control
+ size 145006 bytes: control archive=937 bytes.
+ 712 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 335
+ Installed-Size: 336
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -736,26 +775,28 @@ libbam-dev_0.1.18-3_armhf.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/include/samtools/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/include/samtools/
+-rw-r--r-- root/root 24732 2012-12-23 04:57 ./usr/include/samtools/bam.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 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/lib/
--rw-r--r-- root/root 200906 2012-07-27 15:46 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:46 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./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 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/lib/
+-rw-r--r-- root/root 201058 2012-12-23 05:02 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -769,7 +810,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-b65709ff-8ea2-4ff6-a981-4312e96ea285/build/buildd-samtools_0.1.18-3-armhf-XcQV5o
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-6d05ad6f-19a9-4623-b5e3-70d3193a6028/build/buildd-samtools_0.1.18-4-armhf-OvDkY3
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -777,19 +818,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armhf
-Build-Space: 9480
-Build-Time: 327
+Build-Space: 9404
+Build-Time: 338
Distribution: sid
-Install-Time: 69
-Job: samtools_0.1.18-3
+Install-Time: 85
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 515
-Source-Version: 0.1.18-3
-Space: 9480
+Package-Time: 539
+Source-Version: 0.1.18-4
+Space: 9404
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1547
-Build needed 00:08:35, 9480k disc space
-Signature with key '3CE79B5E' requested:
+Finished at 20121223-0502
+Build needed 00:08:59, 9404k disc space
+Signature with key '0B213A80' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index 2944255..6c6cc89 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,64 +1,85 @@
-From buildd at ironforge.sceen.net Fri Jul 27 16:25:30 2012
+From buildd at ironforge.sceen.net Sun Dec 23 05:24:57 2012
Return-path: <buildd at ironforge.sceen.net>
Received: from ironforge.sceen.net ([46.105.42.111])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at ironforge.sceen.net>)
- id 1SunM0-0003gm-Pm
- for logs at buildd.debian.org; Fri, 27 Jul 2012 16:25:29 +0000
+ id 1Tme3U-0004ox-Mu
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:24:57 +0000
Received: from buildd by ironforge.sceen.net with local (Exim 4.77)
(envelope-from <buildd at ironforge.sceen.net>)
- id 1SunLy-0000lN-2u; Fri, 27 Jul 2012 18:25:26 +0200
+ id 1TmdfK-0006lO-5U; Sun, 23 Dec 2012 05:59:58 +0100
Content-Transfer-Encoding: binary
MIME-Version: 1.0
X-Mailer: MIME::Lite 3.027 (F2.82; B3.13; Q3.13)
-Date: Fri, 27 Jul 2012 18:25:26 +0200
+Date: Sun, 23 Dec 2012 05:59:58 +0100
From: Build Daemon <buildd at ironforge.sceen.net>
-To: samuel.thibault at ens-lyon.org,mbanck at gmx.net,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on hurd-i386 (dist=sid)
-Message-Id: <E1SunLy-0000lN-2u at ironforge.sceen.net>
+To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian.org,
+ debian-hurd-build-logs at lists.alioth.debian.org
+Subject: Log for successful build of samtools_0.1.18-4 on hurd-i386 (dist=sid)
+Message-Id: <E1TmdfK-0006lO-5U at ironforge.sceen.net>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ironforge.sceen.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (hurd-i386) 27 Jul 2012 18:23 ║
+║ samtools 0.1.18-4 (hurd-i386) 23 Dec 2012 05:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: hurd-i386
Ign file: ./ InRelease
Ign file: ./ Release.gpg
Ign file: ./ Release
Ign file: ./ Translation-en
-Get:1 http://ftp.fr.debian.org sid InRelease [249 kB]
-Hit http://incoming.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
-Hit http://incoming.debian.org sid/main Translation-en/DiffIndex
+Get:1 http://ftp.fr.debian.org sid InRelease [227 kB]
Get:2 http://ftp.fr.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org sid InRelease [227 kB]
+Ign http://incoming.debian.org InRelease
Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
Get:4 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
Hit http://ftp.fr.debian.org sid/contrib Translation-en/DiffIndex
-Get:5 http://ftp.fr.debian.org sid/main Translation-en [4032 kB]
-Get:6 http://ftp.fr.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
-Get:7 http://incoming.debian.org Release [1601 B]
-Get:8 http://ftp.fr.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
-Get:9 http://ftp.fr.debian.org sid/main hurd-i386 2012-07-27-1414.10.pdiff [2019 B]
-Get:10 http://incoming.debian.org Sources [14.9 kB]
-Get:11 http://incoming.debian.org Packages [121 kB]
+Get:5 http://ftp.fr.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:6 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:9 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:10 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
+Get:11 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
+Get:12 http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
+Hit http://incoming.debian.org sid/contrib hurd-i386 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
+Get:13 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:16 http://incoming.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
+Get:17 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
+Get:18 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
+Get:19 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:20 http://incoming.debian.org Sources [14.0 kB]
+Get:21 http://incoming.debian.org Packages [118 kB]
+Get:22 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
+Get:23 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
Ign http://incoming.debian.org Translation-en
-Get:12 http://ftp.fr.debian.org sid/main hurd-i386 2012-07-27-1414.10.pdiff [2019 B]
-Fetched 4439 kB in 28s (154 kB/s)
+Get:24 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:25 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Get:26 http://incoming.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
+Get:27 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:28 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
+Get:29 http://incoming.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
+Get:30 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:31 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Get:32 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
+Get:33 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Get:34 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:35 http://incoming.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
+Get:36 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Fetched 657 kB in 59s (10.9 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -79,11 +100,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (215 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 3s (106 kB/s)
Download complete and in download only mode
Check arch
@@ -108,7 +129,7 @@ The following packages were automatically installed and are no longer required:
libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -118,46 +139,47 @@ The following packages were automatically installed and are no longer required:
libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+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, 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
+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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.11)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-3)
+bash: already installed (4.2-5)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3+b1)
-debianutils: already installed (4.3.2)
+debianutils: already installed (4.3.3)
diffutils: already installed (1:3.2-6+b1)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4+b1)
grep: already installed (2.12-2)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11+b1)
-hurd: already installed (20120605-2)
+hurd: already installed (20120710-3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-15)
sed: already installed (4.2.1-10)
sysvinit-utils: already installed (2.88dsf-22)
sysvinit: already installed (2.88dsf-22)
tar: already installed (1.26-4+b1)
bsdutils: already installed (1:2.20.1-5.1)
util-linux: already installed (2.20.1-5.1)
-libc0.3-dev: already installed (2.13-34)
-gcc: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
+libc0.3-dev: already installed (2.13-37)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2+b1)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
-hurd-dev: already installed (20120605-2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+hurd-dev: already installed (20120710-3)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: already installed (1:2.0-1)
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -172,64 +194,68 @@ The following packages were automatically installed and are no longer required:
libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libasprintf0c2
- libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0 libmagic1
- libtinfo-dev libunistring0 libxml2 po-debconf
+ diffstat file gettext gettext-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo-dev libgettextpo0
+ libglib2.0-0 libmagic1 libtinfo-dev libunistring0 libxml2 po-debconf
Suggested packages:
devscripts dh-make gettext-doc ncurses-doc libmail-box-perl procmail
graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ libmail-sendmail-perl
The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libtinfo-dev libunistring0 libxml2 po-debconf
- quilt zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 25 not upgraded.
-Need to get 0 B/8216 kB of archives.
-After this operation, 22.5 MB of additional disk space will be used.
+ libasprintf-dev libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo-dev
+ libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev libtinfo-dev
+ libunistring0 libxml2 po-debconf quilt zlib1g-dev
+0 upgraded, 24 newly installed, 0 to remove and 36 not upgraded.
+Need to get 0 B/8011 kB of archives.
+After this operation, 22.7 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
libasprintf0c2 libmagic1 libxml2 libffi5 libglib2.0-0 libcroco3 libexpat1
- libunistring0 libgettextpo0 file gettext-base cdbs html2text gettext
- intltool-debian po-debconf debhelper diffstat libtinfo-dev libncurses5-dev
- quilt zlib1g-dev
+ libunistring0 libgettextpo0 file gettext-base cdbs html2text libasprintf-dev
+ libgettextpo-dev gettext intltool-debian po-debconf debhelper diffstat
+ libtinfo-dev libncurses5-dev quilt zlib1g-dev
Authentication warning overridden.
Selecting previously unselected package libasprintf0c2:hurd-i386.
-(Reading database ... 14550 files and directories currently installed.)
-Unpacking libasprintf0c2:hurd-i386 (from .../libasprintf0c2_0.18.1.1-9_hurd-i386.deb) ...
+(Reading database ... 15363 files and directories currently installed.)
+Unpacking libasprintf0c2:hurd-i386 (from .../libasprintf0c2_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package libmagic1:hurd-i386.
Unpacking libmagic1:hurd-i386 (from .../libmagic1_5.11-2_hurd-i386.deb) ...
Selecting previously unselected package libxml2:hurd-i386.
-Unpacking libxml2:hurd-i386 (from .../libxml2_2.8.0+dfsg1-5_hurd-i386.deb) ...
+Unpacking libxml2:hurd-i386 (from .../libxml2_2.8.0+dfsg1-7_hurd-i386.deb) ...
Selecting previously unselected package libffi5:hurd-i386.
Unpacking libffi5:hurd-i386 (from .../libffi5_3.0.10-3+b1_hurd-i386.deb) ...
Selecting previously unselected package libglib2.0-0:hurd-i386.
-Unpacking libglib2.0-0:hurd-i386 (from .../libglib2.0-0_2.32.3-1+b2_hurd-i386.deb) ...
+Unpacking libglib2.0-0:hurd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-3_hurd-i386.deb) ...
Selecting previously unselected package libcroco3:hurd-i386.
-Unpacking libcroco3:hurd-i386 (from .../libcroco3_0.6.5-1+b1_hurd-i386.deb) ...
+Unpacking libcroco3:hurd-i386 (from .../libcroco3_0.6.6-2_hurd-i386.deb) ...
Selecting previously unselected package libexpat1:hurd-i386.
Unpacking libexpat1:hurd-i386 (from .../libexpat1_2.1.0-1+b1_hurd-i386.deb) ...
Selecting previously unselected package libunistring0:hurd-i386.
Unpacking libunistring0:hurd-i386 (from .../libunistring0_0.9.3-5+b1_hurd-i386.deb) ...
Selecting previously unselected package libgettextpo0:hurd-i386.
-Unpacking libgettextpo0:hurd-i386 (from .../libgettextpo0_0.18.1.1-9_hurd-i386.deb) ...
+Unpacking libgettextpo0:hurd-i386 (from .../libgettextpo0_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.11-2_hurd-i386.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_hurd-i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b2_hurd-i386.deb) ...
+Selecting previously unselected package libasprintf-dev:hurd-i386.
+Unpacking libasprintf-dev:hurd-i386 (from .../libasprintf-dev_0.18.1.1-10_hurd-i386.deb) ...
+Selecting previously unselected package libgettextpo-dev:hurd-i386.
+Unpacking libgettextpo-dev:hurd-i386 (from .../libgettextpo-dev_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_hurd-i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_hurd-i386.deb) ...
Selecting previously unselected package libtinfo-dev:hurd-i386.
@@ -241,24 +267,26 @@ Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:hurd-i386.
Unpacking zlib1g-dev:hurd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_hurd-i386.deb) ...
Processing triggers for man-db ...
-Setting up libasprintf0c2:hurd-i386 (0.18.1.1-9) ...
+Setting up libasprintf0c2:hurd-i386 (0.18.1.1-10) ...
Setting up libmagic1:hurd-i386 (5.11-2) ...
-Setting up libxml2:hurd-i386 (2.8.0+dfsg1-5) ...
+Setting up libxml2:hurd-i386 (2.8.0+dfsg1-7) ...
Setting up libffi5:hurd-i386 (3.0.10-3+b1) ...
-Setting up libglib2.0-0:hurd-i386 (2.32.3-1+b2) ...
+Setting up libglib2.0-0:hurd-i386 (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:hurd-i386 (0.6.5-1+b1) ...
+Setting up libcroco3:hurd-i386 (0.6.6-2) ...
Setting up libexpat1:hurd-i386 (2.1.0-1+b1) ...
Setting up libunistring0:hurd-i386 (0.9.3-5+b1) ...
-Setting up libgettextpo0:hurd-i386 (0.18.1.1-9) ...
+Setting up libgettextpo0:hurd-i386 (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15+b2) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:hurd-i386 (0.18.1.1-10) ...
+Setting up libgettextpo-dev:hurd-i386 (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:hurd-i386 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -272,11 +300,11 @@ The following packages were automatically installed and are no longer required:
adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.7_4.7.1-5 gcc-4.7_4.7.1-5 gnumach-dev_2:1.3.99.dfsg.git20120610-1 hurd-dev_20120605-2 libc0.3-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5
-Package versions: adduser_3.113+nmu3 apt_0.9.7.1 apt-utils_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 bash-completion_1:2.0-1 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpio_2.11-8 cpp_4:4.7.1-1 cpp-4.7_4.7.1-5 dash_0.5.7-3+b1 debconf_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.01.08 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6+b1 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4+b1 g++_4:4.7.1-1 g++-4.7_4.7.1-5 gawk_1:4.0.1+dfsg-2 gcc_4:4.7.1-1 gcc-4.4-base_4.4.7-1+b1 gcc-4.5-base_4.5.4-1 gcc-4.6-base_4.6.3-8 gcc-4.7_4.7.1-5 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnumach-dev_2:1.3.99.dfsg.git20120610-1 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11+b1 html2text_1.3.2a-15+b2 hurd_20120605-2 hurd-dev_20120605-2 initscripts_2.88dsf-22 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-inst1.5_0.9.7.1 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libboost-iostreams1.46.1_1.46.1-8+b1 libboost-iostreams1.48.0_1.48.0-3+b1 libboost-iostreams1.49.0_1.49.0-3.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc0.3_2.13-34 libc0.3-dev_2.13-34 libc0.3-i686_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1+b1 libcwidget3_0.5.16-3.4 libdb5.1_5.1.29-5+b1 libdpkg-perl_1.16.7 libexpat1_2.1.0-1+b1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-5 libgcrypt11_1.5.0-3+b1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1+b2 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.20-1 libgomp1_4.7.1-5 libgpg-error0_1.10-3+b1 libldap-2.4-2_2.4.28-1.3+b2 liblocale-gettext-perl_1.05-7+b2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libncursesw5_5.9-10 libp11-kit0_0.12-3+b1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libparted0debian1_2.3-10 libpciaccess0_0.13.1-2+b1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1+b1 libpng12-0_1.2.49-2 libpopt0_1.16-7 libprocps0_1:3.3.3-2 libquadmath0_4.7.1-5 libreadline6_6.2-8+b1 libsasl2-2_2.1.25.dfsg1-4+b2 libsigc++-2.0-0c2a_2.2.10-0.2 libsigsegv2_2.9-4+b1 libslang2_2.2.4-15 libss2_1.42.4-3 libssl1.0.0_1.0.1c-3 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1.2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libuuid1_2.20.1-5.1 libxapian22_1.2.8-1 libxml2_2.8.0+dfsg1-5 lsb-base_4.1+Debian7 make_3.81-8.2+b1 man-db_2.6.2-1 mawk_1.3.3-17+b1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 netbase_5.0 netcat-traditional_1.10-40 netdde_0.0.20120520-2 passwd_1:4.1.5.1-1 patch_2.6.1-3+b1 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 procps_1:3.3.3-2 psmisc_22.19-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4+b1 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 gnumach-dev_2:1.3.99.dfsg.git20120923-1 hurd-dev_20120710-3 libc0.3-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
+Package versions: adduser_3.113+nmu3 apt_0.9.7.4 apt-utils_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpio_2.11-8 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3+b1 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.01.08 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6+b1 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4+b1 g++_4:4.7.1-1 g++-4.7_4.7.2-4 gawk_1:4.0.1+dfsg-2 gcc_4:4.7.2-1 gcc-4.5-base_4.5.4-1 gcc-4.6-base_4.6.3-14 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnumach-dev_2:1.3.99.dfsg.git20120923-1 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11+b1 html2text_1.3.2a-15+b2 hurd_20120710-3 hurd-dev_20120710-3 initscripts_2.88dsf-22 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-inst1.5_0.9.7.5 libapt-pkg4.12_0.9.7.5 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libboost-iostreams1.46.1_1.46.1-8+b1 libboost-iostreams1.48.0_1.48.0-3+b1 libboost-iostreams1.49.0_1.49.0-3.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc0.3_2.13-37 libc0.3-dev_2.13-37 libc0.3-i686_2.13-37 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libcwidget3_0.5.16-3.4 libdb5.1_5.1.29-5+b1 libdpkg-perl_1.16.9 libexpat1_2.1.0-1+b1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgcrypt11_1.5.0-3+b1 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.20-2 libgomp1_4.7.2-4 libgpg-error0_1.10-3.1 libldap-2.4-2_2.4.28-1.3+b2 liblocale-gettext-perl_1.05-7+b2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libncursesw5_5.9-10 libp11-kit0_0.12-3+b1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libparted0debian1_2.3-11 libpciaccess0_0.13.1-2+b2 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libpng12-0_1.2.49-3 libpopt0_1.16-7 libprocps0_1:3.3.3-2 libpthread-stubs0_0.3-3 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsasl2-2_2.1.25.dfsg1-6 libsigc++-2.0-0c2a_2.2.10-0.2 libsigsegv2_2.9-4+b1 libslang2_2.2.4-15 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1.2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libuuid1_2.20.1-5.3 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxapian22_1.2.8-1 libxau6_1:1.0.7-1+b1 libxcb1_1.8.1-2 libxdmcp6_1:1.1.1-1+b1 libxml2_2.8.0+dfsg1-7 lsb-base_4.1+Debian7 make_3.81-8.2+b1 man-db_2.6.2-1 mawk_1.3.3-17+b1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 netbase_5.0 netcat-traditional_1.10-40 netdde_0.0.20120710-1 passwd_1:4.1.5.1-1 patch_2.6.1-3+b1 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 procps_1:3.3.3-2 psmisc_22.19-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sgml-base_1.26+nmu4 sudo_1.8.5p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4+b1 tzdata_2012e-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xkb-data_2.5.1-2 xml-core_0.13+nmu1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -287,15 +315,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -305,7 +334,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
@@ -313,26 +342,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -348,13 +380,14 @@ 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-arch
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
test -x debian/rules
mkdir -p "."
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -364,18 +397,21 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
@@ -407,8 +443,8 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -423,10 +459,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -447,38 +483,31 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
seqtk.c: In function 'stk_subseq':
@@ -489,30 +518,37 @@ seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but ar
seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/examples'
-../samtools faidx ex1.fa
[sam_header_read2] 2 sequences loaded.
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/examples'
+../samtools faidx ex1.fa
+../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[bam_rmdup_core] processing reference seq1...
+../samtools index ex1.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
[bam_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 import ex1.fa.fai ex1.sam.gz ex1.bam
-../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"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
@@ -525,7 +561,7 @@ 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_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -534,6 +570,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -560,8 +597,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -584,12 +623,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -602,27 +641,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_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=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../samtools_0.1.18-3_hurd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1825
+Build finished at 20121223-0559
-samtools_0.1.18-3_hurd-i386.changes:
+samtools_0.1.18-4_hurd-i386.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org>
@@ -630,40 +669,51 @@ Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- f71b952addac0c145b43b14b692a17402669ef2e 534442 samtools_0.1.18-3_hurd-i386.deb
- c2a33de935822b4ffd9d70160cf7dfa7b296e132 160908 libbam-dev_0.1.18-3_hurd-i386.deb
+ 74250d587f2dd74b74c42b7719bd1e8dfdc9362f 535120 samtools_0.1.18-4_hurd-i386.deb
+ a14e60c2064d1cc9e52d9ba45d2910b0e315f9b9 161108 libbam-dev_0.1.18-4_hurd-i386.deb
Checksums-Sha256:
- 65bfafcd6251e4985631a5a6e3cd75300333440be055329531dd9073c1521e96 534442 samtools_0.1.18-3_hurd-i386.deb
- 118c152b18028edce4a8019446eacb806a34d0bafde868a012b523bf71238b8d 160908 libbam-dev_0.1.18-3_hurd-i386.deb
+ 4a0742873f65bae405f701ac4552bf07cc778ce6069241930e198c18ca3f5d36 535120 samtools_0.1.18-4_hurd-i386.deb
+ e90cab8dc79b9af30fed0f84be9fdc603820a54981f4aa23c97b36a4d2793786 161108 libbam-dev_0.1.18-4_hurd-i386.deb
Files:
- b29980c288d7398951be60d50cd83582 534442 science optional samtools_0.1.18-3_hurd-i386.deb
- 342f588266c0e963b7c1c465e3a190d1 160908 libdevel optional libbam-dev_0.1.18-3_hurd-i386.deb
+ 5d49505b36a598f3fc19c23853bcc2ab 535120 science optional samtools_0.1.18-4_hurd-i386.deb
+ c81412b0eae985be76b3b6f07548344a 161108 libdevel optional libbam-dev_0.1.18-4_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_hurd-i386.deb
+samtools_0.1.18-4_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 534442 bytes: control archive= 1761 bytes.
+ size 535120 bytes: control archive= 1815 bytes.
+ 32 bytes, 1 lines conffiles
798 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1041
+ Installed-Size: 1050
Depends: libc0.3 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -676,31 +726,31 @@ samtools_0.1.18-3_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 2012-07-27 18:24 ./
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-09-06 09:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 09:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5502 2011-09-06 09:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2012-12-23 04:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-12-23 04:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5522 2012-12-23 04:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126583 2012-12-23 05:58 ./usr/share/doc/samtools/examples/ex1.bam
-rw-r--r-- root/root 3225 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 05:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 05:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2012-07-27 18:24 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 20:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-07-27 18:24 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-12-23 05:59 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 18:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 17:15 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 18:24 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 18:24 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 18:25 ./usr/share/samtools/
+-rw-r--r-- root/root 2067 2012-12-23 04:33 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 05:59 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 05:59 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 04:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 05:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 05:16 ./usr/share/samtools/bowtie2sam.pl
@@ -713,31 +763,34 @@ drwxr-xr-x root/root 0 2012-07-27 18:25 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 05:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 05:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 05:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-07-27 18:25 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/bin/
--rwxr-xr-x root/root 137508 2012-07-27 18:24 ./usr/bin/bcftools
--rwxr-xr-x root/root 25104 2012-07-27 18:24 ./usr/bin/razip
--rwxr-xr-x root/root 400116 2012-07-27 18:24 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/lib/samtools/
--rwxr-xr-x root/root 16696 2012-07-27 18:24 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7128 2012-07-27 18:24 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7128 2012-07-27 18:24 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10876 2012-07-27 18:24 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7816 2012-07-27 18:24 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_hurd-i386.deb
+-rwxr-xr-x root/root 5778 2012-12-23 05:59 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/bin/
+-rwxr-xr-x root/root 137508 2012-12-23 05:59 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25104 2012-12-23 05:59 ./usr/bin/razip
+-rwxr-xr-x root/root 400148 2012-12-23 05:59 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/lib/samtools/
+-rwxr-xr-x root/root 16696 2012-12-23 05:59 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7128 2012-12-23 05:59 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7128 2012-12-23 05:59 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10876 2012-12-23 05:59 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7816 2012-12-23 05:59 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 04:33 ./etc/bash_completion.d/samtools
+lrwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 160908 bytes: control archive= 924 bytes.
- 678 bytes, 15 lines control
+ size 161108 bytes: control archive= 943 bytes.
+ 716 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 432
@@ -750,22 +803,24 @@ libbam-dev_0.1.18-3_hurd-i386.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 18:25 ./usr/share/doc/libbam-dev/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 09:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5522 2012-12-23 04:33 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 33578 2011-03-01 20:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 10122 2011-09-02 18:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 17:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 18:25 ./usr/lib/
--rw-r--r-- root/root 300240 2012-07-27 18:25 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 18:24 ./usr/include/samtools/
--rw-r--r-- root/root 24720 2011-09-02 18:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 2067 2012-12-23 04:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/lib/
+-rw-r--r-- root/root 300292 2012-12-23 05:59 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/include/samtools/
+-rw-r--r-- root/root 24732 2012-12-23 05:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 4617 2011-04-11 00:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 17815 2011-03-01 20:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 05:16 ./usr/include/samtools/faidx.h
@@ -783,7 +838,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.18-3-hurd-i386-v19YQk
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_
Reading package lists...
Building dependency tree...
Reading state information...
@@ -791,23 +846,23 @@ The following packages were automatically installed and are no longer required:
adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
- adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
- libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
- man-db
+ adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
+ libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
The following packages will be REMOVED:
cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libasprintf0c2* libcroco3* libexpat1* libffi5*
- libgettextpo0* libglib2.0-0* libmagic1* libncurses5-dev* libtinfo-dev*
- libunistring0* libxml2* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 22 to remove and 25 not upgraded.
-After this operation, 22.5 MB disk space will be freed.
-(Reading database ... 15646 files and directories currently installed.)
+ intltool-debian* libasprintf-dev* libasprintf0c2* libcroco3* libexpat1*
+ libffi5* libgettextpo-dev* libgettextpo0* libglib2.0-0* libmagic1*
+ libncurses5-dev* libtinfo-dev* libunistring0* libxml2* po-debconf* quilt*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 24 to remove and 36 not upgraded.
+After this operation, 22.7 MB disk space will be freed.
+(Reading database ... 16465 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -820,6 +875,7 @@ Removing gettext ...
Removing gettext-base ...
Removing html2text ...
Purging configuration files for html2text ...
+Removing libasprintf-dev:hurd-i386 ...
Removing libasprintf0c2:hurd-i386 ...
Removing libcroco3:hurd-i386 ...
Purging configuration files for libcroco3:hurd-i386 ...
@@ -829,6 +885,7 @@ Removing libglib2.0-0:hurd-i386 ...
Purging configuration files for libglib2.0-0:hurd-i386 ...
Removing libffi5:hurd-i386 ...
Purging configuration files for libffi5:hurd-i386 ...
+Removing libgettextpo-dev:hurd-i386 ...
Removing libgettextpo0:hurd-i386 ...
Removing libmagic1:hurd-i386 ...
Purging configuration files for libmagic1:hurd-i386 ...
@@ -846,17 +903,17 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 11400
-Build-Time: 85
+Build-Space: 11460
+Build-Time: 114
Distribution: sid
-Install-Time: 15
-Job: samtools_0.1.18-3
+Install-Time: 12
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 137
-Source-Version: 0.1.18-3
-Space: 11400
+Package-Time: 199
+Source-Version: 0.1.18-4
+Space: 11460
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1825
-Build needed 00:02:17, 11400k disc space
+Finished at 20121223-0559
+Build needed 00:03:19, 11460k disc space
diff --git a/ia64.log b/ia64.log
index b24f02b..69721db 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,60 +1,88 @@
-From buildd at alkman.debian.org Fri Jul 27 15:43:03 2012
-Return-path: <buildd at alkman.debian.org>
+From buildd at caballero.debian.org Sun Dec 23 04:58:15 2012
+Return-path: <buildd at caballero.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=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 alkman.debian.org>)
- id 1Sumgw-00057W-Nn
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:03 +0000
-Received: from alkman.debian.org ([192.25.206.63])
+ (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
+ id 1Tmdde-0007aZ-Pi
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 04:58:15 +0000
+Received: from caballero.debian.org ([193.201.200.200])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
+ 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 alkman.debian.org>)
- id 1Sumgu-0005hX-VG
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:01 +0000
-Received: from buildd by alkman.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alkman.debian.org>)
- id 1Sumgs-0004XD-PR; Fri, 27 Jul 2012 15:42:58 +0000
-Date: Fri, 27 Jul 2012 15:42:58 +0000
-Message-Id: <E1Sumgs-0004XD-PR 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_0.1.18-3 on ia64 (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
+ id 1Tmddc-00083W-KO; Sun, 23 Dec 2012 04:58:12 +0000
+Received: from buildd by caballero.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at caballero.debian.org>) id 1Tmddb-0001fs-KX
+ for buildd-porters at caballero.debian.org; Sun, 23 Dec 2012 04:58:11 +0000
+Date: Sun, 23 Dec 2012 04:58:11 +0000
+Message-Id: <E1Tmddb-0001fs-KX at caballero.debian.org>
+From: buildd on caballero <buildd at caballero.debian.org>
+To: buildd-porters at caballero.debian.org
+Subject: Log for successful build of samtools_0.1.18-4 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+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 alkman.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on caballero.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (ia64) 27 Jul 2012 15:37 ║
+║ samtools 0.1.18-4 (ia64) 23 Dec 2012 04:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: ia64
-Get:1 http://spohr.debian.org unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://spohr.debian.org unstable/main Sources [6315 kB]
+Get:1 http://ftp.uk.debian.org sid InRelease [227 kB]
+Get:2 http://ftp.uk.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:3 http://incoming.debian.org sid InRelease [227 kB]
+Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:5 http://spohr.debian.org unstable/contrib Sources [53.9 kB]
-Get:6 http://spohr.debian.org unstable/non-free Sources [98.1 kB]
-Get:7 http://spohr.debian.org unstable/main ia64 Packages [5831 kB]
-Get:8 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:9 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:10 http://incoming.debian.org unstable/main ia64 Packages [5831 kB]
-Get:11 http://spohr.debian.org unstable/contrib ia64 Packages [38.3 kB]
-Get:12 http://incoming.debian.org unstable/contrib ia64 Packages [38.3 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.3 MB in 28s (876 kB/s)
+Get:4 http://ftp.uk.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
+Hit http://ftp.uk.debian.org sid/contrib ia64 Packages/DiffIndex
+Hit http://ftp.uk.debian.org sid/contrib Translation-en/DiffIndex
+Get:5 http://ftp.uk.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:6 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:9 http://ftp.uk.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
+Get:10 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
+Get:11 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
+Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:12 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
+Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
+Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
+Get:13 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:16 http://incoming.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
+Get:17 http://ftp.uk.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
+Get:18 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:19 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
+Get:20 http://incoming.debian.org Sources [14.0 kB]
+Get:21 http://incoming.debian.org Packages [118 kB]
+Ign http://incoming.debian.org Translation-en
+Get:22 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
+Get:23 http://ftp.uk.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
+Get:24 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
+Get:25 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Get:26 http://incoming.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
+Get:27 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:28 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:29 http://incoming.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
+Get:30 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
+Get:31 http://ftp.uk.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
+Get:32 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Get:33 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Get:34 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
+Get:35 http://incoming.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
+Get:36 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
+Fetched 672 kB in 28s (23.3 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -75,11 +103,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (327 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (385 kB/s)
Download complete and in download only mode
Check arch
@@ -99,19 +127,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 119 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.11)
base-passwd: already installed (3.5.26)
@@ -121,14 +149,14 @@ dash: already installed (0.5.7-3)
debianutils: already installed (4.3.2)
diffutils: already installed (1:3.2-6)
dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
grep: already installed (2.12-2)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-16)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
sysvinit-utils: already installed (2.88dsf-28)
@@ -137,113 +165,36 @@ tar: already installed (1.26-4)
bsdutils: already installed (1:2.20.1-5.1)
mount: already installed (2.20.1-5.1)
util-linux: already installed (2.20.1-5.1)
-libc6.1-dev: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+libc6.1-dev: already installed (2.13-36)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120608
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+debhelper: already installed (9.20120909 >= 9 is satisfied)
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
-zlib1g-dev: missing
+zlib1g-dev: already installed (1:1.2.7.dfsg-13)
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: bash-completion cdbs quilt libncurses5-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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ diffstat libtinfo-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
+ devscripts ncurses-doc procmail graphviz default-mta mail-transport-agent
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 23 not upgraded.
-Need to get 12.7 MB of archives.
-After this operation, 38.2 MB of additional disk space will be used.
-Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.1-1 [48.2 kB]
-Get:2 http://spohr.debian.org/debian/ unstable/main libasprintf0c2 ia64 0.18.1.1-9 [27.3 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.11-2 [220 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 1:8.30-5 [294 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.8.0+dfsg1-5 [1185 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main libffi5 ia64 3.0.10-3 [35.5 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.32.3-1 [2434 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.5-1 [175 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-5 [463 kB]
-Get:10 http://spohr.debian.org/debian/ unstable/main libgettextpo0 ia64 0.18.1.1-9 [206 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 9.0.3 [240 kB]
-Get:12 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-9 [1419 kB]
-Get:13 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.2-1 [1160 kB]
-Get:14 http://spohr.debian.org/debian/ unstable/main file ia64 5.11-2 [53.2 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-9 [173 kB]
-Get:16 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-9 [2265 kB]
-Get:19 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://spohr.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.55-3 [37.4 kB]
-Get:23 http://spohr.debian.org/debian/ unstable/main libtinfo-dev ia64 5.9-10 [135 kB]
-Get:24 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.9-10 [298 kB]
-Get:25 http://spohr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.7.dfsg-13 [252 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.7 MB in 13s (951 kB/s)
-Selecting previously unselected package libpipeline1:ia64.
-(Reading database ... 10682 files and directories currently installed.)
-Unpacking libpipeline1:ia64 (from .../libpipeline1_1.2.1-1_ia64.deb) ...
-Selecting previously unselected package libasprintf0c2:ia64.
-Unpacking libasprintf0c2:ia64 (from .../libasprintf0c2_0.18.1.1-9_ia64.deb) ...
-Selecting previously unselected package libmagic1:ia64.
-Unpacking libmagic1:ia64 (from .../libmagic1_5.11-2_ia64.deb) ...
-Selecting previously unselected package libpcre3:ia64.
-Unpacking libpcre3:ia64 (from .../libpcre3_1%3a8.30-5_ia64.deb) ...
-Selecting previously unselected package libxml2:ia64.
-Unpacking libxml2:ia64 (from .../libxml2_2.8.0+dfsg1-5_ia64.deb) ...
-Selecting previously unselected package libffi5:ia64.
-Unpacking libffi5:ia64 (from .../libffi5_3.0.10-3_ia64.deb) ...
-Selecting previously unselected package libglib2.0-0:ia64.
-Unpacking libglib2.0-0:ia64 (from .../libglib2.0-0_2.32.3-1_ia64.deb) ...
-Selecting previously unselected package libcroco3:ia64.
-Unpacking libcroco3:ia64 (from .../libcroco3_0.6.5-1_ia64.deb) ...
-Selecting previously unselected package libunistring0:ia64.
-Unpacking libunistring0:ia64 (from .../libunistring0_0.9.3-5_ia64.deb) ...
-Selecting previously unselected package libgettextpo0:ia64.
-Unpacking libgettextpo0:ia64 (from .../libgettextpo0_0.18.1.1-9_ia64.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_ia64.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_ia64.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_ia64.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_ia64.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_ia64.deb) ...
+ bash-completion cdbs diffstat libncurses5-dev libtinfo-dev quilt
+0 upgraded, 6 newly installed, 0 to remove and 119 not upgraded.
+Need to get 0 B/1121 kB of archives.
+After this operation, 3871 kB of additional disk space will be used.
+Selecting previously unselected package bash-completion.
+(Reading database ... 28142 files and directories currently installed.)
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_ia64.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_ia64.deb) ...
Selecting previously unselected package libtinfo-dev:ia64.
@@ -252,47 +203,22 @@ Selecting previously unselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_ia64.deb) ...
Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev:ia64.
-Unpacking zlib1g-dev:ia64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_ia64.deb) ...
-Setting up libpipeline1:ia64 (1.2.1-1) ...
-Setting up libasprintf0c2:ia64 (0.18.1.1-9) ...
-Setting up libmagic1:ia64 (5.11-2) ...
-Setting up libpcre3:ia64 (1:8.30-5) ...
-Setting up libxml2:ia64 (2.8.0+dfsg1-5) ...
-Setting up libffi5:ia64 (3.0.10-3) ...
-Setting up libglib2.0-0:ia64 (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:ia64 (0.6.5-1) ...
-Setting up libunistring0:ia64 (0.9.3-5) ...
-Setting up libgettextpo0:ia64 (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
-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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
-Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Processing triggers for man-db ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up cdbs (0.4.119) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:ia64 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev:ia64 (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6.1-dev_2.13-34 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
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+Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -303,15 +229,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -321,7 +248,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
@@ -329,26 +256,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/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_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -366,11 +296,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -380,15 +311,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -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]
@@ -417,8 +351,8 @@ 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 -Wformat -Werror=format-security -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 -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_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -433,10 +367,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -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_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
@@ -457,24 +391,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -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_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -488,14 +422,14 @@ gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-ia64-5Oj98m/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -521,7 +455,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -530,6 +464,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -556,8 +491,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -580,86 +517,99 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-ia64-5Oj98m/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
dh_perl -psamtools
dh_shlibdeps -psamtools
+dh_girepository -psamtools
dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
+dh_girepository -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_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=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.18-3_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1542
+Build finished at 20121223-0458
-samtools_0.1.18-3_ia64.changes:
+samtools_0.1.18-4_ia64.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
+Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
+ .
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
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- 9aff0a6300b11d3411923da9ebd22d2ecebea523 194500 libbam-dev_0.1.18-3_ia64.deb
+ 45172beb6c41b5f181c5cc21ad82fc75daec2a40 604308 samtools_0.1.18-4_ia64.deb
+ 7c71de38769e2a2646862621d617234963a49fab 195258 libbam-dev_0.1.18-4_ia64.deb
Checksums-Sha256:
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- 16371abafac995a01d52c3407e9f8c5fde97e40db96d23fbff273474775f6a66 194500 libbam-dev_0.1.18-3_ia64.deb
+ ae1b6fbc654cde12b271df03af334a8cb9768fa099cd469f40103988f92a6816 604308 samtools_0.1.18-4_ia64.deb
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Files:
- 53a16dd9c18be2dedc1e9dedbf810b0d 604856 science optional samtools_0.1.18-3_ia64.deb
- 7f775e9b785114b641b4c9635fdf0cc5 194500 libdevel optional libbam-dev_0.1.18-3_ia64.deb
+ 9c45d25cbf505dc27e239b776da69950 604308 science optional samtools_0.1.18-4_ia64.deb
+ e3027eaac8d82994998ea490b9a7ae1b 195258 libdevel optional libbam-dev_0.1.18-4_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_ia64.deb
+samtools_0.1.18-4_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 604856 bytes: control archive= 1759 bytes.
+ size 604308 bytes: control archive= 1815 bytes.
+ 32 bytes, 1 lines conffiles
793 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1638
+ Installed-Size: 1697
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -672,71 +622,74 @@ samtools_0.1.18-3_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 2012-07-27 15:42 ./
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/lib/samtools/
--rwxr-xr-x root/root 30976 2012-07-27 15:42 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13136 2012-07-27 15:42 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13136 2012-07-27 15:42 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 21952 2012-07-27 15:42 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2012-07-27 15:42 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/bin/
--rwxr-xr-x root/root 303936 2012-07-27 15:42 ./usr/bin/bcftools
--rwxr-xr-x root/root 50640 2012-07-27 15:42 ./usr/bin/razip
--rwxr-xr-x root/root 826608 2012-07-27 15:42 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2012-07-27 15:42 ./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 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 2012-07-27 15:42 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:42 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:42 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/samtools/
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./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 2012-07-27 15:42 ./usr/share/doc/samtools/README.bcftools
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2012-07-27 15:42 ./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 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-lrwxrwxrwx root/root 0 2012-07-27 15:42 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_ia64.deb
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126583 2012-12-23 04:57 ./usr/share/doc/samtools/examples/ex1.bam
+-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 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2012-12-23 04:57 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 04:57 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 04:57 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./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
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2012-12-23 04:57 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/bin/
+-rwxr-xr-x root/root 303936 2012-12-23 04:57 ./usr/bin/bcftools
+-rwxr-xr-x root/root 50640 2012-12-23 04:57 ./usr/bin/razip
+-rwxr-xr-x root/root 826736 2012-12-23 04:57 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30976 2012-12-23 04:57 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13136 2012-12-23 04:57 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13136 2012-12-23 04:57 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 21952 2012-12-23 04:57 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2012-12-23 04:57 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2012-12-23 04:57 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 194500 bytes: control archive= 923 bytes.
- 673 bytes, 15 lines control
+ size 195258 bytes: control archive= 941 bytes.
+ 711 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 672
+ Installed-Size: 707
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -746,26 +699,28 @@ libbam-dev_0.1.18-3_ia64.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./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 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/lib/
--rw-r--r-- root/root 581530 2012-07-27 15:42 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:42 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./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 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./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 5522 2012-12-23 03:33 ./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 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/lib/
+-rw-r--r-- root/root 581690 2012-12-23 04:57 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/include/samtools/
+-rw-r--r-- root/root 24732 2012-12-23 04:55 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -779,27 +734,46 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-d882d7c1-376a-484a-a7b5-ea9c093d4d7f/build/buildd-samtools_0.1.18-3-ia64-5Oj98m
-Not cleaning session: cloned chroot in use
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-1e30fda6-a8b8-4d82-8ebc-fef7a1b61ffb/build/buildd-samtools_0.1.18-4-ia64-N8G1wM
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ bash-completion* cdbs* diffstat* libncurses5-dev* libtinfo-dev* quilt*
+0 upgraded, 0 newly installed, 6 to remove and 119 not upgraded.
+After this operation, 3871 kB disk space will be freed.
+(Reading database ... 28873 files and directories currently installed.)
+Removing bash-completion ...
+Purging configuration files for bash-completion ...
+Removing cdbs ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
+Removing libncurses5-dev ...
+Removing libtinfo-dev:ia64 ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 17976
-Build-Time: 160
+Build-Space: 15720
+Build-Time: 149
Distribution: sid
-Install-Time: 81
-Job: samtools_0.1.18-3
+Install-Time: 18
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 295
-Source-Version: 0.1.18-3
-Space: 17976
+Package-Time: 209
+Source-Version: 0.1.18-4
+Space: 15720
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1542
-Build needed 00:04:55, 17976k disc space
-Signature with key '94AE7BC0' requested:
+Finished at 20121223-0458
+Build needed 00:03:29, 15720k disc space
diff --git a/info b/info
index ff7bd35..714cce6 100644
--- a/info
+++ b/info
@@ -1,14 +1,13 @@
-i386~1343403644~sid~successful
-ia64~1343403784~sid~successful
-powerpc~1343403802~sid~successful
-kfreebsd-amd64~1343403831~sid~successful
-kfreebsd-i386~1343403844~sid~successful
-sparc~1343403938~sid~failed
-mipsel~1343403951~sid~successful
-s390x~1343403961~sid~failed
-s390~1343403978~sid~successful
-armhf~1343404044~sid~successful
-armel~1343404148~sid~failed
-mips~1343405070~sid~successful
-hurd-i386~1343406337~sid~successful
-s390x~1346209716~sid~failed
+amd64~1356238515~sid~successful
+s390x~1356238574~sid~failed
+powerpc~1356238584~sid~successful
+s390~1356238691~sid~successful
+ia64~1356238695~sid~successful
+kfreebsd-i386~1356238784~sid~successful
+sparc~1356238821~sid~failed
+kfreebsd-amd64~1356238866~sid~successful
+armel~1356238970~sid~failed
+armhf~1356238971~sid~successful
+mipsel~1356239092~sid~successful
+mips~1356239928~sid~successful
+hurd-i386~1356240303~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 28554fa..95fa07f 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,4 +1,4 @@
-From buildd at fano.debian.org Fri Jul 27 15:43:51 2012
+From buildd at fano.debian.org Sun Dec 23 05:01:05 2012
Return-path: <buildd at fano.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -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 fano.debian.org>)
- id 1Sumhj-0005L9-6D
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:51 +0000
+ id 1TmdgP-0008AA-N2
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:01:05 +0000
Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1Sumhh-0005iT-OW; Fri, 27 Jul 2012 15:43:50 +0000
+ id 1TmdgO-0008GF-5F; Sun, 23 Dec 2012 05:01:04 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1Sumhf-00064E-FF; Fri, 27 Jul 2012 15:43:47 +0000
-Message-Id: <E1Sumhf-00064E-FF at fano.debian.org>
+ id 1TmdgL-000OD4-OH; Sun, 23 Dec 2012 05:01:01 +0000
+Message-Id: <E1TmdgL-000OD4-OH at fano.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:43:47 +0000
+Date: Sun, 23 Dec 2012 05:01:01 +0000
From: buildd on fano <buildd at fano.debian.org>
To: logs at buildd.debian.org,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on kfreebsd-amd64
+Subject: Log for successful build of samtools_0.1.18-4 on kfreebsd-amd64
(dist=sid)
Key-Id: 4584BE29
Delivered-To: logs at buildd.debian.org
@@ -32,31 +32,31 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (kfreebsd-amd64) 27 Jul 2012 15:39 ║
+║ samtools 0.1.18-4 (kfreebsd-amd64) 23 Dec 2012 04:57 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: kfreebsd-amd64
-Get:1 http://incoming.debian.org unstable InRelease [249 kB]
-Get:2 http://mirror-ubc.debian.org unstable InRelease [249 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [6315 kB]
-Get:4 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
-Get:5 http://mirror-ubc.debian.org unstable/non-free Sources [98.1 kB]
-Get:6 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5657 kB]
+Get:1 http://incoming.debian.org unstable InRelease [227 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [37.4 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main kfreebsd-amd64 Packages [5657 kB]
-Get:12 http://incoming.debian.org unstable/contrib kfreebsd-amd64 Packages [37.4 kB]
+Get:2 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:3 http://mirror-ubc.debian.org unstable InRelease [227 kB]
+Get:4 http://mirror-ubc.debian.org unstable/main Sources [6458 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [53.0 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5770 kB]
+Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [36.4 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main kfreebsd-amd64 Packages [5770 kB]
+Get:12 http://incoming.debian.org unstable/contrib kfreebsd-amd64 Packages [36.4 kB]
Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.0 MB in 16s (1471 kB/s)
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 25.4 MB in 13s (1900 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,11 +77,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (364 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 0s (391 kB/s)
Download complete and in download only mode
Check arch
@@ -101,64 +101,66 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (6.12)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-4)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
-findutils: already installed (4.4.2-4)
-freebsd-utils: already installed (9.0+ds1-7)
-grep: already installed (2.12-2)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+freebsd-utils: already installed (9.0+ds1-8)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-15)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-28)
-sysvinit: already installed (2.88dsf-28)
+sysvinit-utils: already installed (2.88dsf-34)
+sysvinit: already installed (2.88dsf-34)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
+bsdutils: already installed (1:2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libmagic1
- libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ libasprintf-dev libasprintf0c2 libcroco3 libffi5 libgettextpo-dev
+ libgettextpo0 libglib2.0-0 libmagic1 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf
Suggested packages:
devscripts dh-make gettext-doc groff ncurses-doc less www-browser
libmail-box-perl procmail graphviz default-mta mail-transport-agent
@@ -166,78 +168,88 @@ 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 diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0 libxml2
- man-db po-debconf quilt zlib1g-dev
-0 upgraded, 24 newly installed, 0 to remove and 13 not upgraded.
-Need to get 10.4 MB of archives.
-After this operation, 26.4 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.2.1-1 [39.0 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.18.1.1-9 [26.8 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 5.11-2 [202 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.8.0+dfsg1-5 [914 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-amd64 3.0.10-3 [23.9 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.32.3-1 [2071 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.5-1 [150 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5 [434 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-amd64 0.18.1.1-9 [145 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.21-9 [1113 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.6.2-1 [1052 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 5.11-2 [51.8 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.18.1.1-9 [153 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-amd64 1.3.2a-15 [104 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.18.1.1-9 [1965 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-amd64 1.55-3 [29.9 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9-10 [105 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9-10 [220 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.7.dfsg-13 [215 kB]
+ bash-completion cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev
+ libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
+0 upgraded, 27 newly installed, 0 to remove and 17 not upgraded.
+Need to get 10.3 MB of archives.
+After this operation, 27.3 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.2.2-1 [39.8 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.21-9 [1113 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.6.3-3 [893 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.18.1.1-10 [27.2 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 5.11-2 [202 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.8.0+dfsg1-7 [914 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-amd64 3.0.10-3 [23.9 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.33.12+really2.32.4-3 [1831 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.6-2 [133 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5 [434 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-amd64 0.18.1.1-10 [145 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 5.11-2 [51.8 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.18.1.1-10 [153 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-amd64 1.3.2a-15 [104 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev kfreebsd-amd64 0.18.1.1-10 [27.0 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev kfreebsd-amd64 0.18.1.1-10 [184 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.18.1.1-10 [1805 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-amd64 1.55-3 [29.9 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9-10 [105 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9-10 [220 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 0s (16.3 MB/s)
+Fetched 10.3 MB in 2s (3923 kB/s)
Selecting previously unselected package libpipeline1:kfreebsd-amd64.
-(Reading database ... 11559 files and directories currently installed.)
-Unpacking libpipeline1:kfreebsd-amd64 (from .../libpipeline1_1.2.1-1_kfreebsd-amd64.deb) ...
+(Reading database ... 11630 files and directories currently installed.)
+Unpacking libpipeline1:kfreebsd-amd64 (from .../libpipeline1_1.2.2-1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-amd64.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_kfreebsd-amd64.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:kfreebsd-amd64.
-Unpacking libasprintf0c2:kfreebsd-amd64 (from .../libasprintf0c2_0.18.1.1-9_kfreebsd-amd64.deb) ...
+Unpacking libasprintf0c2:kfreebsd-amd64 (from .../libasprintf0c2_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package libmagic1:kfreebsd-amd64.
Unpacking libmagic1:kfreebsd-amd64 (from .../libmagic1_5.11-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libxml2:kfreebsd-amd64.
-Unpacking libxml2:kfreebsd-amd64 (from .../libxml2_2.8.0+dfsg1-5_kfreebsd-amd64.deb) ...
+Unpacking libxml2:kfreebsd-amd64 (from .../libxml2_2.8.0+dfsg1-7_kfreebsd-amd64.deb) ...
Selecting previously unselected package libffi5:kfreebsd-amd64.
Unpacking libffi5:kfreebsd-amd64 (from .../libffi5_3.0.10-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package libglib2.0-0:kfreebsd-amd64.
-Unpacking libglib2.0-0:kfreebsd-amd64 (from .../libglib2.0-0_2.32.3-1_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0:kfreebsd-amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package libcroco3:kfreebsd-amd64.
-Unpacking libcroco3:kfreebsd-amd64 (from .../libcroco3_0.6.5-1_kfreebsd-amd64.deb) ...
+Unpacking libcroco3:kfreebsd-amd64 (from .../libcroco3_0.6.6-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libunistring0:kfreebsd-amd64.
Unpacking libunistring0:kfreebsd-amd64 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package libgettextpo0:kfreebsd-amd64.
-Unpacking libgettextpo0:kfreebsd-amd64 (from .../libgettextpo0_0.18.1.1-9_kfreebsd-amd64.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-amd64.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_kfreebsd-amd64.deb) ...
+Unpacking libgettextpo0:kfreebsd-amd64 (from .../libgettextpo0_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.11-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_kfreebsd-amd64.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libasprintf-dev:kfreebsd-amd64.
+Unpacking libasprintf-dev:kfreebsd-amd64 (from .../libasprintf-dev_0.18.1.1-10_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libgettextpo-dev:kfreebsd-amd64.
+Unpacking libgettextpo-dev:kfreebsd-amd64 (from .../libgettextpo-dev_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_kfreebsd-amd64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
@@ -248,27 +260,30 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:kfreebsd-amd64.
Unpacking zlib1g-dev:kfreebsd-amd64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_kfreebsd-amd64.deb) ...
-Setting up libpipeline1:kfreebsd-amd64 (1.2.1-1) ...
-Setting up libasprintf0c2:kfreebsd-amd64 (0.18.1.1-9) ...
+Setting up libpipeline1:kfreebsd-amd64 (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-3) ...
+Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:kfreebsd-amd64 (0.18.1.1-10) ...
Setting up libmagic1:kfreebsd-amd64 (5.11-2) ...
-Setting up libxml2:kfreebsd-amd64 (2.8.0+dfsg1-5) ...
+Setting up libxml2:kfreebsd-amd64 (2.8.0+dfsg1-7) ...
Setting up libffi5:kfreebsd-amd64 (3.0.10-3) ...
-Setting up libglib2.0-0:kfreebsd-amd64 (2.32.3-1) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:kfreebsd-amd64 (0.6.5-1) ...
+Setting up libcroco3:kfreebsd-amd64 (0.6.6-2) ...
Setting up libunistring0:kfreebsd-amd64 (0.9.3-5) ...
-Setting up libgettextpo0:kfreebsd-amd64 (0.18.1.1-9) ...
-Setting up groff-base (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
+Setting up libgettextpo0:kfreebsd-amd64 (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:kfreebsd-amd64 (0.18.1.1-10) ...
+Setting up libgettextpo-dev:kfreebsd-amd64 (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:kfreebsd-amd64 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -278,11 +293,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.7 g++-4.7_4.7.1-5 gcc-4.7_4.7.1-5 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5
-Package versions: apt_0.9.7.2 base-files_6.11 base-passwd_3.5.26 bash_4.2-4 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.7.1-1 cpp-4.7_4.7.1-5 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 freebsd-utils_9.0+ds1-7 g++_4:4.7.1-1 g++-4.7_4.7.1-5 gcc_4:4.7.1-1 gcc-4.7_4.7.1-5 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-7 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.2 libasprintf0c2_0.18.1.1-9 libblkid1_2.20.1-5.1 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc0.1_2.13-34 libc0.1-dev_2.13-34 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-5 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-5 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libquadmath0_4.7.1-5 libreadline6_6.2-8 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 freebsd-utils_9.0+ds1-8 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-34 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-8 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libblkid1_2.20.1-5.2 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc0.1_2.13-37 libc0.1-dev_2.13-37 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -293,15 +308,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -311,7 +327,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
@@ -319,26 +335,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -356,11 +375,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -370,15 +390,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -407,8 +430,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -423,10 +446,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -447,24 +470,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
@@ -484,14 +507,14 @@ gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -517,7 +540,7 @@ 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_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -526,6 +549,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -552,8 +576,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -576,12 +602,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -594,27 +620,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_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=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.18-3_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1543
+Build finished at 20121223-0500
-samtools_0.1.18-3_kfreebsd-amd64.changes:
+samtools_0.1.18-4_kfreebsd-amd64.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
@@ -622,40 +648,51 @@ Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- d7dcbda7c1b14e7936a007915c21285e451e756a 532312 samtools_0.1.18-3_kfreebsd-amd64.deb
- 14198a76d6077e1c30accb7f547de10886a77a51 156480 libbam-dev_0.1.18-3_kfreebsd-amd64.deb
+ 51fac14f1315cc152443896ec0f2192f1323eeb4 532760 samtools_0.1.18-4_kfreebsd-amd64.deb
+ b4a056c0a13dff3710cd4a20c6d4753a7d1c1123 156700 libbam-dev_0.1.18-4_kfreebsd-amd64.deb
Checksums-Sha256:
- 31a120bd7599bbda862e18d910e80fc9338a08d17e310443d6099cd0a5a03dc0 532312 samtools_0.1.18-3_kfreebsd-amd64.deb
- 82e2abd996ea077becb0afcda2823e4d762633d220ccf4b6f07f72d9ff2b2dc7 156480 libbam-dev_0.1.18-3_kfreebsd-amd64.deb
+ 765b5352bd24b050d7b39a5aea5e51d6bc2eef6ec33b3e9ec6ec681effa69928 532760 samtools_0.1.18-4_kfreebsd-amd64.deb
+ 247833939f60e02970b8c915fc8c59f59235b67d84a0457478653539b5f9afa8 156700 libbam-dev_0.1.18-4_kfreebsd-amd64.deb
Files:
- 504f6102707976bbacc29245dd416f61 532312 science optional samtools_0.1.18-3_kfreebsd-amd64.deb
- 474366270710ae0b25ec14ddaa1b2edb 156480 libdevel optional libbam-dev_0.1.18-3_kfreebsd-amd64.deb
+ 48ddfb74dd07c26e6b8eb385489a79fc 532760 science optional samtools_0.1.18-4_kfreebsd-amd64.deb
+ 1dc14418bd4cb404378cf8a0bd73db9f 156700 libdevel optional libbam-dev_0.1.18-4_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_kfreebsd-amd64.deb
+samtools_0.1.18-4_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 532312 bytes: control archive= 1767 bytes.
+ size 532760 bytes: control archive= 1820 bytes.
+ 32 bytes, 1 lines conffiles
802 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 968
+ Installed-Size: 969
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -668,31 +705,31 @@ samtools_0.1.18-3_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 2012-07-27 15:43 ./
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./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 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126583 2012-12-23 05:00 ./usr/share/doc/samtools/examples/ex1.bam
-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 2012-07-27 15:43 ./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 2012-07-27 15:43 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-12-23 05:00 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:43 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:43 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/samtools/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 05:00 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 05:00 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./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
@@ -705,31 +742,34 @@ drwxr-xr-x root/root 0 2012-07-27 15:43 ./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 2012-07-27 15:43 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/bin/
--rwxr-xr-x root/root 130696 2012-07-27 15:43 ./usr/bin/bcftools
--rwxr-xr-x root/root 24912 2012-07-27 15:43 ./usr/bin/razip
--rwxr-xr-x root/root 372576 2012-07-27 15:43 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/samtools/
--rwxr-xr-x root/root 18208 2012-07-27 15:43 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8440 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8360 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12104 2012-07-27 15:43 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8896 2012-07-27 15:43 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2012-12-23 05:00 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/bin/
+-rwxr-xr-x root/root 130696 2012-12-23 05:00 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24912 2012-12-23 05:00 ./usr/bin/razip
+-rwxr-xr-x root/root 372448 2012-12-23 05:00 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18208 2012-12-23 05:00 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8440 2012-12-23 05:00 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8360 2012-12-23 05:00 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12104 2012-12-23 05:00 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8896 2012-12-23 05:00 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 156480 bytes: control archive= 928 bytes.
- 683 bytes, 15 lines control
+ size 156700 bytes: control archive= 947 bytes.
+ 721 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 432
@@ -742,22 +782,24 @@ libbam-dev_0.1.18-3_kfreebsd-amd64.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/libbam-dev/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./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 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./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 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
--rw-r--r-- root/root 332474 2012-07-27 15:43 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/samtools/
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/lib/
+-rw-r--r-- root/root 332346 2012-12-23 05:00 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/include/samtools/
+-rw-r--r-- root/root 24732 2012-12-23 05:00 ./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
@@ -775,7 +817,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1343403586-20770/build/buildd-samtools_0.1.18-3-kfreebsd-amd64-pjjcgf
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1356238677-90509/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -783,18 +825,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 13452
-Build-Time: 61
+Build-Space: 13492
+Build-Time: 62
Distribution: sid
-Install-Time: 39
-Job: samtools_0.1.18-3
+Install-Time: 32
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 237
-Source-Version: 0.1.18-3
-Space: 13452
+Package-Time: 180
+Source-Version: 0.1.18-4
+Space: 13492
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1543
-Build needed 00:03:57, 13452k disc space
+Finished at 20121223-0500
+Build needed 00:03:00, 13492k disc space
Signature with key '4584BE29' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index aa86631..6465bde 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,30 +1,30 @@
-From buildd at finzi.debian.org Fri Jul 27 15:44:04 2012
+From buildd at finzi.debian.org Sun Dec 23 04:59:44 2012
Return-path: <buildd at finzi.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+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 finzi.debian.org>)
- id 1Sumhw-0005Qe-4O
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:44:04 +0000
+ id 1Tmdf5-0007t2-RS
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 04:59:44 +0000
Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=finzi.debian.org, EMAIL=hostmaster at finzi.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 finzi.debian.org>)
- id 1Sumhu-0001rE-RA; Fri, 27 Jul 2012 15:44:03 +0000
+ id 1Tmdf3-00083t-M1; Sun, 23 Dec 2012 04:59:42 +0000
Received: from buildd by finzi.debian.org with local (Exim 4.72)
(envelope-from <buildd at finzi.debian.org>)
- id 1Sumhs-000Lq2-Oh; Fri, 27 Jul 2012 15:44:00 +0000
-Message-Id: <E1Sumhs-000Lq2-Oh at finzi.debian.org>
+ id 1Tmdf1-0004Lm-Ag; Sun, 23 Dec 2012 04:59:39 +0000
+Message-Id: <E1Tmdf1-0004Lm-Ag at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:44:00 +0000
+Date: Sun, 23 Dec 2012 04:59:39 +0000
From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on kfreebsd-i386
+Subject: Log for successful build of samtools_0.1.18-4 on kfreebsd-i386
(dist=sid)
Key-Id: B3DA9773
Delivered-To: logs at buildd.debian.org
@@ -32,31 +32,31 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (kfreebsd-i386) 27 Jul 2012 15:40 ║
+║ samtools 0.1.18-4 (kfreebsd-i386) 23 Dec 2012 04:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: kfreebsd-i386
-Get:1 http://incoming.debian.org unstable InRelease [249 kB]
-Get:2 http://mirror-ubc.debian.org unstable InRelease [249 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [6315 kB]
-Get:4 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
-Get:5 http://mirror-ubc.debian.org unstable/non-free Sources [98.1 kB]
-Get:6 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [5652 kB]
+Get:1 http://incoming.debian.org unstable InRelease [227 kB]
+Get:2 http://mirror-ubc.debian.org unstable InRelease [227 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [6458 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org Release [1601 B]
-Get:9 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [37.0 kB]
-Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:13 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5652 kB]
-Get:14 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [37.0 kB]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 24.9 MB in 18s (1380 kB/s)
+Get:4 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [53.0 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [5765 kB]
+Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [36.4 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5765 kB]
+Get:12 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [36.4 kB]
+Get:13 http://incoming.debian.org Release.gpg [836 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 25.4 MB in 15s (1667 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,11 +77,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (359 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (360 kB/s)
Download complete and in download only mode
Check arch
@@ -101,65 +101,66 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (6.12)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-4)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
-findutils: already installed (4.4.2-4)
-freebsd-utils: already installed (9.0+ds1-7)
-grep: already installed (2.12-2)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+freebsd-utils: already installed (9.0+ds1-8)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-15)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-28)
-sysvinit: already installed (2.88dsf-28)
+sysvinit-utils: already installed (2.88dsf-34)
+sysvinit: already installed (2.88dsf-34)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
+bsdutils: already installed (1:2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
@@ -168,84 +169,94 @@ 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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 13 not upgraded.
-Need to get 10.7 MB of archives.
-After this operation, 26.4 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.1-1 [38.4 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-9 [26.7 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 5.11-2 [204 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.30-5 [241 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-5 [904 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.32.3-1 [2060 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.5-1 [151 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-9 [140 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.3 [204 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.21-9 [1095 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.6.2-1 [1038 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 5.11-2 [51.5 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-9 [131 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.18.1.1-9 [1894 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9-10 [93.1 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9-10 [210 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.7.dfsg-13 [213 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 17 not upgraded.
+Need to get 10.5 MB of archives.
+After this operation, 27.3 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.2-1 [38.8 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.21-9 [1095 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.3 [204 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.6.3-3 [889 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-10 [27.0 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 5.11-2 [204 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.31-1 [247 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-7 [904 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.33.12+really2.32.4-3 [1819 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.6-2 [133 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-10 [141 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 5.11-2 [51.5 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-10 [131 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev kfreebsd-i386 0.18.1.1-10 [26.6 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev kfreebsd-i386 0.18.1.1-10 [170 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.18.1.1-10 [1747 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9-10 [93.1 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9-10 [210 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.7 MB in 1s (10.6 MB/s)
+Fetched 10.5 MB in 2s (4996 kB/s)
Selecting previously unselected package libpipeline1:kfreebsd-i386.
-(Reading database ... 11227 files and directories currently installed.)
-Unpacking libpipeline1:kfreebsd-i386 (from .../libpipeline1_1.2.1-1_kfreebsd-i386.deb) ...
+(Reading database ... 11298 files and directories currently installed.)
+Unpacking libpipeline1:kfreebsd-i386 (from .../libpipeline1_1.2.2-1_kfreebsd-i386.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-i386.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_kfreebsd-i386.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_kfreebsd-i386.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:kfreebsd-i386.
-Unpacking libasprintf0c2:kfreebsd-i386 (from .../libasprintf0c2_0.18.1.1-9_kfreebsd-i386.deb) ...
+Unpacking libasprintf0c2:kfreebsd-i386 (from .../libasprintf0c2_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package libmagic1:kfreebsd-i386.
Unpacking libmagic1:kfreebsd-i386 (from .../libmagic1_5.11-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libpcre3:kfreebsd-i386.
-Unpacking libpcre3:kfreebsd-i386 (from .../libpcre3_1%3a8.30-5_kfreebsd-i386.deb) ...
+Unpacking libpcre3:kfreebsd-i386 (from .../libpcre3_1%3a8.31-1_kfreebsd-i386.deb) ...
Selecting previously unselected package libxml2:kfreebsd-i386.
-Unpacking libxml2:kfreebsd-i386 (from .../libxml2_2.8.0+dfsg1-5_kfreebsd-i386.deb) ...
+Unpacking libxml2:kfreebsd-i386 (from .../libxml2_2.8.0+dfsg1-7_kfreebsd-i386.deb) ...
Selecting previously unselected package libffi5:kfreebsd-i386.
Unpacking libffi5:kfreebsd-i386 (from .../libffi5_3.0.10-3_kfreebsd-i386.deb) ...
Selecting previously unselected package libglib2.0-0:kfreebsd-i386.
-Unpacking libglib2.0-0:kfreebsd-i386 (from .../libglib2.0-0_2.32.3-1_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0:kfreebsd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-3_kfreebsd-i386.deb) ...
Selecting previously unselected package libcroco3:kfreebsd-i386.
-Unpacking libcroco3:kfreebsd-i386 (from .../libcroco3_0.6.5-1_kfreebsd-i386.deb) ...
+Unpacking libcroco3:kfreebsd-i386 (from .../libcroco3_0.6.6-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libunistring0:kfreebsd-i386.
Unpacking libunistring0:kfreebsd-i386 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
Selecting previously unselected package libgettextpo0:kfreebsd-i386.
-Unpacking libgettextpo0:kfreebsd-i386 (from .../libgettextpo0_0.18.1.1-9_kfreebsd-i386.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_kfreebsd-i386.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-i386.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_kfreebsd-i386.deb) ...
+Unpacking libgettextpo0:kfreebsd-i386 (from .../libgettextpo0_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.11-2_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_kfreebsd-i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
+Selecting previously unselected package libasprintf-dev:kfreebsd-i386.
+Unpacking libasprintf-dev:kfreebsd-i386 (from .../libasprintf-dev_0.18.1.1-10_kfreebsd-i386.deb) ...
+Selecting previously unselected package libgettextpo-dev:kfreebsd-i386.
+Unpacking libgettextpo-dev:kfreebsd-i386 (from .../libgettextpo-dev_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_kfreebsd-i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_kfreebsd-i386.deb) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-i386.
@@ -256,31 +267,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:kfreebsd-i386.
Unpacking zlib1g-dev:kfreebsd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_kfreebsd-i386.deb) ...
-Setting up libpipeline1:kfreebsd-i386 (1.2.1-1) ...
-Setting up libasprintf0c2:kfreebsd-i386 (0.18.1.1-9) ...
-Setting up libmagic1:kfreebsd-i386 (5.11-2) ...
-Setting up libpcre3:kfreebsd-i386 (1:8.30-5) ...
-Setting up libxml2:kfreebsd-i386 (2.8.0+dfsg1-5) ...
-Setting up libffi5:kfreebsd-i386 (3.0.10-3) ...
-Setting up libglib2.0-0:kfreebsd-i386 (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:kfreebsd-i386 (0.6.5-1) ...
-Setting up libunistring0:kfreebsd-i386 (0.9.3-5) ...
-Setting up libgettextpo0:kfreebsd-i386 (0.18.1.1-9) ...
+Setting up libpipeline1:kfreebsd-i386 (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
Setting up bsdmainutils (9.0.3) ...
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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
+Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:kfreebsd-i386 (0.18.1.1-10) ...
+Setting up libmagic1:kfreebsd-i386 (5.11-2) ...
+Setting up libpcre3:kfreebsd-i386 (1:8.31-1) ...
+Setting up libxml2:kfreebsd-i386 (2.8.0+dfsg1-7) ...
+Setting up libffi5:kfreebsd-i386 (3.0.10-3) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.33.12+really2.32.4-3) ...
+No schema files found: doing nothing.
+Setting up libcroco3:kfreebsd-i386 (0.6.6-2) ...
+Setting up libunistring0:kfreebsd-i386 (0.9.3-5) ...
+Setting up libgettextpo0:kfreebsd-i386 (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:kfreebsd-i386 (0.18.1.1-10) ...
+Setting up libgettextpo-dev:kfreebsd-i386 (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:kfreebsd-i386 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -290,11 +304,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.7 g++-4.7_4.7.1-5 gcc-4.7_4.7.1-5 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5
-Package versions: apt_0.9.7.2 base-files_6.11 base-passwd_3.5.26 bash_4.2-4 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.7.1-1 cpp-4.7_4.7.1-5 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 freebsd-utils_9.0+ds1-7 g++_4:4.7.1-1 g++-4.7_4.7.1-5 gcc_4:4.7.1-1 gcc-4.7_4.7.1-5 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-7 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.2 libasprintf0c2_0.18.1.1-9 libblkid1_2.20.1-5.1 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc0.1_2.13-34 libc0.1-dev_2.13-34 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-5 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-5 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libquadmath0_4.7.1-5 libreadline6_6.2-8 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 freebsd-utils_9.0+ds1-8 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-34 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-8 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libblkid1_2.20.1-5.2 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc0.1_2.13-37 libc0.1-dev_2.13-37 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -305,15 +319,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -323,7 +338,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
@@ -331,26 +346,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -368,11 +386,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -382,15 +401,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -425,8 +447,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -441,10 +463,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -465,24 +487,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
@@ -510,14 +532,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -543,7 +565,7 @@ 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_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -552,6 +574,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -578,8 +601,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -602,12 +627,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -620,27 +645,27 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_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=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.18-3_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1543
+Build finished at 20121223-0459
-samtools_0.1.18-3_kfreebsd-i386.changes:
+samtools_0.1.18-4_kfreebsd-i386.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
@@ -648,40 +673,51 @@ Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- 62d5dd1176b665472c645ed79219ba0916b9043b 533734 samtools_0.1.18-3_kfreebsd-i386.deb
- 301e198be416c2fbc53c0fb898c221d98e7a8383 160710 libbam-dev_0.1.18-3_kfreebsd-i386.deb
+ 8f5b3ae4cbe37d42d0acb3fa121e89d72c50b081 534414 samtools_0.1.18-4_kfreebsd-i386.deb
+ daeb3b47e6efa643c4ebe62a90623b39a5d9d308 160998 libbam-dev_0.1.18-4_kfreebsd-i386.deb
Checksums-Sha256:
- 4b7593ea23b756d10e6c1abfe96c8c5721f78e44853216228d142ad1012d0263 533734 samtools_0.1.18-3_kfreebsd-i386.deb
- 2269e3ee3c2e9486b9715e754aa0e1212e09f3880c835a9380c9d60d883d3883 160710 libbam-dev_0.1.18-3_kfreebsd-i386.deb
+ ba217ba846aa5abd85dcb03fa1509b6ccdbe7ca709dbb199045ee021fa4b5c4c 534414 samtools_0.1.18-4_kfreebsd-i386.deb
+ e5e6e16b17ac42608e37b95146ff1ee355cc36f712338a40f27548206735bd01 160998 libbam-dev_0.1.18-4_kfreebsd-i386.deb
Files:
- 176fe81a452f916674dbf0d376eb4d7e 533734 science optional samtools_0.1.18-3_kfreebsd-i386.deb
- f10f8b19b1ff958d5aaaee2b3449ff8e 160710 libdevel optional libbam-dev_0.1.18-3_kfreebsd-i386.deb
+ 15e3c265d578110987dfea084ed8dfd6 534414 science optional samtools_0.1.18-4_kfreebsd-i386.deb
+ 45e5729f94233e78cd653d45271a6c5f 160998 libdevel optional libbam-dev_0.1.18-4_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_kfreebsd-i386.deb
+samtools_0.1.18-4_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 533734 bytes: control archive= 1766 bytes.
+ size 534414 bytes: control archive= 1813 bytes.
+ 32 bytes, 1 lines conffiles
801 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 990
+ Installed-Size: 992
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -694,31 +730,31 @@ samtools_0.1.18-3_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 2012-07-27 15:43 ./
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126583 2012-12-23 04:59 ./usr/share/doc/samtools/examples/ex1.bam
-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 2012-07-27 15:43 ./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 2012-07-27 15:43 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-12-23 04:59 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:43 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:43 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/samtools/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 04:59 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 04:59 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./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
@@ -731,34 +767,37 @@ drwxr-xr-x root/root 0 2012-07-27 15:43 ./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 2012-07-27 15:43 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/bin/
--rwxr-xr-x root/root 134212 2012-07-27 15:43 ./usr/bin/bcftools
--rwxr-xr-x root/root 24676 2012-07-27 15:43 ./usr/bin/razip
--rwxr-xr-x root/root 399924 2012-07-27 15:43 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/samtools/
--rwxr-xr-x root/root 16472 2012-07-27 15:43 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6844 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6844 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10576 2012-07-27 15:43 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7452 2012-07-27 15:43 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2012-12-23 04:59 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/bin/
+-rwxr-xr-x root/root 134212 2012-12-23 04:59 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24676 2012-12-23 04:59 ./usr/bin/razip
+-rwxr-xr-x root/root 399988 2012-12-23 04:59 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/lib/samtools/
+-rwxr-xr-x root/root 16472 2012-12-23 04:59 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6844 2012-12-23 04:59 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6844 2012-12-23 04:59 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10576 2012-12-23 04:59 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7452 2012-12-23 04:59 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 160710 bytes: control archive= 929 bytes.
- 682 bytes, 15 lines control
+ size 160998 bytes: control archive= 946 bytes.
+ 720 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 400
+ Installed-Size: 401
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -768,22 +807,24 @@ libbam-dev_0.1.18-3_kfreebsd-i386.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/libbam-dev/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./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 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./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 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
--rw-r--r-- root/root 299796 2012-07-27 15:43 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/samtools/
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/lib/
+-rw-r--r-- root/root 299848 2012-12-23 04:59 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/include/samtools/
+-rw-r--r-- root/root 24732 2012-12-23 04:58 ./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
@@ -801,7 +842,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1343403637-81390/build/buildd-samtools_0.1.18-3-kfreebsd-i386-VzPl6z
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1356238605-13802/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -809,18 +850,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 11026
-Build-Time: 71
+Build-Space: 11086
+Build-Time: 72
Distribution: sid
-Install-Time: 23
-Job: samtools_0.1.18-3
+Install-Time: 35
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 199
-Source-Version: 0.1.18-3
-Space: 11026
+Package-Time: 169
+Source-Version: 0.1.18-4
+Space: 11086
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1543
-Build needed 00:03:19, 11026k disc space
+Finished at 20121223-0459
+Build needed 00:02:49, 11086k disc space
Signature with key 'B3DA9773' requested:
diff --git a/mips.log b/mips.log
index 410e135..36e3ad0 100644
--- a/mips.log
+++ b/mips.log
@@ -1,29 +1,29 @@
-From buildd at lucatelli.debian.org Fri Jul 27 16:04:29 2012
-Return-path: <buildd at lucatelli.debian.org>
+From buildd2 at lucatelli.debian.org Sun Dec 23 05:18:47 2012
+Return-path: <buildd2 at lucatelli.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 lucatelli.debian.org>)
- id 1Sun1h-0000IO-EZ
- for logs at buildd.debian.org; Fri, 27 Jul 2012 16:04:29 +0000
+ (Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
+ id 1TmdxX-0003Ro-IT
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:18:47 +0000
Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=lucatelli.debian.org,
EMAIL=hostmaster at lucatelli.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
- id 1Sun1f-0006Qs-DS
- for logs at buildd.debian.org; Fri, 27 Jul 2012 16:04:28 +0000
-Received: from buildd by lucatelli.debian.org with local (Exim 4.72)
- (envelope-from <buildd at lucatelli.debian.org>) id 1Sun1c-0006ab-Lp
- for logs at buildd.debian.org; Fri, 27 Jul 2012 16:04:24 +0000
-Date: Fri, 27 Jul 2012 16:04:24 +0000
-Message-Id: <E1Sun1c-0006ab-Lp at lucatelli.debian.org>
-From: buildd on lucatelli <buildd at lucatelli.debian.org>
+ (Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
+ id 1TmdxW-00014y-5G
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:18:46 +0000
+Received: from buildd2 by lucatelli.debian.org with local (Exim 4.72)
+ (envelope-from <buildd2 at lucatelli.debian.org>) id 1TmdxT-0007jO-8m
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:18:43 +0000
+Date: Sun, 23 Dec 2012 05:18:43 +0000
+Message-Id: <E1TmdxT-0007jO-8m at lucatelli.debian.org>
+From: buildd on lucatelli <buildd2 at lucatelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on mips (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-4 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -31,31 +31,31 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (mips) 27 Jul 2012 15:38 ║
+║ samtools 0.1.18-4 (mips) 23 Dec 2012 04:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [6315 kB]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [227 kB]
+Get:2 http://incoming.debian.org unstable InRelease [227 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [6458 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 [6315 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [98.1 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [5964 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main mips Packages [5964 kB]
-Get:12 http://mirror-ubc.debian.org unstable/contrib mips Packages [38.3 kB]
-Get:13 http://incoming.debian.org unstable/contrib mips Packages [38.3 kB]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.6 MB in 1min 39s (256 kB/s)
+Get:5 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [53.0 kB]
+Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [6059 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main mips Packages [6059 kB]
+Get:12 http://mirror-ubc.debian.org unstable/contrib mips Packages [37.1 kB]
+Get:13 http://incoming.debian.org unstable/contrib mips Packages [37.1 kB]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 26.0 MB in 1min 38s (264 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,11 +76,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (347 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (347 kB/s)
Download complete and in download only mode
Check arch
@@ -100,178 +100,162 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 70 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 56 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 70 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 56 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.10)
-base-passwd: already installed (3.5.24)
-bash: already installed (4.2-2)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-5)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.1)
+debianutils: already installed (4.3.3)
diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.4.2)
-e2fsprogs: already installed (1.42.2-2)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
grep: already installed (2.12-2)
-gzip: already installed (1.4-5)
+gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
-ncurses-base: already installed (5.9-8)
-ncurses-bin: already installed (5.9-8)
-perl-base: already installed (5.14.2-11)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-12)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-27)
-sysvinit: already installed (2.88dsf-27)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5)
-mount: already installed (2.20.1-5)
-util-linux: already installed (2.20.1-5)
-libc6-dev: already installed (2.13-33)
-gcc: already installed (4:4.6.3-6 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-6 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.20.1-5.1)
+mount: already installed (2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
+libc6-dev: already installed (2.13-35)
+gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.4.2 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- liblzma5 libmagic1 libncurses5 libpcre3 libpipeline1 libtinfo-dev libtinfo5
- libunistring0 libxml2 man-db ncurses-bin po-debconf zlib1g
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libgpm2 xml-core libmail-sendmail-perl
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-The following packages will be upgraded:
- liblzma5 libncurses5 libtinfo5 ncurses-bin zlib1g
-5 upgraded, 26 newly installed, 0 to remove and 65 not upgraded.
-Need to get 11.7 MB of archives.
-After this operation, 29.3 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin mips 5.9-10 [331 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main liblzma5 mips 5.1.1alpha+20120614-1 [209 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 mips 5.9-10 [268 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 mips 5.9-10 [99.7 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g mips 1:1.2.7.dfsg-13 [87.4 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.1-1 [36.7 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 mips 0.18.1.1-9 [26.7 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.11-2 [201 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 1:8.30-5 [245 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-5 [869 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.32.3-1 [1991 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.5-1 [140 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 mips 0.18.1.1-9 [139 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.3 [208 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-9 [1156 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.2-1 [1029 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.11-2 [51.5 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-9 [141 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-9 [1918 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev mips 5.9-10 [104 kB]
-Get:29 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-10 [223 kB]
-Get:30 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:31 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.7.dfsg-13 [213 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 56 not upgraded.
+Need to get 10.4 MB of archives.
+After this operation, 30.3 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.2-1 [37.1 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-9 [1156 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.3 [208 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.3-3 [867 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 mips 0.18.1.1-10 [27.1 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.11-2 [201 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 1:8.31-1 [250 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-7 [870 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.33.12+really2.32.4-3 [1685 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.6-2 [118 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 mips 0.18.1.1-10 [140 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.11-2 [51.5 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-10 [141 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev mips 0.18.1.1-10 [26.9 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev mips 0.18.1.1-10 [189 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-10 [1753 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev mips 5.9-10 [104 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-10 [223 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.7 MB in 5s (2208 kB/s)
-(Reading database ... 10710 files and directories currently installed.)
-Preparing to replace ncurses-bin 5.9-8 (using .../ncurses-bin_5.9-10_mips.deb) ...
-Unpacking replacement ncurses-bin ...
-Setting up ncurses-bin (5.9-10) ...
-(Reading database ... 10710 files and directories currently installed.)
-Preparing to replace liblzma5:mips 5.1.1alpha+20110809-3 (using .../liblzma5_5.1.1alpha+20120614-1_mips.deb) ...
-Unpacking replacement liblzma5:mips ...
-Setting up liblzma5:mips (5.1.1alpha+20120614-1) ...
-(Reading database ... 10710 files and directories currently installed.)
-Preparing to replace libtinfo5:mips 5.9-8 (using .../libtinfo5_5.9-10_mips.deb) ...
-Unpacking replacement libtinfo5:mips ...
-Setting up libtinfo5:mips (5.9-10) ...
-(Reading database ... 10710 files and directories currently installed.)
-Preparing to replace libncurses5:mips 5.9-8 (using .../libncurses5_5.9-10_mips.deb) ...
-Unpacking replacement libncurses5:mips ...
-Setting up libncurses5:mips (5.9-10) ...
-(Reading database ... 10710 files and directories currently installed.)
-Preparing to replace zlib1g:mips 1:1.2.7.dfsg-11 (using .../zlib1g_1%3a1.2.7.dfsg-13_mips.deb) ...
-Unpacking replacement zlib1g:mips ...
-Setting up zlib1g:mips (1:1.2.7.dfsg-13) ...
+Fetched 10.4 MB in 10s (1000 kB/s)
Selecting previously unselected package libpipeline1:mips.
-(Reading database ... 10710 files and directories currently installed.)
-Unpacking libpipeline1:mips (from .../libpipeline1_1.2.1-1_mips.deb) ...
+(Reading database ... 10735 files and directories currently installed.)
+Unpacking libpipeline1:mips (from .../libpipeline1_1.2.2-1_mips.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_mips.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_mips.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_mips.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:mips.
-Unpacking libasprintf0c2:mips (from .../libasprintf0c2_0.18.1.1-9_mips.deb) ...
+Unpacking libasprintf0c2:mips (from .../libasprintf0c2_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package libmagic1:mips.
Unpacking libmagic1:mips (from .../libmagic1_5.11-2_mips.deb) ...
Selecting previously unselected package libpcre3:mips.
-Unpacking libpcre3:mips (from .../libpcre3_1%3a8.30-5_mips.deb) ...
+Unpacking libpcre3:mips (from .../libpcre3_1%3a8.31-1_mips.deb) ...
Selecting previously unselected package libxml2:mips.
-Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-5_mips.deb) ...
+Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-7_mips.deb) ...
Selecting previously unselected package libffi5:mips.
Unpacking libffi5:mips (from .../libffi5_3.0.10-3_mips.deb) ...
Selecting previously unselected package libglib2.0-0:mips.
-Unpacking libglib2.0-0:mips (from .../libglib2.0-0_2.32.3-1_mips.deb) ...
+Unpacking libglib2.0-0:mips (from .../libglib2.0-0_2.33.12+really2.32.4-3_mips.deb) ...
Selecting previously unselected package libcroco3:mips.
-Unpacking libcroco3:mips (from .../libcroco3_0.6.5-1_mips.deb) ...
+Unpacking libcroco3:mips (from .../libcroco3_0.6.6-2_mips.deb) ...
Selecting previously unselected package libunistring0:mips.
Unpacking libunistring0:mips (from .../libunistring0_0.9.3-5_mips.deb) ...
Selecting previously unselected package libgettextpo0:mips.
-Unpacking libgettextpo0:mips (from .../libgettextpo0_0.18.1.1-9_mips.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_mips.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_mips.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_mips.deb) ...
+Unpacking libgettextpo0:mips (from .../libgettextpo0_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.11-2_mips.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_mips.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
+Selecting previously unselected package libasprintf-dev:mips.
+Unpacking libasprintf-dev:mips (from .../libasprintf-dev_0.18.1.1-10_mips.deb) ...
+Selecting previously unselected package libgettextpo-dev:mips.
+Unpacking libgettextpo-dev:mips (from .../libgettextpo-dev_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_mips.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_mips.deb) ...
Selecting previously unselected package libtinfo-dev:mips.
@@ -282,31 +266,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:mips.
Unpacking zlib1g-dev:mips (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mips.deb) ...
-Setting up libpipeline1:mips (1.2.1-1) ...
-Setting up libasprintf0c2:mips (0.18.1.1-9) ...
+Setting up libpipeline1:mips (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
+Setting up bsdmainutils (9.0.3) ...
+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 man-db (2.6.3-3) ...
+Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:mips (0.18.1.1-10) ...
Setting up libmagic1:mips (5.11-2) ...
-Setting up libpcre3:mips (1:8.30-5) ...
-Setting up libxml2:mips (2.8.0+dfsg1-5) ...
+Setting up libpcre3:mips (1:8.31-1) ...
+Setting up libxml2:mips (2.8.0+dfsg1-7) ...
Setting up libffi5:mips (3.0.10-3) ...
-Setting up libglib2.0-0:mips (2.32.3-1) ...
+Setting up libglib2.0-0:mips (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:mips (0.6.5-1) ...
+Setting up libcroco3:mips (0.6.6-2) ...
Setting up libunistring0:mips (0.9.3-5) ...
-Setting up libgettextpo0:mips (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
-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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
+Setting up libgettextpo0:mips (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:mips (0.18.1.1-10) ...
+Setting up libgettextpo-dev:mips (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:mips (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -316,11 +303,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 65 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 56 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 3.2.0-0.bpo.1-octeon mips (mips64)
-Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.2 g++-4.6_4.6.3-7 gcc-4.6_4.6.3-7 libc6-dev_2.13-33 libstdc++6_4.7.0-12 libstdc++6-4.6-dev_4.6.3-7 linux-libc-dev_3.2.19-1
-Package versions: apt_0.9.5.1 base-files_6.10 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-6 cpp-4.6_4.6.3-7 dash_0.5.7-3 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.2 dpkg-dev_1.16.4.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-6 g++-4.6_4.6.3-7 gcc_4:4.6.3-6 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7-base_4.7.0-12 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-9 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-7 libapt-pkg4.12_0.9.5.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-7 libblkid1_2.20.1-5 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.2 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-1+b1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-12 libgdbm3_1.8.3-10 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.0-12 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-4 libsemanage-common_2.1.6-5 libsemanage1_2.1.6-5 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.2-2 libstdc++6_4.7.0-12 libstdc++6-4.6-dev_4.6.3-7 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.19-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian6 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5 multiarch-support_2.13-33 ncurses-base_5.9-8 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-11 perl-base_5.14.2-11 perl-modules_5.14.2-11 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.3p2-1.1 sysv-rc_2.88dsf-26 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Kernel: Linux 3.2.0-0.bpo.3-octeon mips (mips64)
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -330,16 +317,17 @@ Package versions: apt_0.9.5.1 base-files_6.10 base-passwd_3.5.24 bash_4.2-2 binu
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -349,7 +337,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
@@ -357,26 +345,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/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_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -394,11 +385,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -408,15 +400,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -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]
@@ -451,8 +446,8 @@ 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 -Wformat -Werror=format-security -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 -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_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -467,10 +462,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -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_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
@@ -491,24 +486,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -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_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mips-BQrOiu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -530,14 +525,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mips-BQrOiu/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -563,7 +558,7 @@ 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_0.1.18-3-mips-BQrOiu/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -572,6 +567,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -598,8 +594,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -622,12 +620,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-mips-BQrOiu/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -640,68 +638,79 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_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=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.18-3_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1604
+Build finished at 20121223-0518
-samtools_0.1.18-3_mips.changes:
+samtools_0.1.18-4_mips.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
+Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
+ .
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- b19cd0fcbd83a2600a37b447235b9303c9615e60 525342 samtools_0.1.18-3_mips.deb
- 1fbd24bf59e3d470f67e6788a151e25233d06090 163210 libbam-dev_0.1.18-3_mips.deb
+ 293e544fe85a2978220887552b654ee1fe51c1a4 525938 samtools_0.1.18-4_mips.deb
+ 9a3aef658319c24ab965ea8a4e291d33833f87ef 163590 libbam-dev_0.1.18-4_mips.deb
Checksums-Sha256:
- ce993d4a71e36b984a273334831442e7d33018ac1e861bd90894220f2007c945 525342 samtools_0.1.18-3_mips.deb
- df94beee0cd0c7a2fbfd92a2ca6eae14fcd8f34b53d381236597b62331de7483 163210 libbam-dev_0.1.18-3_mips.deb
+ 01bc7f18c1d1ec407511bf5fed18b7189f4d1af2febb3a921501d682ad217f4d 525938 samtools_0.1.18-4_mips.deb
+ c93149d09a6b57e5a629957e98d7cdc63ad5becf57665aecc5ebc83dec384d22 163590 libbam-dev_0.1.18-4_mips.deb
Files:
- 866934ed8a0d7da77b303fcfe430dde6 525342 science optional samtools_0.1.18-3_mips.deb
- fce1cc71ae8f79e4a460f40c6d3bef90 163210 libdevel optional libbam-dev_0.1.18-3_mips.deb
+ 3d619f6a934917cb1eac0369633839e4 525938 science optional samtools_0.1.18-4_mips.deb
+ 2f8476f717beb2f942766d073de51831 163590 libdevel optional libbam-dev_0.1.18-4_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_mips.deb
+samtools_0.1.18-4_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 525342 bytes: control archive= 1765 bytes.
+ size 525938 bytes: control archive= 1810 bytes.
+ 32 bytes, 1 lines conffiles
791 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1106
+ Installed-Size: 1115
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -714,21 +723,21 @@ samtools_0.1.18-3_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 2012-07-27 16:02 ./
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/lib/samtools/
--rwxr-xr-x root/root 7472 2012-07-27 16:03 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9252 2012-07-27 16:03 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 12432 2012-07-27 16:03 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2012-07-27 16:03 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 17692 2012-07-27 16:03 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/bin/
--rwxr-xr-x root/root 155204 2012-07-27 16:03 ./usr/bin/bcftools
--rwxr-xr-x root/root 440320 2012-07-27 16:03 ./usr/bin/samtools
--rwxr-xr-x root/root 29296 2012-07-27 16:03 ./usr/bin/razip
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7472 2012-12-23 05:17 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9252 2012-12-23 05:17 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 12432 2012-12-23 05:17 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2012-12-23 05:17 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 17692 2012-12-23 05:17 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/bin/
+-rwxr-xr-x root/root 155204 2012-12-23 05:17 ./usr/bin/bcftools
+-rwxr-xr-x root/root 440320 2012-12-23 05:17 ./usr/bin/samtools
+-rwxr-xr-x root/root 29296 2012-12-23 05:17 ./usr/bin/razip
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/samtools/
-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
@@ -736,46 +745,49 @@ drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/samtools/
-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 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2012-07-27 16:03 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2012-12-23 05:17 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-drwxr-xr-x root/root 0 2012-07-27 16:02 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126609 2012-07-27 15:50 ./usr/share/doc/samtools/examples/ex1.bam.gz
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./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 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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126583 2012-12-23 05:04 ./usr/share/doc/samtools/examples/ex1.bam
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2012-07-27 16:03 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1966 2012-12-23 05:17 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2012-07-27 16:02 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 16:02 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 16:02 ./usr/share/man/man1/samtools.1.gz
-lrwxrwxrwx root/root 0 2012-07-27 16:03 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_mips.deb
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 05:17 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 05:17 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2012-12-23 05:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 163210 bytes: control archive= 925 bytes.
- 673 bytes, 15 lines control
+ size 163590 bytes: control archive= 946 bytes.
+ 711 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 467
@@ -788,25 +800,27 @@ libbam-dev_0.1.18-3_mips.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/lib/
--rw-r--r-- root/root 335554 2012-07-27 16:03 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/include/samtools/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/lib/
+-rw-r--r-- root/root 335618 2012-12-23 05:17 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/include/samtools/
-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 24732 2012-12-23 04:58 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.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
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 16:03 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
@@ -821,55 +835,57 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-5e383676-c884-4bd9-8f03-7932a12a9603/build/buildd-samtools_0.1.18-3-mips-BQrOiu
+Purging /var/lib/schroot/mount/sid-mips-sbuild-cb17ab87-f16e-4459-bb11-3f44ac7e51c0/build/buildd2-samtools_0.1.18-4-mips-UhvVCE
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: 10956
-Build-Time: 1302
+Build-Space: 11012
+Build-Time: 1286
Distribution: sid
-Install-Time: 93
-Job: samtools_0.1.18-3
+Install-Time: 87
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 1543
-Source-Version: 0.1.18-3
-Space: 10956
+Package-Time: 1519
+Source-Version: 0.1.18-4
+Space: 11012
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1604
-Build needed 00:25:43, 10956k disc space
+Finished at 20121223-0518
+Build needed 00:25:19, 11012k disc space
Signature with key '86ADA8B4' requested:
-From buildd at mayer.debian.org Fri Jul 27 15:45:41 2012
+From buildd at mayer.debian.org Sun Dec 23 05:04:52 2012
Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+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 mayer.debian.org>)
- id 1SumjU-0005sg-GU
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:40 +0000
+ id 1Tmdk4-0000P2-3B
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:52 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1SumjS-0001vj-Ou
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:39 +0000
+ id 1Tmdk2-0008JB-FH
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:51 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mayer.debian.org>) id 1SumjQ-0000sF-Fd
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:36 +0000
-Date: Fri, 27 Jul 2012 15:45:36 +0000
-Message-Id: <E1SumjQ-0000sF-Fd at mayer.debian.org>
+ (envelope-from <buildd at mayer.debian.org>) id 1Tmdjz-00014d-0i
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:47 +0000
+Date: Sun, 23 Dec 2012 05:04:47 +0000
+Message-Id: <E1Tmdjz-00014d-0i at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-4 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -877,29 +893,29 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (mipsel) 27 Jul 2012 15:38 ║
+║ samtools 0.1.18-4 (mipsel) 23 Dec 2012 04:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [249 kB]
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org sid InRelease [227 kB]
+Get:2 http://debian.oregonstate.edu sid InRelease [227 kB]
+Get:3 http://debian.oregonstate.edu sid/main Sources [6458 kB]
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org Release [1601 B]
-Get:4 http://debian.oregonstate.edu sid/main Sources [6315 kB]
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Get:5 http://incoming.debian.org Sources [14.5 kB]
-Get:6 http://incoming.debian.org Packages [117 kB]
-Get:7 http://debian.oregonstate.edu sid/contrib Sources [53.9 kB]
-Get:8 http://debian.oregonstate.edu sid/main mipsel Packages [5971 kB]
-Get:9 http://debian.oregonstate.edu sid/contrib mipsel Packages [38.3 kB]
-Fetched 12.8 MB in 35s (359 kB/s)
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org sid/main Sources [6458 kB]
+Get:6 http://debian.oregonstate.edu sid/contrib Sources [53.0 kB]
+Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [6064 kB]
+Get:8 http://incoming.debian.org sid/contrib Sources [53.0 kB]
+Get:9 http://incoming.debian.org sid/main mipsel Packages [6064 kB]
+Get:10 http://debian.oregonstate.edu sid/contrib mipsel Packages [37.1 kB]
+Get:11 http://incoming.debian.org sid/contrib mipsel Packages [37.1 kB]
+Get:12 http://incoming.debian.org Release [1141 B]
+Get:13 http://incoming.debian.org Sources [14.0 kB]
+Get:14 http://incoming.debian.org Packages [118 kB]
+Fetched 25.8 MB in 1min 25s (301 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -920,11 +936,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (350 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (378 kB/s)
Download complete and in download only mode
Check arch
@@ -944,64 +960,66 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.11)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-3)
+bash: already installed (4.2-5)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
+debianutils: already installed (4.3.3)
diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
grep: already installed (2.12-2)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-16)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-28)
-sysvinit: already installed (2.88dsf-28)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
bsdutils: already installed (1:2.20.1-5.1)
mount: already installed (2.20.1-5.1)
util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-37)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libmagic1
- libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ libasprintf-dev libasprintf0c2 libcroco3 libffi5 libgettextpo-dev
+ libgettextpo0 libglib2.0-0 libmagic1 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf
Suggested packages:
devscripts dh-make gettext-doc groff ncurses-doc less www-browser
libmail-box-perl procmail graphviz default-mta mail-transport-agent
@@ -1009,53 +1027,60 @@ 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 diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0 libxml2
- man-db po-debconf quilt zlib1g-dev
+ bash-completion cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev
+ libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 24 newly installed, 0 to remove and 17 not upgraded.
-Need to get 0 B/10.2 MB of archives.
-After this operation, 28.3 MB of additional disk space will be used.
+0 upgraded, 27 newly installed, 0 to remove and 30 not upgraded.
+Need to get 0 B/9966 kB of archives.
+After this operation, 29.2 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10891 files and directories currently installed.)
-Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
+(Reading database ... 10942 files and directories currently installed.)
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-1_mipsel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_mipsel.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:mipsel.
-Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
+Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package libmagic1:mipsel.
Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
Selecting previously unselected package libxml2:mipsel.
-Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-5_mipsel.deb) ...
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7_mipsel.deb) ...
Selecting previously unselected package libffi5:mipsel.
Unpacking libffi5:mipsel (from .../libffi5_3.0.10-3_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0:mipsel.
-Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.32.3-1_mipsel.deb) ...
+Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-3_mipsel.deb) ...
Selecting previously unselected package libcroco3:mipsel.
-Unpacking libcroco3:mipsel (from .../libcroco3_0.6.5-1_mipsel.deb) ...
+Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-2_mipsel.deb) ...
Selecting previously unselected package libunistring0:mipsel.
Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
Selecting previously unselected package libgettextpo0:mipsel.
-Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-9_mipsel.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_mipsel.deb) ...
+Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.11-2_mipsel.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Selecting previously unselected package libasprintf-dev:mipsel.
+Unpacking libasprintf-dev:mipsel (from .../libasprintf-dev_0.18.1.1-10_mipsel.deb) ...
+Selecting previously unselected package libgettextpo-dev:mipsel.
+Unpacking libgettextpo-dev:mipsel (from .../libgettextpo-dev_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
Selecting previously unselected package libtinfo-dev:mipsel.
@@ -1066,27 +1091,30 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:mipsel.
Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) ...
-Setting up libpipeline1:mipsel (1.2.1-1) ...
-Setting up libasprintf0c2:mipsel (0.18.1.1-9) ...
+Setting up libpipeline1:mipsel (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-3) ...
+Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:mipsel (0.18.1.1-10) ...
Setting up libmagic1:mipsel (5.11-2) ...
-Setting up libxml2:mipsel (2.8.0+dfsg1-5) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-7) ...
Setting up libffi5:mipsel (3.0.10-3) ...
-Setting up libglib2.0-0:mipsel (2.32.3-1) ...
+Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:mipsel (0.6.5-1) ...
+Setting up libcroco3:mipsel (0.6.6-2) ...
Setting up libunistring0:mipsel (0.9.3-5) ...
-Setting up libgettextpo0:mipsel (0.18.1.1-9) ...
-Setting up groff-base (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
+Setting up libgettextpo0:mipsel (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:mipsel (0.18.1.1-10) ...
+Setting up libgettextpo-dev:mipsel (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:mipsel (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -1096,11 +1124,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012d-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-14 gcc_4:4.6.3-8 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-16 perl-base_5.14.2-16 perl-modules_5.14.2-16 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1111,15 +1139,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -1129,7 +1158,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
@@ -1137,26 +1166,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -1174,11 +1206,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -1188,15 +1221,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -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]
@@ -1231,8 +1267,8 @@ 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 -Wformat -Werror=format-security -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 -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -1247,10 +1283,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
@@ -1271,24 +1307,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -1310,14 +1346,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1343,7 +1379,7 @@ 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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -1352,6 +1388,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -1378,8 +1415,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1402,12 +1441,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -1421,28 +1460,28 @@ dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is no
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-3_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1545
+Build finished at 20121223-0504
-samtools_0.1.18-3_mipsel.changes:
+samtools_0.1.18-4_mipsel.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -1450,40 +1489,51 @@ Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- fbdad8c7b943d06b23a609601851719c79ae8249 528128 samtools_0.1.18-3_mipsel.deb
- 0c31cedee12156cdaf9a3243b6979cdec73f0c43 165534 libbam-dev_0.1.18-3_mipsel.deb
+ e38f3d105ff9aec1e46a1cf7df50d9d690daa854 528822 samtools_0.1.18-4_mipsel.deb
+ e3bac066a176abf71ac601f7cc5b7f6a8115b949 165950 libbam-dev_0.1.18-4_mipsel.deb
Checksums-Sha256:
- 10eff2a972b78b93caaa55f5fc7de3b34299ece6a0741d144d069d7c70ce2170 528128 samtools_0.1.18-3_mipsel.deb
- b2a1d344243fe3d3d9aed637f9f5570911f574b48b3923db3bf28fa67f94276e 165534 libbam-dev_0.1.18-3_mipsel.deb
+ deeeaee3478547fe36bf464cd72db5a97f311564984c636f1d526d583edbf645 528822 samtools_0.1.18-4_mipsel.deb
+ 755ab8c730bd35963f3d8c2ff6d6e4a53e0819099742a8a1d994d1f983628ece 165950 libbam-dev_0.1.18-4_mipsel.deb
Files:
- 366461221d46aa8a679a50c0e0cfe449 528128 science optional samtools_0.1.18-3_mipsel.deb
- 0a5933504f5a307ad579a6a7de287738 165534 libdevel optional libbam-dev_0.1.18-3_mipsel.deb
+ 9654a2be2233c1816ecc00d751ce655c 528822 science optional samtools_0.1.18-4_mipsel.deb
+ 0f8f4860ecf69157bff1f30b8435bf0a 165950 libdevel optional libbam-dev_0.1.18-4_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_mipsel.deb
+samtools_0.1.18-4_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 528128 bytes: control archive= 1760 bytes.
+ size 528822 bytes: control archive= 1809 bytes.
+ 32 bytes, 1 lines conffiles
793 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1106
+ Installed-Size: 1115
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -1496,31 +1546,31 @@ samtools_0.1.18-3_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 2012-07-27 15:44 ./
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./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 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126583 2012-12-23 05:03 ./usr/share/doc/samtools/examples/ex1.bam
-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 2012-07-27 15:44 ./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 2012-07-27 15:44 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-12-23 05:03 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:44 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:44 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/samtools/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 05:03 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 05:03 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./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
@@ -1533,31 +1583,34 @@ drwxr-xr-x root/root 0 2012-07-27 15:44 ./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 2012-07-27 15:44 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/bin/
--rwxr-xr-x root/root 155204 2012-07-27 15:44 ./usr/bin/bcftools
--rwxr-xr-x root/root 29168 2012-07-27 15:44 ./usr/bin/razip
--rwxr-xr-x root/root 440320 2012-07-27 15:44 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/samtools/
--rwxr-xr-x root/root 17692 2012-07-27 15:44 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12432 2012-07-27 15:44 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9252 2012-07-27 15:44 ./usr/lib/samtools/md5sum-lite
-lrwxrwxrwx root/root 0 2012-07-27 15:44 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_mipsel.deb
+-rwxr-xr-x root/root 5778 2012-12-23 05:03 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/bin/
+-rwxr-xr-x root/root 155204 2012-12-23 05:03 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29168 2012-12-23 05:03 ./usr/bin/razip
+-rwxr-xr-x root/root 440320 2012-12-23 05:03 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17692 2012-12-23 05:03 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12432 2012-12-23 05:03 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9252 2012-12-23 05:03 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2012-12-23 05:03 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165534 bytes: control archive= 922 bytes.
- 675 bytes, 15 lines control
+ size 165950 bytes: control archive= 942 bytes.
+ 713 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 467
@@ -1570,22 +1623,24 @@ libbam-dev_0.1.18-3_mipsel.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/libbam-dev/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./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 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./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 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
--rw-r--r-- root/root 335626 2012-07-27 15:44 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/samtools/
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
+-rw-r--r-- root/root 335698 2012-12-23 05:03 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/samtools/
+-rw-r--r-- root/root 24732 2012-12-23 04:59 ./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
@@ -1603,22 +1658,25 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-94144eca-09d3-4eb1-9fdc-0354750509b2/build/buildd-samtools_0.1.18-3-mipsel-zDspvi
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-3334b19a-a1bc-4c57-a8db-8e6c3252fce1/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libasprintf0c2* libcroco3* libffi5*
- libgettextpo0* libglib2.0-0* libmagic1* libncurses5-dev* libpipeline1*
- libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 24 to remove and 17 not upgraded.
-After this operation, 28.3 MB disk space will be freed.
-(Reading database ... 12379 files and directories currently installed.)
+ bash-completion* cdbs* debhelper* diffstat* file* gettext* gettext-base*
+ groff-base* html2text* intltool-debian* libasprintf-dev* libasprintf0c2*
+ libcroco3* libffi5* libgettextpo-dev* libgettextpo0* libglib2.0-0*
+ libmagic1* libncurses5-dev* libpipeline1* libtinfo-dev* libunistring0*
+ libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 27 to remove and 30 not upgraded.
+After this operation, 29.2 MB disk space will be freed.
+(Reading database ... 12988 files and directories currently installed.)
+Removing bash-completion ...
+Purging configuration files for bash-completion ...
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -1635,6 +1693,7 @@ Removing groff-base ...
Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
+Removing libasprintf-dev:mipsel ...
Removing libasprintf0c2:mipsel ...
Removing libcroco3:mipsel ...
Purging configuration files for libcroco3:mipsel ...
@@ -1642,6 +1701,7 @@ Removing libglib2.0-0:mipsel ...
Purging configuration files for libglib2.0-0:mipsel ...
Removing libffi5:mipsel ...
Purging configuration files for libffi5:mipsel ...
+Removing libgettextpo-dev:mipsel ...
Removing libgettextpo0:mipsel ...
Removing libmagic1:mipsel ...
Purging configuration files for libmagic1:mipsel ...
@@ -1660,19 +1720,19 @@ Removing zlib1g-dev:mipsel ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10956
-Build-Time: 309
+Build-Space: 11016
+Build-Time: 320
Distribution: sid
-Install-Time: 48
-Job: samtools_0.1.18-3
+Install-Time: 54
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 428
-Source-Version: 0.1.18-3
-Space: 10956
+Package-Time: 496
+Source-Version: 0.1.18-4
+Space: 11016
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1545
-Build needed 00:07:08, 10956k disc space
+Finished at 20121223-0504
+Build needed 00:08:16, 11016k disc space
Signature with key '8C9FAB20' requested:
diff --git a/mipsel.log b/mipsel.log
index 92e8f50..eb807a8 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,28 +1,28 @@
-From buildd at mayer.debian.org Fri Jul 27 15:45:41 2012
+From buildd at mayer.debian.org Sun Dec 23 05:04:52 2012
Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+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 mayer.debian.org>)
- id 1SumjU-0005sg-GU
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:40 +0000
+ id 1Tmdk4-0000P2-3B
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:52 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1SumjS-0001vj-Ou
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:39 +0000
+ id 1Tmdk2-0008JB-FH
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:51 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mayer.debian.org>) id 1SumjQ-0000sF-Fd
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:36 +0000
-Date: Fri, 27 Jul 2012 15:45:36 +0000
-Message-Id: <E1SumjQ-0000sF-Fd at mayer.debian.org>
+ (envelope-from <buildd at mayer.debian.org>) id 1Tmdjz-00014d-0i
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:47 +0000
+Date: Sun, 23 Dec 2012 05:04:47 +0000
+Message-Id: <E1Tmdjz-00014d-0i at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-4 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,29 +30,29 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (mipsel) 27 Jul 2012 15:38 ║
+║ samtools 0.1.18-4 (mipsel) 23 Dec 2012 04:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [249 kB]
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org sid InRelease [227 kB]
+Get:2 http://debian.oregonstate.edu sid InRelease [227 kB]
+Get:3 http://debian.oregonstate.edu sid/main Sources [6458 kB]
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org Release [1601 B]
-Get:4 http://debian.oregonstate.edu sid/main Sources [6315 kB]
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Get:5 http://incoming.debian.org Sources [14.5 kB]
-Get:6 http://incoming.debian.org Packages [117 kB]
-Get:7 http://debian.oregonstate.edu sid/contrib Sources [53.9 kB]
-Get:8 http://debian.oregonstate.edu sid/main mipsel Packages [5971 kB]
-Get:9 http://debian.oregonstate.edu sid/contrib mipsel Packages [38.3 kB]
-Fetched 12.8 MB in 35s (359 kB/s)
+Get:4 http://incoming.debian.org Release.gpg [836 B]
+Get:5 http://incoming.debian.org sid/main Sources [6458 kB]
+Get:6 http://debian.oregonstate.edu sid/contrib Sources [53.0 kB]
+Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [6064 kB]
+Get:8 http://incoming.debian.org sid/contrib Sources [53.0 kB]
+Get:9 http://incoming.debian.org sid/main mipsel Packages [6064 kB]
+Get:10 http://debian.oregonstate.edu sid/contrib mipsel Packages [37.1 kB]
+Get:11 http://incoming.debian.org sid/contrib mipsel Packages [37.1 kB]
+Get:12 http://incoming.debian.org Release [1141 B]
+Get:13 http://incoming.debian.org Sources [14.0 kB]
+Get:14 http://incoming.debian.org Packages [118 kB]
+Fetched 25.8 MB in 1min 25s (301 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -73,11 +73,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (350 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (378 kB/s)
Download complete and in download only mode
Check arch
@@ -97,64 +97,66 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.11)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-3)
+bash: already installed (4.2-5)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
+debianutils: already installed (4.3.3)
diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
grep: already installed (2.12-2)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-16)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-28)
-sysvinit: already installed (2.88dsf-28)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
bsdutils: already installed (1:2.20.1-5.1)
mount: already installed (2.20.1-5.1)
util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-37)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
diffstat file gettext gettext-base groff-base html2text intltool-debian
- libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0 libmagic1
- libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ libasprintf-dev libasprintf0c2 libcroco3 libffi5 libgettextpo-dev
+ libgettextpo0 libglib2.0-0 libmagic1 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf
Suggested packages:
devscripts dh-make gettext-doc groff ncurses-doc less www-browser
libmail-box-perl procmail graphviz default-mta mail-transport-agent
@@ -162,53 +164,60 @@ 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 diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0 libxml2
- man-db po-debconf quilt zlib1g-dev
+ bash-completion cdbs debhelper diffstat file gettext gettext-base groff-base
+ html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev
+ libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf quilt
+ zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 24 newly installed, 0 to remove and 17 not upgraded.
-Need to get 0 B/10.2 MB of archives.
-After this operation, 28.3 MB of additional disk space will be used.
+0 upgraded, 27 newly installed, 0 to remove and 30 not upgraded.
+Need to get 0 B/9966 kB of archives.
+After this operation, 29.2 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10891 files and directories currently installed.)
-Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
+(Reading database ... 10942 files and directories currently installed.)
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-1_mipsel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_mipsel.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:mipsel.
-Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
+Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package libmagic1:mipsel.
Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
Selecting previously unselected package libxml2:mipsel.
-Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-5_mipsel.deb) ...
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7_mipsel.deb) ...
Selecting previously unselected package libffi5:mipsel.
Unpacking libffi5:mipsel (from .../libffi5_3.0.10-3_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0:mipsel.
-Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.32.3-1_mipsel.deb) ...
+Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-3_mipsel.deb) ...
Selecting previously unselected package libcroco3:mipsel.
-Unpacking libcroco3:mipsel (from .../libcroco3_0.6.5-1_mipsel.deb) ...
+Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-2_mipsel.deb) ...
Selecting previously unselected package libunistring0:mipsel.
Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
Selecting previously unselected package libgettextpo0:mipsel.
-Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-9_mipsel.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_mipsel.deb) ...
+Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.11-2_mipsel.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_mipsel.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
+Selecting previously unselected package libasprintf-dev:mipsel.
+Unpacking libasprintf-dev:mipsel (from .../libasprintf-dev_0.18.1.1-10_mipsel.deb) ...
+Selecting previously unselected package libgettextpo-dev:mipsel.
+Unpacking libgettextpo-dev:mipsel (from .../libgettextpo-dev_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_mipsel.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
Selecting previously unselected package libtinfo-dev:mipsel.
@@ -219,27 +228,30 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:mipsel.
Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) ...
-Setting up libpipeline1:mipsel (1.2.1-1) ...
-Setting up libasprintf0c2:mipsel (0.18.1.1-9) ...
+Setting up libpipeline1:mipsel (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.3-3) ...
+Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:mipsel (0.18.1.1-10) ...
Setting up libmagic1:mipsel (5.11-2) ...
-Setting up libxml2:mipsel (2.8.0+dfsg1-5) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-7) ...
Setting up libffi5:mipsel (3.0.10-3) ...
-Setting up libglib2.0-0:mipsel (2.32.3-1) ...
+Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:mipsel (0.6.5-1) ...
+Setting up libcroco3:mipsel (0.6.6-2) ...
Setting up libunistring0:mipsel (0.9.3-5) ...
-Setting up libgettextpo0:mipsel (0.18.1.1-9) ...
-Setting up groff-base (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
+Setting up libgettextpo0:mipsel (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:mipsel (0.18.1.1-10) ...
+Setting up libgettextpo-dev:mipsel (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:mipsel (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -249,11 +261,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-4 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-4 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012d-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-14 gcc_4:4.6.3-8 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-16 perl-base_5.14.2-16 perl-modules_5.14.2-16 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -264,15 +276,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -282,7 +295,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
@@ -290,26 +303,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -327,11 +343,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -341,15 +358,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
gcc -c -g -O2 -Wformat -Werror=format-security -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]
@@ -384,8 +404,8 @@ 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 -Wformat -Werror=format-security -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 -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -400,10 +420,10 @@ gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=6
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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
@@ -424,24 +444,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -g -O2 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -463,14 +483,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
gcc -c -g -O2 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -496,7 +516,7 @@ 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_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -505,6 +525,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -531,8 +552,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -555,12 +578,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-mipsel-zDspvi/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -574,28 +597,28 @@ dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is no
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-3_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1545
+Build finished at 20121223-0504
-samtools_0.1.18-3_mipsel.changes:
+samtools_0.1.18-4_mipsel.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
@@ -603,40 +626,51 @@ Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- fbdad8c7b943d06b23a609601851719c79ae8249 528128 samtools_0.1.18-3_mipsel.deb
- 0c31cedee12156cdaf9a3243b6979cdec73f0c43 165534 libbam-dev_0.1.18-3_mipsel.deb
+ e38f3d105ff9aec1e46a1cf7df50d9d690daa854 528822 samtools_0.1.18-4_mipsel.deb
+ e3bac066a176abf71ac601f7cc5b7f6a8115b949 165950 libbam-dev_0.1.18-4_mipsel.deb
Checksums-Sha256:
- 10eff2a972b78b93caaa55f5fc7de3b34299ece6a0741d144d069d7c70ce2170 528128 samtools_0.1.18-3_mipsel.deb
- b2a1d344243fe3d3d9aed637f9f5570911f574b48b3923db3bf28fa67f94276e 165534 libbam-dev_0.1.18-3_mipsel.deb
+ deeeaee3478547fe36bf464cd72db5a97f311564984c636f1d526d583edbf645 528822 samtools_0.1.18-4_mipsel.deb
+ 755ab8c730bd35963f3d8c2ff6d6e4a53e0819099742a8a1d994d1f983628ece 165950 libbam-dev_0.1.18-4_mipsel.deb
Files:
- 366461221d46aa8a679a50c0e0cfe449 528128 science optional samtools_0.1.18-3_mipsel.deb
- 0a5933504f5a307ad579a6a7de287738 165534 libdevel optional libbam-dev_0.1.18-3_mipsel.deb
+ 9654a2be2233c1816ecc00d751ce655c 528822 science optional samtools_0.1.18-4_mipsel.deb
+ 0f8f4860ecf69157bff1f30b8435bf0a 165950 libdevel optional libbam-dev_0.1.18-4_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_mipsel.deb
+samtools_0.1.18-4_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 528128 bytes: control archive= 1760 bytes.
+ size 528822 bytes: control archive= 1809 bytes.
+ 32 bytes, 1 lines conffiles
793 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1106
+ Installed-Size: 1115
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -649,31 +683,31 @@ samtools_0.1.18-3_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 2012-07-27 15:44 ./
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./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 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126583 2012-12-23 05:03 ./usr/share/doc/samtools/examples/ex1.bam
-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 2012-07-27 15:44 ./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 2012-07-27 15:44 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-12-23 05:03 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:44 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:44 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/samtools/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 05:03 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 05:03 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./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
@@ -686,31 +720,34 @@ drwxr-xr-x root/root 0 2012-07-27 15:44 ./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 2012-07-27 15:44 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/bin/
--rwxr-xr-x root/root 155204 2012-07-27 15:44 ./usr/bin/bcftools
--rwxr-xr-x root/root 29168 2012-07-27 15:44 ./usr/bin/razip
--rwxr-xr-x root/root 440320 2012-07-27 15:44 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/samtools/
--rwxr-xr-x root/root 17692 2012-07-27 15:44 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2012-07-27 15:44 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12432 2012-07-27 15:44 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9252 2012-07-27 15:44 ./usr/lib/samtools/md5sum-lite
-lrwxrwxrwx root/root 0 2012-07-27 15:44 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_mipsel.deb
+-rwxr-xr-x root/root 5778 2012-12-23 05:03 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/bin/
+-rwxr-xr-x root/root 155204 2012-12-23 05:03 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29168 2012-12-23 05:03 ./usr/bin/razip
+-rwxr-xr-x root/root 440320 2012-12-23 05:03 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17692 2012-12-23 05:03 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12432 2012-12-23 05:03 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9252 2012-12-23 05:03 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2012-12-23 05:03 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165534 bytes: control archive= 922 bytes.
- 675 bytes, 15 lines control
+ size 165950 bytes: control archive= 942 bytes.
+ 713 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 467
@@ -723,22 +760,24 @@ libbam-dev_0.1.18-3_mipsel.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/share/doc/libbam-dev/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./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 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./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 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/lib/
--rw-r--r-- root/root 335626 2012-07-27 15:44 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:44 ./usr/include/samtools/
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
+-rw-r--r-- root/root 335698 2012-12-23 05:03 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/samtools/
+-rw-r--r-- root/root 24732 2012-12-23 04:59 ./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
@@ -756,22 +795,25 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-94144eca-09d3-4eb1-9fdc-0354750509b2/build/buildd-samtools_0.1.18-3-mipsel-zDspvi
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-3334b19a-a1bc-4c57-a8db-8e6c3252fce1/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
- html2text* intltool-debian* libasprintf0c2* libcroco3* libffi5*
- libgettextpo0* libglib2.0-0* libmagic1* libncurses5-dev* libpipeline1*
- libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 24 to remove and 17 not upgraded.
-After this operation, 28.3 MB disk space will be freed.
-(Reading database ... 12379 files and directories currently installed.)
+ bash-completion* cdbs* debhelper* diffstat* file* gettext* gettext-base*
+ groff-base* html2text* intltool-debian* libasprintf-dev* libasprintf0c2*
+ libcroco3* libffi5* libgettextpo-dev* libgettextpo0* libglib2.0-0*
+ libmagic1* libncurses5-dev* libpipeline1* libtinfo-dev* libunistring0*
+ libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 27 to remove and 30 not upgraded.
+After this operation, 29.2 MB disk space will be freed.
+(Reading database ... 12988 files and directories currently installed.)
+Removing bash-completion ...
+Purging configuration files for bash-completion ...
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -788,6 +830,7 @@ Removing groff-base ...
Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
+Removing libasprintf-dev:mipsel ...
Removing libasprintf0c2:mipsel ...
Removing libcroco3:mipsel ...
Purging configuration files for libcroco3:mipsel ...
@@ -795,6 +838,7 @@ Removing libglib2.0-0:mipsel ...
Purging configuration files for libglib2.0-0:mipsel ...
Removing libffi5:mipsel ...
Purging configuration files for libffi5:mipsel ...
+Removing libgettextpo-dev:mipsel ...
Removing libgettextpo0:mipsel ...
Removing libmagic1:mipsel ...
Purging configuration files for libmagic1:mipsel ...
@@ -813,19 +857,19 @@ Removing zlib1g-dev:mipsel ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10956
-Build-Time: 309
+Build-Space: 11016
+Build-Time: 320
Distribution: sid
-Install-Time: 48
-Job: samtools_0.1.18-3
+Install-Time: 54
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 428
-Source-Version: 0.1.18-3
-Space: 10956
+Package-Time: 496
+Source-Version: 0.1.18-4
+Space: 11016
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1545
-Build needed 00:07:08, 10956k disc space
+Finished at 20121223-0504
+Build needed 00:08:16, 11016k disc space
Signature with key '8C9FAB20' requested:
diff --git a/powerpc.log b/powerpc.log
index de49be6..5324f13 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,62 +1,62 @@
-From buildd at poulenc.debian.org Fri Jul 27 15:43:22 2012
-Return-path: <buildd at poulenc.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at porpora.debian.org Sun Dec 23 04:56:24 2012
+Return-path: <buildd at porpora.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 poulenc.debian.org>)
- id 1SumhF-0005Dv-RK
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:43:21 +0000
-Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
- helo=poulenc.debian.org)
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1Tmdbs-0007LE-7V
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 04:56:24 +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=poulenc.debian.org, EMAIL=hostmaster at poulenc.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at poulenc.debian.org>)
- id 1SumhE-0001pt-RZ; Fri, 27 Jul 2012 15:43:20 +0000
-Received: from buildd by poulenc.debian.org with local (Exim 4.72)
- (envelope-from <buildd at poulenc.debian.org>)
- id 1SumhE-0008KF-Dq; Fri, 27 Jul 2012 15:43:20 +0000
-Message-Id: <E1SumhE-0008KF-Dq at poulenc.debian.org>
+ 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)
+ (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
+ id 1Tmdbr-00082h-58; Sun, 23 Dec 2012 04:56:23 +0000
+Received: from buildd by porpora.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at porpora.debian.org>)
+ id 1Tmdbq-0003nE-9Q; Sun, 23 Dec 2012 04:56:22 +0000
+Message-Id: <E1Tmdbq-0003nE-9Q at porpora.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:43:20 +0000
-From: buildd on poulenc <buildd at poulenc.debian.org>
+Date: Sun, 23 Dec 2012 04:56:22 +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_0.1.18-3 on powerpc (dist=sid)
-Key-Id: 050CE77C
+Subject: Log for successful build of samtools_0.1.18-4 on powerpc (dist=sid)
+Key-Id: EABF3A35
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on poulenc.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on porpora.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (powerpc) 27 Jul 2012 15:40 ║
+║ samtools 0.1.18-4 (powerpc) 23 Dec 2012 04:53 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [249 kB]
-Get:2 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
-Get:3 http://incoming.debian.org unstable InRelease [249 kB]
-Get:4 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
-Get:5 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
-Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [6016 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [227 kB]
+Get:2 http://incoming.debian.org unstable InRelease [227 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6458 kB]
+Get:4 http://ftp.uk.debian.org unstable/contrib Sources [53.0 kB]
+Get:5 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
+Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [6131 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:8 http://ftp.uk.debian.org unstable/contrib powerpc Packages [37.7 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main powerpc Packages [6016 kB]
-Get:12 http://incoming.debian.org unstable/contrib powerpc Packages [37.7 kB]
+Get:7 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:8 http://ftp.uk.debian.org unstable/contrib powerpc Packages [36.8 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main powerpc Packages [6131 kB]
+Get:12 http://incoming.debian.org unstable/contrib powerpc Packages [36.8 kB]
Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.7 MB in 30s (836 kB/s)
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 26.1 MB in 28s (933 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,11 +77,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 2s (144 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (196 kB/s)
Download complete and in download only mode
Check arch
@@ -101,65 +101,66 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 35 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 35 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (6.12)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-2)
+bash: already installed (4.2-5)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.4.3)
-e2fsprogs: already installed (1.42.4-3)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-15)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-27)
-sysvinit: already installed (2.88dsf-27)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-mount: already installed (2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-33)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.20.1-5.2)
+mount: already installed (2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
+libc6-dev: already installed (2.13-36)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.4.3 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
@@ -168,84 +169,94 @@ 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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 28 not upgraded.
-Need to get 10.8 MB of archives.
-After this operation, 28.9 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.1-1 [38.5 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-9 [27.0 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.11-2 [201 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 1:8.30-5 [240 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-5 [851 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.32.3-1 [2044 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.5-1 [143 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-9 [137 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.3 [208 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-9 [1179 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.2-1 [1062 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.11-2 [51.7 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-9 [131 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-9 [1929 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev powerpc 5.9-10 [105 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-10 [211 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.7.dfsg-13 [213 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 35 not upgraded.
+Need to get 10.5 MB of archives.
+After this operation, 29.8 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.2-1 [39.0 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-9 [1179 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.3 [208 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.3-3 [872 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-10 [27.4 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.11-2 [201 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 1:8.31-1 [246 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-7 [852 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.33.12+really2.32.4-3 [1713 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.6-2 [121 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-10 [138 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.11-2 [51.7 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-10 [130 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev powerpc 0.18.1.1-10 [26.9 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev powerpc 0.18.1.1-10 [184 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-10 [1766 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
+Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev powerpc 5.9-10 [105 kB]
+Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-10 [211 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.8 MB in 3s (3574 kB/s)
+Fetched 10.5 MB in 1s (5887 kB/s)
Selecting previously unselected package libpipeline1:powerpc.
-(Reading database ... 10700 files and directories currently installed.)
-Unpacking libpipeline1:powerpc (from .../libpipeline1_1.2.1-1_powerpc.deb) ...
+(Reading database ... 10804 files and directories currently installed.)
+Unpacking libpipeline1:powerpc (from .../libpipeline1_1.2.2-1_powerpc.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_powerpc.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_powerpc.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_powerpc.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:powerpc.
-Unpacking libasprintf0c2:powerpc (from .../libasprintf0c2_0.18.1.1-9_powerpc.deb) ...
+Unpacking libasprintf0c2:powerpc (from .../libasprintf0c2_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package libmagic1:powerpc.
Unpacking libmagic1:powerpc (from .../libmagic1_5.11-2_powerpc.deb) ...
Selecting previously unselected package libpcre3:powerpc.
-Unpacking libpcre3:powerpc (from .../libpcre3_1%3a8.30-5_powerpc.deb) ...
+Unpacking libpcre3:powerpc (from .../libpcre3_1%3a8.31-1_powerpc.deb) ...
Selecting previously unselected package libxml2:powerpc.
-Unpacking libxml2:powerpc (from .../libxml2_2.8.0+dfsg1-5_powerpc.deb) ...
+Unpacking libxml2:powerpc (from .../libxml2_2.8.0+dfsg1-7_powerpc.deb) ...
Selecting previously unselected package libffi5:powerpc.
Unpacking libffi5:powerpc (from .../libffi5_3.0.10-3_powerpc.deb) ...
Selecting previously unselected package libglib2.0-0:powerpc.
-Unpacking libglib2.0-0:powerpc (from .../libglib2.0-0_2.32.3-1_powerpc.deb) ...
+Unpacking libglib2.0-0:powerpc (from .../libglib2.0-0_2.33.12+really2.32.4-3_powerpc.deb) ...
Selecting previously unselected package libcroco3:powerpc.
-Unpacking libcroco3:powerpc (from .../libcroco3_0.6.5-1_powerpc.deb) ...
+Unpacking libcroco3:powerpc (from .../libcroco3_0.6.6-2_powerpc.deb) ...
Selecting previously unselected package libunistring0:powerpc.
Unpacking libunistring0:powerpc (from .../libunistring0_0.9.3-5_powerpc.deb) ...
Selecting previously unselected package libgettextpo0:powerpc.
-Unpacking libgettextpo0:powerpc (from .../libgettextpo0_0.18.1.1-9_powerpc.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_powerpc.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_powerpc.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_powerpc.deb) ...
+Unpacking libgettextpo0:powerpc (from .../libgettextpo0_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.11-2_powerpc.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_powerpc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
+Selecting previously unselected package libasprintf-dev:powerpc.
+Unpacking libasprintf-dev:powerpc (from .../libasprintf-dev_0.18.1.1-10_powerpc.deb) ...
+Selecting previously unselected package libgettextpo-dev:powerpc.
+Unpacking libgettextpo-dev:powerpc (from .../libgettextpo-dev_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_powerpc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_powerpc.deb) ...
Selecting previously unselected package libtinfo-dev:powerpc.
@@ -256,31 +267,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:powerpc.
Unpacking zlib1g-dev:powerpc (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_powerpc.deb) ...
-Setting up libpipeline1:powerpc (1.2.1-1) ...
-Setting up libasprintf0c2:powerpc (0.18.1.1-9) ...
+Setting up libpipeline1:powerpc (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
+Setting up bsdmainutils (9.0.3) ...
+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 man-db (2.6.3-3) ...
+Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:powerpc (0.18.1.1-10) ...
Setting up libmagic1:powerpc (5.11-2) ...
-Setting up libpcre3:powerpc (1:8.30-5) ...
-Setting up libxml2:powerpc (2.8.0+dfsg1-5) ...
+Setting up libpcre3:powerpc (1:8.31-1) ...
+Setting up libxml2:powerpc (2.8.0+dfsg1-7) ...
Setting up libffi5:powerpc (3.0.10-3) ...
-Setting up libglib2.0-0:powerpc (2.32.3-1) ...
+Setting up libglib2.0-0:powerpc (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:powerpc (0.6.5-1) ...
+Setting up libcroco3:powerpc (0.6.6-2) ...
Setting up libunistring0:powerpc (0.9.3-5) ...
-Setting up libgettextpo0:powerpc (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
-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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
+Setting up libgettextpo0:powerpc (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:powerpc (0.18.1.1-10) ...
+Setting up libgettextpo-dev:powerpc (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:powerpc (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -290,11 +304,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 35 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-33 libstdc++6_4.7.1-2 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-2
-Package versions: apt_0.9.6 base-files_6.11 base-passwd_3.5.26 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-2 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.6 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-4 libdpkg-perl_1.16.4.3 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-2 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-2 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-33 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.3p2-1.1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -305,15 +319,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -323,7 +338,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
@@ -331,26 +346,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -368,11 +386,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -382,15 +401,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -425,8 +447,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -441,10 +463,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -465,24 +487,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -504,14 +526,14 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -537,7 +559,7 @@ 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_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -546,6 +568,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -572,8 +595,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -596,12 +621,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -611,73 +636,82 @@ dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_powerpc.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.18-3_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1543
+Build finished at 20121223-0456
-samtools_0.1.18-3_powerpc.changes:
+samtools_0.1.18-4_powerpc.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
+Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
+ .
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- 201aa0d6e1cc27d7bdd24748bec86638e73a77db 513056 samtools_0.1.18-3_powerpc.deb
- 8c590ff0ae64ab17f3590dbaf616af5246ea439f 149972 libbam-dev_0.1.18-3_powerpc.deb
+ 7bb08ccce05f69ee084da8679dccab57311a93ee 514514 samtools_0.1.18-4_powerpc.deb
+ e2f269d69d62772bcc2c66f70580ffef7a4384f2 150306 libbam-dev_0.1.18-4_powerpc.deb
Checksums-Sha256:
- 9dced67a3b8160cbd39cf8f0bb1da3fe7593a9b3596ad8785c26875659004e3c 513056 samtools_0.1.18-3_powerpc.deb
- e7e63cedf73288e26dbe039cdf5f85999412efa73404c856c7090cfcc2b388cf 149972 libbam-dev_0.1.18-3_powerpc.deb
+ 6193e557996e6254ab95be4b513423f5c798324bdaa583039941d7fb8d8c6408 514514 samtools_0.1.18-4_powerpc.deb
+ 86c8d69e99f4aea11551af696ee8bae614459446722c4e4e7f9f9d71983fca62 150306 libbam-dev_0.1.18-4_powerpc.deb
Files:
- 78ad583f99e101926045d97bc30ac0be 513056 science optional samtools_0.1.18-3_powerpc.deb
- f749f74ac053d1d83c8077ae9c3438d1 149972 libdevel optional libbam-dev_0.1.18-3_powerpc.deb
+ 53d98ebf397242f3efd11db5b21a124f 514514 science optional samtools_0.1.18-4_powerpc.deb
+ 40ba965ac8b1fdc393ea53c9a1c2d3ac 150306 libdevel optional libbam-dev_0.1.18-4_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_powerpc.deb
+samtools_0.1.18-4_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 513056 bytes: control archive= 1764 bytes.
+ size 514514 bytes: control archive= 1806 bytes.
+ 32 bytes, 1 lines conffiles
794 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1013
+ Installed-Size: 1022
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -690,68 +724,71 @@ samtools_0.1.18-3_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 2012-07-27 15:43 ./
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2012-07-27 15:43 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2012-07-27 15:43 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/samtools/
--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 5778 2012-07-27 15:43 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/bin/
+-rwxr-xr-x root/root 130976 2012-12-23 04:56 ./usr/bin/bcftools
+-rwxr-xr-x root/root 375144 2012-12-23 04:56 ./usr/bin/samtools
+-rwxr-xr-x root/root 25484 2012-12-23 04:56 ./usr/bin/razip
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./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 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 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5778 2012-12-23 04:56 ./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 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/samtools/
+-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 2012-12-23 04:56 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2012-12-23 04:56 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2012-12-23 04:56 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/samtools/
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 1966 2012-07-27 15:43 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126609 2012-07-27 15:42 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126583 2012-12-23 04:55 ./usr/share/doc/samtools/examples/ex1.bam
+-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 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/samtools/
--rwxr-xr-x root/root 7348 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11080 2012-07-27 15:43 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8036 2012-07-27 15:43 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7348 2012-07-27 15:43 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 18528 2012-07-27 15:43 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/bin/
--rwxr-xr-x root/root 375080 2012-07-27 15:43 ./usr/bin/samtools
--rwxr-xr-x root/root 25484 2012-07-27 15:43 ./usr/bin/razip
--rwxr-xr-x root/root 130976 2012-07-27 15:43 ./usr/bin/bcftools
-lrwxrwxrwx root/root 0 2012-07-27 15:43 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_powerpc.deb
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1966 2012-12-23 04:56 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18528 2012-12-23 04:56 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8036 2012-12-23 04:56 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7348 2012-12-23 04:56 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7348 2012-12-23 04:56 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11080 2012-12-23 04:56 ./usr/lib/samtools/md5fa
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2012-12-23 04:56 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 149972 bytes: control archive= 928 bytes.
- 676 bytes, 15 lines control
+ size 150306 bytes: control archive= 941 bytes.
+ 714 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 409
@@ -764,26 +801,28 @@ libbam-dev_0.1.18-3_powerpc.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/share/doc/libbam-dev/
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./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 5522 2012-12-23 03:33 ./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 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/include/samtools/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/include/samtools/
-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 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./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 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-drwxr-xr-x root/root 0 2012-07-27 15:43 ./usr/lib/
--rw-r--r-- root/root 276222 2012-07-27 15:43 ./usr/lib/libbam.a
+-rw-r--r-- root/root 24732 2012-12-23 04:54 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/lib/
+-rw-r--r-- root/root 276306 2012-12-23 04:56 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -797,7 +836,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-d948fd80-97e7-4ef9-88d6-d6707400a517/build/buildd-samtools_0.1.18-3-powerpc-3qKtFZ
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-28506304-0b95-400a-b3e5-77aab2cbf363/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -805,18 +844,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 10504
-Build-Time: 81
+Build-Space: 10560
+Build-Time: 91
Distribution: sid
-Install-Time: 49
-Job: samtools_0.1.18-3
+Install-Time: 57
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 177
-Source-Version: 0.1.18-3
-Space: 10504
+Package-Time: 192
+Source-Version: 0.1.18-4
+Space: 10560
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1543
-Build needed 00:02:57, 10504k disc space
-Signature with key '050CE77C' requested:
+Finished at 20121223-0456
+Build needed 00:03:12, 10560k disc space
+Signature with key 'EABF3A35' requested:
diff --git a/s390.log b/s390.log
index 26f4ee3..29de407 100644
--- a/s390.log
+++ b/s390.log
@@ -1,61 +1,62 @@
-From buildd at zappa.debian.org Fri Jul 27 15:46:08 2012
-Return-path: <buildd at zappa.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at zemlinsky.debian.org Sun Dec 23 04:58:10 2012
+Return-path: <buildd at zemlinsky.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 zappa.debian.org>)
- id 1Sumjw-00062B-5r
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:46:08 +0000
-Received: from [148.100.96.103] (helo=zappa.debian.org)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1Tmdda-0007ZI-3r
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 04:58:10 +0000
+Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zappa.debian.org, EMAIL=hostmaster at zappa.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zappa.debian.org>)
- id 1Sumju-0001zC-Us; Fri, 27 Jul 2012 15:46:07 +0000
-Received: from buildd by zappa.debian.org with local (Exim 4.72)
- (envelope-from <buildd at zappa.debian.org>)
- id 1Sumjt-0007cl-KT; Fri, 27 Jul 2012 15:46:05 +0000
-Message-Id: <E1Sumjt-0007cl-KT at zappa.debian.org>
+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1TmddZ-00083S-1Z; Sun, 23 Dec 2012 04:58:09 +0000
+Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1TmddY-0007r5-Dr; Sun, 23 Dec 2012 04:58:08 +0000
+Message-Id: <E1TmddY-0007r5-Dr at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:46:05 +0000
-From: buildd on zappa <buildd at zappa.debian.org>
+Date: Sun, 23 Dec 2012 04:58:08 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-3 on s390 (dist=sid)
-Key-Id: 0C4D1E93
+Subject: Log for successful build of samtools_0.1.18-4 on s390 (dist=sid)
+Key-Id: E0AC2C92
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zappa.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (s390) 27 Jul 2012 15:42 ║
+║ samtools 0.1.18-4 (s390) 23 Dec 2012 04:56 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: s390
-Get:1 http://incoming.debian.org unstable InRelease [249 kB]
-Get:2 http://ftp.us.debian.org unstable InRelease [249 kB]
+Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [227 kB]
+Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [6458 kB]
+Get:3 http://incoming.debian.org unstable InRelease [227 kB]
+Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [53.0 kB]
+Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
+Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390 Packages [6028 kB]
Ign http://incoming.debian.org InRelease
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://incoming.debian.org Release [1601 B]
-Get:5 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:6 http://ftp.us.debian.org unstable/main Sources [6315 kB]
-Get:7 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:8 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:9 http://incoming.debian.org unstable/main s390 Packages [5930 kB]
-Get:10 http://incoming.debian.org unstable/contrib s390 Packages [37.5 kB]
-Get:11 http://incoming.debian.org Sources [14.5 kB]
-Get:12 http://incoming.debian.org Packages [117 kB]
-Get:13 http://ftp.us.debian.org unstable/contrib Sources [53.9 kB]
-Get:14 http://ftp.us.debian.org unstable/non-free Sources [98.1 kB]
-Get:15 http://ftp.us.debian.org unstable/main s390 Packages [5930 kB]
-Get:16 http://ftp.us.debian.org unstable/contrib s390 Packages [37.5 kB]
-Fetched 25.5 MB in 53s (476 kB/s)
+Get:7 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:8 http://ftp-stud.hs-esslingen.de unstable/contrib s390 Packages [36.3 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main s390 Packages [6028 kB]
+Get:12 http://incoming.debian.org unstable/contrib s390 Packages [36.3 kB]
+Get:13 http://incoming.debian.org Release.gpg [836 B]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 25.9 MB in 22s (1166 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -73,13 +74,14 @@ Download source files with APT
Reading package lists...
Building dependency tree...
+Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 0s (523 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (313 kB/s)
Download complete and in download only mode
Check arch
@@ -98,28 +100,30 @@ Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 58 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 58 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.11)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-4)
+bash: already installed (4.2-5)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
+debianutils: already installed (4.3.3)
diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
+dpkg: already installed (1.16.8)
+e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-4)
grep: already installed (2.12-2)
gzip: already installed (1.5-1.1)
@@ -129,32 +133,34 @@ ncurses-bin: already installed (5.9-10)
perl-base: already installed (5.14.2-12)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-28)
-sysvinit: already installed (2.88dsf-28)
+sysvinit-utils: already installed (2.88dsf-32)
+sysvinit: already installed (2.88dsf-32)
tar: already installed (1.26-4)
bsdutils: already installed (1:2.20.1-5.1)
mount: already installed (2.20.1-5.1)
util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-34)
+libc6-dev: already installed (2.13-35)
gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
@@ -163,84 +169,94 @@ 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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 14 not upgraded.
-Need to get 11.0 MB of archives.
-After this operation, 29.1 MB of additional disk space will be used.
-Get:1 http://ftp.us.debian.org/debian/ unstable/main libpipeline1 s390 1.2.1-1 [40.0 kB]
-Get:2 http://ftp.us.debian.org/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-9 [26.8 kB]
-Get:3 http://ftp.us.debian.org/debian/ unstable/main libmagic1 s390 5.11-2 [205 kB]
-Get:4 http://ftp.us.debian.org/debian/ unstable/main libpcre3 s390 1:8.30-5 [248 kB]
-Get:5 http://ftp.us.debian.org/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-5 [892 kB]
-Get:6 http://ftp.us.debian.org/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
-Get:7 http://ftp.us.debian.org/debian/ unstable/main libglib2.0-0 s390 2.32.3-1 [2122 kB]
-Get:8 http://ftp.us.debian.org/debian/ unstable/main libcroco3 s390 0.6.5-1 [150 kB]
-Get:9 http://ftp.us.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
-Get:10 http://ftp.us.debian.org/debian/ unstable/main libgettextpo0 s390 0.18.1.1-9 [146 kB]
-Get:11 http://ftp.us.debian.org/debian/ unstable/main bsdmainutils s390 9.0.3 [213 kB]
-Get:12 http://ftp.us.debian.org/debian/ unstable/main groff-base s390 1.21-9 [1148 kB]
-Get:13 http://ftp.us.debian.org/debian/ unstable/main man-db s390 2.6.2-1 [1074 kB]
-Get:14 http://ftp.us.debian.org/debian/ unstable/main file s390 5.11-2 [52.0 kB]
-Get:15 http://ftp.us.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-9 [152 kB]
-Get:16 http://ftp.us.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.us.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:18 http://ftp.us.debian.org/debian/ unstable/main gettext s390 0.18.1.1-9 [1959 kB]
-Get:19 http://ftp.us.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.us.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.us.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.us.debian.org/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
-Get:23 http://ftp.us.debian.org/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
-Get:24 http://ftp.us.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 kB]
-Get:25 http://ftp.us.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.us.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.7.dfsg-13 [215 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 58 not upgraded.
+Need to get 10.7 MB of archives.
+After this operation, 30.1 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390 1.2.2-1 [40.6 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390 1.21-9 [1148 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390 9.0.3 [213 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390 2.6.3-3 [884 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-10 [27.2 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390 5.11-2 [205 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390 1:8.31-1 [253 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-7 [892 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390 2.33.12+really2.32.4-3 [1785 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390 0.6.6-2 [128 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390 0.18.1.1-10 [147 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390 5.11-2 [52.0 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390 0.18.1.1-10 [152 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390 0.18.1.1-10 [27.1 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390 0.18.1.1-10 [182 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390 0.18.1.1-10 [1800 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
+Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.0 MB in 10s (1056 kB/s)
+Fetched 10.7 MB in 1s (5921 kB/s)
Selecting previously unselected package libpipeline1:s390.
-(Reading database ... 10773 files and directories currently installed.)
-Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.1-1_s390.deb) ...
+(Reading database ... 10815 files and directories currently installed.)
+Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.2-1_s390.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_s390.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_s390.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:s390.
-Unpacking libasprintf0c2:s390 (from .../libasprintf0c2_0.18.1.1-9_s390.deb) ...
+Unpacking libasprintf0c2:s390 (from .../libasprintf0c2_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package libmagic1:s390.
Unpacking libmagic1:s390 (from .../libmagic1_5.11-2_s390.deb) ...
Selecting previously unselected package libpcre3:s390.
-Unpacking libpcre3:s390 (from .../libpcre3_1%3a8.30-5_s390.deb) ...
+Unpacking libpcre3:s390 (from .../libpcre3_1%3a8.31-1_s390.deb) ...
Selecting previously unselected package libxml2:s390.
-Unpacking libxml2:s390 (from .../libxml2_2.8.0+dfsg1-5_s390.deb) ...
+Unpacking libxml2:s390 (from .../libxml2_2.8.0+dfsg1-7_s390.deb) ...
Selecting previously unselected package libffi5:s390.
Unpacking libffi5:s390 (from .../libffi5_3.0.10-3_s390.deb) ...
Selecting previously unselected package libglib2.0-0:s390.
-Unpacking libglib2.0-0:s390 (from .../libglib2.0-0_2.32.3-1_s390.deb) ...
+Unpacking libglib2.0-0:s390 (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390.deb) ...
Selecting previously unselected package libcroco3:s390.
-Unpacking libcroco3:s390 (from .../libcroco3_0.6.5-1_s390.deb) ...
+Unpacking libcroco3:s390 (from .../libcroco3_0.6.6-2_s390.deb) ...
Selecting previously unselected package libunistring0:s390.
Unpacking libunistring0:s390 (from .../libunistring0_0.9.3-5_s390.deb) ...
Selecting previously unselected package libgettextpo0:s390.
-Unpacking libgettextpo0:s390 (from .../libgettextpo0_0.18.1.1-9_s390.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_s390.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_s390.deb) ...
+Unpacking libgettextpo0:s390 (from .../libgettextpo0_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.11-2_s390.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
+Selecting previously unselected package libasprintf-dev:s390.
+Unpacking libasprintf-dev:s390 (from .../libasprintf-dev_0.18.1.1-10_s390.deb) ...
+Selecting previously unselected package libgettextpo-dev:s390.
+Unpacking libgettextpo-dev:s390 (from .../libgettextpo-dev_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_s390.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_s390.deb) ...
Selecting previously unselected package libtinfo-dev:s390.
@@ -251,31 +267,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:s390.
Unpacking zlib1g-dev:s390 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390.deb) ...
-Setting up libpipeline1:s390 (1.2.1-1) ...
-Setting up libasprintf0c2:s390 (0.18.1.1-9) ...
-Setting up libmagic1:s390 (5.11-2) ...
-Setting up libpcre3:s390 (1:8.30-5) ...
-Setting up libxml2:s390 (2.8.0+dfsg1-5) ...
-Setting up libffi5:s390 (3.0.10-3) ...
-Setting up libglib2.0-0:s390 (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:s390 (0.6.5-1) ...
-Setting up libunistring0:s390 (0.9.3-5) ...
-Setting up libgettextpo0:s390 (0.18.1.1-9) ...
+Setting up libpipeline1:s390 (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
Setting up bsdmainutils (9.0.3) ...
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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
+Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:s390 (0.18.1.1-10) ...
+Setting up libmagic1:s390 (5.11-2) ...
+Setting up libpcre3:s390 (1:8.31-1) ...
+Setting up libxml2:s390 (2.8.0+dfsg1-7) ...
+Setting up libffi5:s390 (3.0.10-3) ...
+Setting up libglib2.0-0:s390 (2.33.12+really2.32.4-3) ...
+No schema files found: doing nothing.
+Setting up libcroco3:s390 (0.6.6-2) ...
+Setting up libunistring0:s390 (0.9.3-5) ...
+Setting up libgettextpo0:s390 (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:s390 (0.18.1.1-10) ...
+Setting up libgettextpo-dev:s390 (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:s390 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -285,11 +304,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 58 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.2 base-files_6.11 base-passwd_3.5.26 bash_4.2-4 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-5 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.2 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-5 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-5 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
+Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-2 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -300,15 +319,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -318,7 +338,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
@@ -326,26 +346,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/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_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -363,11 +386,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -377,15 +401,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -414,8 +441,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -430,10 +457,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -454,24 +481,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390-vNgSph/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390-vNgSph/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -485,14 +512,14 @@ gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390-vNgSph/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -518,7 +545,7 @@ 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_0.1.18-3-s390-vNgSph/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -527,6 +554,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -553,8 +581,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -577,12 +607,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-s390-vNgSph/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -592,73 +622,82 @@ dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_s390.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-3_s390.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zappa) <buildd_s390x-zappa at buildd.debian.org> >../samtools_0.1.18-3_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_s390.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../samtools_0.1.18-4_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-0.1.18
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1546
+Build finished at 20121223-0458
-samtools_0.1.18-3_s390.changes:
+samtools_0.1.18-4_s390.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Fri, 21 Dec 2012 12:09:18 -0500
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.18-3
+Version: 0.1.18-4
Distribution: sid
Urgency: low
-Maintainer: s390/s390x Build Daemon (zappa) <buildd_s390x-zappa at buildd.debian.org>
+Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
Changed-By: Dominique Belhachemi <domibel 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: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.18-4) unstable; urgency=low
+ .
+ [Charles Plessy]
+ debian/copyright: Normalised with config-model
+ added bash completion
+ Build-depend on Debhelper 9
+ Pass build flaggs set by dpkg-buildflags via Debhelper
+ Moved DOI and PubMed to the Reference namespace
+ Do not compress the example binary alignment file
+ Mention ‘SAMtools’ in libbam-dev's description
+ .
+ [Andreas Tille]
+ debian/upstream: replaced BibTeX entry
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ [Dominique Belhachemi]
+ added patch to fix float tag bug (upstream bug 71)
Checksums-Sha1:
- 74aa8dc71998f8a42c8b5730f792b94475cb662d 529586 samtools_0.1.18-3_s390.deb
- e0b19292c1b93779765175ae1d06a2a7f0d53f12 156030 libbam-dev_0.1.18-3_s390.deb
+ b2d769caeb5b8884842ba76182403fdc4dc9c821 528596 samtools_0.1.18-4_s390.deb
+ 2c66f9597dd415f351e13a1a5c745041ee1cbe63 156368 libbam-dev_0.1.18-4_s390.deb
Checksums-Sha256:
- b9c1ec4654d69578c24bae721ec1a86561fcde67134949adc18b8f20fa8933d6 529586 samtools_0.1.18-3_s390.deb
- 4f61616acf2511127ed0a6a80d3948b88d3b79352d753e8d2245fc393f6d8e80 156030 libbam-dev_0.1.18-3_s390.deb
+ 4f7784b66c2ac85aeb4c3d8835c063dd85621dcee62e179ccd340f96496b9d63 528596 samtools_0.1.18-4_s390.deb
+ 61d0f830db9ff217e0c41071690eed9513f75a2708ef83cde61ae66e0e57e756 156368 libbam-dev_0.1.18-4_s390.deb
Files:
- 0de00d985611b9e54e5e79dd80d363aa 529586 science optional samtools_0.1.18-3_s390.deb
- ae7354bcaa605dc1430e6cc33d386000 156030 libdevel optional libbam-dev_0.1.18-3_s390.deb
+ a72c1363daaa7998ff9cf38f647d2cbb 528596 science optional samtools_0.1.18-4_s390.deb
+ 31be5fb71631d5c3fb84dfa647c93291 156368 libdevel optional libbam-dev_0.1.18-4_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_s390.deb
+samtools_0.1.18-4_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 529586 bytes: control archive= 1762 bytes.
+ size 528596 bytes: control archive= 1811 bytes.
+ 32 bytes, 1 lines conffiles
791 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2450 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1066
+ Installed-Size: 1075
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -671,68 +710,71 @@ samtools_0.1.18-3_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 2012-07-27 15:45 ./
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/bin/
--rwxr-xr-x root/root 27584 2012-07-27 15:45 ./usr/bin/razip
--rwxr-xr-x root/root 416680 2012-07-27 15:45 ./usr/bin/samtools
--rwxr-xr-x root/root 141452 2012-07-27 15:45 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-07-27 15:45 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-07-27 15:45 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2012-07-27 15:45 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2012-12-23 04:58 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./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 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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126583 2012-12-23 04:57 ./usr/share/doc/samtools/examples/ex1.bam
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 126609 2012-07-27 15:45 ./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 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2012-07-27 15:45 ./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 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 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/samtools/
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.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 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 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 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/lib/samtools/
--rwxr-xr-x root/root 11488 2012-07-27 15:45 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7596 2012-07-27 15:45 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8424 2012-07-27 15:45 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 17340 2012-07-27 15:45 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7596 2012-07-27 15:45 ./usr/lib/samtools/maq2sam-long
-lrwxrwxrwx root/root 0 2012-07-27 15:45 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_s390.deb
+-rwxr-xr-x root/root 5778 2012-12-23 04:58 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 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 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-12-23 04:57 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-12-23 04:57 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/bin/
+-rwxr-xr-x root/root 416744 2012-12-23 04:58 ./usr/bin/samtools
+-rwxr-xr-x root/root 141452 2012-12-23 04:58 ./usr/bin/bcftools
+-rwxr-xr-x root/root 27584 2012-12-23 04:58 ./usr/bin/razip
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/lib/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17340 2012-12-23 04:58 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7596 2012-12-23 04:58 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8424 2012-12-23 04:58 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 11488 2012-12-23 04:58 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7596 2012-12-23 04:58 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./etc/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2012-12-23 04:58 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-4_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 156030 bytes: control archive= 925 bytes.
- 673 bytes, 15 lines control
+ size 156368 bytes: control archive= 943 bytes.
+ 711 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.18-4
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 421
@@ -745,26 +787,28 @@ libbam-dev_0.1.18-3_s390.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5522 2012-12-23 03:33 ./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 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/include/samtools/
--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
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/include/
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/include/samtools/
-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 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 24732 2012-12-23 04:57 ./usr/include/samtools/bam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2012-07-27 15:45 ./usr/lib/
--rw-r--r-- root/root 288978 2012-07-27 15:45 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/lib/
+-rw-r--r-- root/root 289042 2012-12-23 04:58 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -778,7 +822,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-ead94a4a-16f2-48ac-80e6-fb156be5d852/build/buildd-samtools_0.1.18-3-s390-vNgSph
+Purging /var/lib/schroot/mount/sid-s390-sbuild-5192ef59-16ac-48fe-9a5f-9585e6c01c45/build/buildd-samtools_0.1.18-4-s390-fy7gJA
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -786,80 +830,80 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 11100
-Build-Time: 135
+Build-Space: 11148
+Build-Time: 60
Distribution: sid
-Install-Time: 27
-Job: samtools_0.1.18-3
+Install-Time: 16
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 228
-Source-Version: 0.1.18-3
-Space: 11100
+Package-Time: 104
+Source-Version: 0.1.18-4
+Space: 11148
Status: successful
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1546
-Build needed 00:03:48, 11100k disc space
-Signature with key '0C4D1E93' requested:
-From buildd at zandonai.debian.org Fri Jul 27 15:45:49 2012
-Return-path: <buildd at zandonai.debian.org>
+Finished at 20121223-0458
+Build needed 00:01:44, 11148k disc space
+Signature with key 'E0AC2C92' requested:
+From buildd at zemlinsky.debian.org Sun Dec 23 04:56:12 2012
+Return-path: <buildd at zemlinsky.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
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+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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+Message-Id: <E1Tmdbe-00075S-0j at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:45:48 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
+Date: Sun, 23 Dec 2012 04:56:09 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-3 on s390x (dist=sid)
-Key-Id: BE1C5586
+Subject: Log for attempted build of samtools_0.1.18-4 on s390x (dist=sid)
+Key-Id: 6A3F7E2B
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (s390x) 27 Jul 2012 15:43 ║
+║ samtools 0.1.18-4 (s390x) 23 Dec 2012 04:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: s390x
-Get:1 http://ftp.de.debian.org unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://ftp.de.debian.org unstable/main Sources [6315 kB]
+Hit http://ftp-stud.hs-esslingen.de unstable InRelease
+Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
+Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
+Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
+Hit http://incoming.debian.org unstable InRelease
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
-Get:5 http://ftp.de.debian.org unstable/contrib Sources [53.9 kB]
-Get:6 http://ftp.de.debian.org unstable/non-free Sources [98.1 kB]
-Get:7 http://ftp.de.debian.org unstable/main s390x Packages [5879 kB]
-Get:8 http://ftp.de.debian.org unstable/contrib s390x Packages [37.0 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:11 http://incoming.debian.org unstable/main s390x Packages [5879 kB]
-Get:12 http://incoming.debian.org unstable/contrib s390x Packages [37.0 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.4 MB in 22s (1140 kB/s)
+Hit http://incoming.debian.org unstable/main Sources
+Hit http://incoming.debian.org unstable/contrib Sources
+Get:2 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Hit http://incoming.debian.org unstable/main s390x Packages
+Hit http://incoming.debian.org unstable/contrib s390x Packages
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1141 B]
+Get:5 http://incoming.debian.org Sources [14.0 kB]
+Get:6 http://incoming.debian.org Packages [118 kB]
+Fetched 337 kB in 1s (176 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -880,11 +924,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (288 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (339 kB/s)
Download complete and in download only mode
Check arch
@@ -904,41 +948,42 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+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 23 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: 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
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+libc6-dev: already installed (2.13-36)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
@@ -947,84 +992,94 @@ 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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 23 not upgraded.
-Need to get 11.1 MB of archives.
-After this operation, 30.7 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-9 [26.8 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390x 1:8.30-5 [254 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-5 [901 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390x 2.32.3-1 [2105 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390x 0.6.5-1 [151 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-9 [158 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main man-db s390x 2.6.2-1 [1069 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390x 0.18.1.1-9 [156 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390x 0.18.1.1-9 [2037 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
-Get:25 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 36 not upgraded.
+Need to get 10.9 MB of archives.
+After this operation, 31.6 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-1 [41.0 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-3 [888 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-10 [27.2 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-1 [259 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7 [901 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-3 [1798 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-2 [129 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-10 [158 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-10 [156 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390x 0.18.1.1-10 [26.8 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390x 0.18.1.1-10 [195 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-10 [1864 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
+Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.1 MB in 5s (2127 kB/s)
+Fetched 10.9 MB in 1s (10.9 MB/s)
Selecting previously unselected package libpipeline1:s390x.
-(Reading database ... 10787 files and directories currently installed.)
-Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.1-1_s390x.deb) ...
+(Reading database ... 10867 files and directories currently installed.)
+Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-1_s390x.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_s390x.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:s390x.
-Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-9_s390x.deb) ...
+Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package libmagic1:s390x.
Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
Selecting previously unselected package libpcre3:s390x.
-Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.30-5_s390x.deb) ...
+Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-1_s390x.deb) ...
Selecting previously unselected package libxml2:s390x.
-Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-5_s390x.deb) ...
+Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-7_s390x.deb) ...
Selecting previously unselected package libffi5:s390x.
Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
Selecting previously unselected package libglib2.0-0:s390x.
-Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.32.3-1_s390x.deb) ...
+Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390x.deb) ...
Selecting previously unselected package libcroco3:s390x.
-Unpacking libcroco3:s390x (from .../libcroco3_0.6.5-1_s390x.deb) ...
+Unpacking libcroco3:s390x (from .../libcroco3_0.6.6-2_s390x.deb) ...
Selecting previously unselected package libunistring0:s390x.
Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
Selecting previously unselected package libgettextpo0:s390x.
-Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_s390x.deb) ...
+Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390x.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
+Selecting previously unselected package libasprintf-dev:s390x.
+Unpacking libasprintf-dev:s390x (from .../libasprintf-dev_0.18.1.1-10_s390x.deb) ...
+Selecting previously unselected package libgettextpo-dev:s390x.
+Unpacking libgettextpo-dev:s390x (from .../libgettextpo-dev_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_s390x.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
Selecting previously unselected package libtinfo-dev:s390x.
@@ -1035,548 +1090,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:s390x.
Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
-Setting up libpipeline1:s390x (1.2.1-1) ...
-Setting up libasprintf0c2:s390x (0.18.1.1-9) ...
-Setting up libmagic1:s390x (5.11-2) ...
-Setting up libpcre3:s390x (1:8.30-5) ...
-Setting up libxml2:s390x (2.8.0+dfsg1-5) ...
-Setting up libffi5:s390x (3.0.10-3+b1) ...
-Setting up libglib2.0-0:s390x (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:s390x (0.6.5-1) ...
-Setting up libunistring0:s390x (0.9.3-5+b1) ...
-Setting up libgettextpo0:s390x (0.18.1.1-9) ...
+Setting up libpipeline1:s390x (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
Setting up bsdmainutils (9.0.3) ...
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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
+Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
-Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up gettext (0.18.1.1-9) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:s390x (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
-Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
- dpkg-source --before-build samtools-0.1.18
-dpkg-buildpackage: host architecture s390x
- 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-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-arch
-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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
-seqtk.c: In function 'stk_comp':
-seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-8JKR6G/samtools-0.1.18'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-make[1]: *** [ex1f.bam] Killed
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-8JKR6G/samtools-0.1.18/examples'
-make: *** [debian/stamp-makefile-check] Error 2
-dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1545
-FAILED [dpkg-buildpackage died]
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-80ba5657-d6f5-4ca2-931a-cbd3940fc021/sid-s390x-sbuild/build/buildd-samtools_0.1.18-3-s390x-8JKR6G
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: s390x
-Build-Space: 9780
-Build-Time: 109
-Distribution: sid
-Fail-Stage: build
-Install-Time: 11
-Job: samtools_0.1.18-3
-Package: samtools
-Package-Time: 154
-Source-Version: 0.1.18-3
-Space: 9780
-Status: attempted
-Version: 0.1.18-3
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1545
-Build needed 00:02:34, 9780k disc space
-From buildd at zandonai.debian.org Wed Aug 29 03:08:35 2012
-Return-path: <buildd at zandonai.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
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- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
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-Message-Id: <E1T6Ydu-0003zo-1b at zandonai.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Wed, 29 Aug 2012 03:08:33 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-3 on s390x (dist=sid)
-Key-Id: BE1C5586
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (s390x) 29 Aug 2012 03:06 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
-Architecture: s390x
-Get:1 http://ftp.de.debian.org unstable InRelease [257 kB]
-Get:2 http://incoming.debian.org unstable InRelease [257 kB]
-Hit http://ftp.de.debian.org unstable/main Sources
-Hit http://ftp.de.debian.org unstable/contrib Sources
-Hit http://ftp.de.debian.org unstable/non-free Sources
-Hit http://ftp.de.debian.org unstable/main s390x Packages
-Hit http://ftp.de.debian.org unstable/contrib s390x Packages
-Ign http://incoming.debian.org InRelease
-Get:3 http://incoming.debian.org unstable/main Sources [6331 kB]
-Get:4 http://incoming.debian.org unstable/contrib Sources [53.6 kB]
-Get:5 http://incoming.debian.org unstable/non-free Sources [99.4 kB]
-Get:6 http://incoming.debian.org unstable/main s390x Packages [5891 kB]
-Get:7 http://incoming.debian.org unstable/contrib s390x Packages [36.8 kB]
-Get:8 http://incoming.debian.org Release.gpg [836 B]
-Get:9 http://incoming.debian.org Release [1141 B]
-Get:10 http://incoming.debian.org Sources [23.8 kB]
-Get:11 http://incoming.debian.org Packages [284 kB]
-Fetched 13.2 MB in 24s (537 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 390 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 0s (849 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5+b1)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: 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...
-libc6-dev: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120608
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev 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 procmail graphviz default-mta
- mail-transport-agent
-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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 38 not upgraded.
-Need to get 11.1 MB of archives.
-After this operation, 30.7 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390x 1.2.1-1 [40.5 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-9 [26.8 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390x 1:8.30-5 [254 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-5 [901 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390x 2.32.3-1 [2105 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390x 0.6.5-1 [151 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-9 [158 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main man-db s390x 2.6.2-1 [1069 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390x 0.18.1.1-9 [156 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.117 [79.9 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390x 0.18.1.1-9 [2037 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
-Get:25 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.1 MB in 6s (1846 kB/s)
-Selecting previously unselected package libpipeline1:s390x.
-(Reading database ... 10787 files and directories currently installed.)
-Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.1-1_s390x.deb) ...
-Selecting previously unselected package libasprintf0c2:s390x.
-Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package libmagic1:s390x.
-Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
-Selecting previously unselected package libpcre3:s390x.
-Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.30-5_s390x.deb) ...
-Selecting previously unselected package libxml2:s390x.
-Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-5_s390x.deb) ...
-Selecting previously unselected package libffi5:s390x.
-Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
-Selecting previously unselected package libglib2.0-0:s390x.
-Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.32.3-1_s390x.deb) ...
-Selecting previously unselected package libcroco3:s390x.
-Unpacking libcroco3:s390x (from .../libcroco3_0.6.5-1_s390x.deb) ...
-Selecting previously unselected package libunistring0:s390x.
-Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
-Selecting previously unselected package libgettextpo0:s390x.
-Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_s390x.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.117_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_s390x.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
-Selecting previously unselected package libtinfo-dev:s390x.
-Unpacking libtinfo-dev:s390x (from .../libtinfo-dev_5.9-10_s390x.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_s390x.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
-Selecting previously unselected package zlib1g-dev:s390x.
-Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
-Setting up libpipeline1:s390x (1.2.1-1) ...
-Setting up libasprintf0c2:s390x (0.18.1.1-9) ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:s390x (0.18.1.1-10) ...
Setting up libmagic1:s390x (5.11-2) ...
-Setting up libpcre3:s390x (1:8.30-5) ...
-Setting up libxml2:s390x (2.8.0+dfsg1-5) ...
+Setting up libpcre3:s390x (1:8.31-1) ...
+Setting up libxml2:s390x (2.8.0+dfsg1-7) ...
Setting up libffi5:s390x (3.0.10-3+b1) ...
-Setting up libglib2.0-0:s390x (2.32.3-1) ...
+Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:s390x (0.6.5-1) ...
+Setting up libcroco3:s390x (0.6.6-2) ...
Setting up libunistring0:s390x (0.9.3-5+b1) ...
-Setting up libgettextpo0:s390x (0.18.1.1-9) ...
-Setting up bsdmainutils (9.0.3) ...
-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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
-Building database of manual pages ...
+Setting up libgettextpo0:s390x (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.117) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15+b1) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:s390x (0.18.1.1-10) ...
+Setting up libgettextpo-dev:s390x (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:s390x (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -1586,11 +1127,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 38 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-3 cdbs_0.4.117 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debconf-i18n_1.5.45 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8+b1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.20-1 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-34 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1601,15 +1142,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -1619,7 +1161,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture s390x
fakeroot debian/rules clean
@@ -1627,26 +1169,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/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_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -1664,11 +1209,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -1678,15 +1224,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -1715,8 +1264,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -1731,10 +1280,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -1755,24 +1304,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -1786,14 +1335,14 @@ gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-s
seqtk.c: In function 'stk_comp':
seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-s390x-mBlLZO/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1805,14 +1354,14 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtoo
(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
make[1]: *** [ex1f.bam] Killed
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-s390x-mBlLZO/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120829-0308
+Build finished at 20121223-0456
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-fcd0e2de-81bc-415a-8d68-06cb3cc50741/sid-s390x-sbuild/build/buildd-samtools_0.1.18-3-s390x-mBlLZO
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-87753949-4301-408f-ad75-3e402223fe91/build/buildd-samtools_0.1.18-4-s390x-3fMAMA
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1820,18 +1369,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 9780
-Build-Time: 67
+Build-Space: 9652
+Build-Time: 70
Distribution: sid
Fail-Stage: build
-Install-Time: 11
-Job: samtools_0.1.18-3
+Install-Time: 15
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 113
-Source-Version: 0.1.18-3
-Space: 9780
+Package-Time: 94
+Source-Version: 0.1.18-4
+Space: 9652
Status: attempted
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120829-0308
-Build needed 00:01:53, 9780k disc space
+Finished at 20121223-0456
+Build needed 00:01:34, 9652k disc space
diff --git a/s390x.log b/s390x.log
index e69de29..8ed5856 100644
--- a/s390x.log
+++ b/s390x.log
@@ -0,0 +1,539 @@
+From buildd at zemlinsky.debian.org Sun Dec 23 04:56:12 2012
+Return-path: <buildd at zemlinsky.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 zemlinsky.debian.org>)
+ id 1Tmdbg-0007GK-Cf
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 04:56:12 +0000
+Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=zemlinsky.debian.org,
+ EMAIL=hostmaster at zemlinsky.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1Tmdbf-0007z3-9r; Sun, 23 Dec 2012 04:56:11 +0000
+Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1Tmdbe-00075S-0j; Sun, 23 Dec 2012 04:56:10 +0000
+Message-Id: <E1Tmdbe-00075S-0j at zemlinsky.debian.org>
+MIME-Version: 1.0
+Content-Transfer-Encoding: binary
+X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
+Date: Sun, 23 Dec 2012 04:56:09 +0000
+From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
+To: phil+buildd at philkern.de,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.18-4 on s390x (dist=sid)
+Key-Id: 6A3F7E2B
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 0.1.18-4 (s390x) 23 Dec 2012 04:54 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.18-4
+Source Version: 0.1.18-4
+Architecture: s390x
+Hit http://ftp-stud.hs-esslingen.de unstable InRelease
+Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
+Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
+Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
+Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
+Hit http://incoming.debian.org unstable InRelease
+Ign http://incoming.debian.org InRelease
+Hit http://incoming.debian.org unstable/main Sources
+Hit http://incoming.debian.org unstable/contrib Sources
+Get:2 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Hit http://incoming.debian.org unstable/main s390x Packages
+Hit http://incoming.debian.org unstable/contrib s390x Packages
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1141 B]
+Get:5 http://incoming.debian.org Sources [14.0 kB]
+Get:6 http://incoming.debian.org Packages [118 kB]
+Fetched 337 kB in 1s (176 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://git.debian.org/debian-med/samtools.git
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (339 kB/s)
+Download complete and in download only mode
+
+Check arch
+──────────
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: build-essential, fakeroot
+Checking for already installed dependencies...
+build-essential: already installed (11.5+b1)
+fakeroot: already installed (1.18.4-2)
+Checking for dependency conflicts...
+Installing positive dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Checking for already installed dependencies...
+libc6-dev: already installed (2.13-36)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+debhelper: missing
+Using default version 9.20120909
+bash-completion: missing
+cdbs: missing
+quilt: missing
+libncurses5-dev: missing
+zlib1g-dev: missing
+Checking for dependency conflicts...
+Installing positive dependencies: debhelper bash-completion 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 libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
+ mail-transport-agent
+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:
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 36 not upgraded.
+Need to get 10.9 MB of archives.
+After this operation, 31.6 MB of additional disk space will be used.
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-1 [41.0 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
+Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-3 [888 kB]
+Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-10 [27.2 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-1 [259 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7 [901 kB]
+Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-3 [1798 kB]
+Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-2 [129 kB]
+Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
+Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-10 [158 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
+Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-10 [156 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
+Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390x 0.18.1.1-10 [26.8 kB]
+Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390x 0.18.1.1-10 [195 kB]
+Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-10 [1864 kB]
+Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
+Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
+Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 10.9 MB in 1s (10.9 MB/s)
+Selecting previously unselected package libpipeline1:s390x.
+(Reading database ... 10867 files and directories currently installed.)
+Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-1_s390x.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_s390x.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
+Selecting previously unselected package libasprintf0c2:s390x.
+Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-10_s390x.deb) ...
+Selecting previously unselected package libmagic1:s390x.
+Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
+Selecting previously unselected package libpcre3:s390x.
+Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-1_s390x.deb) ...
+Selecting previously unselected package libxml2:s390x.
+Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-7_s390x.deb) ...
+Selecting previously unselected package libffi5:s390x.
+Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
+Selecting previously unselected package libglib2.0-0:s390x.
+Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390x.deb) ...
+Selecting previously unselected package libcroco3:s390x.
+Unpacking libcroco3:s390x (from .../libcroco3_0.6.6-2_s390x.deb) ...
+Selecting previously unselected package libunistring0:s390x.
+Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
+Selecting previously unselected package libgettextpo0:s390x.
+Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-10_s390x.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390x.deb) ...
+Selecting previously unselected package cdbs.
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
+Selecting previously unselected package libasprintf-dev:s390x.
+Unpacking libasprintf-dev:s390x (from .../libasprintf-dev_0.18.1.1-10_s390x.deb) ...
+Selecting previously unselected package libgettextpo-dev:s390x.
+Unpacking libgettextpo-dev:s390x (from .../libgettextpo-dev_0.18.1.1-10_s390x.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-10_s390x.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
+Selecting previously unselected package libtinfo-dev:s390x.
+Unpacking libtinfo-dev:s390x (from .../libtinfo-dev_5.9-10_s390x.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_s390x.deb) ...
+Selecting previously unselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev:s390x.
+Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
+Setting up libpipeline1:s390x (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
+Setting up bsdmainutils (9.0.3) ...
+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 man-db (2.6.3-3) ...
+Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:s390x (0.18.1.1-10) ...
+Setting up libmagic1:s390x (5.11-2) ...
+Setting up libpcre3:s390x (1:8.31-1) ...
+Setting up libxml2:s390x (2.8.0+dfsg1-7) ...
+Setting up libffi5:s390x (3.0.10-3+b1) ...
+Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-3) ...
+No schema files found: doing nothing.
+Setting up libcroco3:s390x (0.6.6-2) ...
+Setting up libunistring0:s390x (0.9.3-5+b1) ...
+Setting up libgettextpo0:s390x (0.18.1.1-10) ...
+Setting up file (5.11-2) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
+Setting up html2text (1.3.2a-15+b1) ...
+Setting up libasprintf-dev:s390x (0.18.1.1-10) ...
+Setting up libgettextpo-dev:s390x (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120909) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:s390x (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 2.6.32-5-s390x s390x (s390x)
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.20-1 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-34 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
+
+Check disc space
+────────────────
+
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 0.1.18-4
+ dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: host architecture s390x
+ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+rm -f debian/stamp-makefile-check
+dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
+Removing patch fix_coverage_cap.patch
+Restoring bam2depth.c
+
+Removing patch fix_segfault_with_small_ref.patch
+Restoring bam_plcmd.c
+
+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-arch
+test -x debian/rules
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch no-pileup-tests.patch
+patching file examples/Makefile
+
+Applying patch fix_segfault_with_small_ref.patch
+patching file bam_plcmd.c
+
+Applying patch fix_coverage_cap.patch
+patching file bam2depth.c
+
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+em.c: In function 'bcf_em1':
+em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+touch debian/stamp-makefile-build
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
+../samtools faidx ex1.fa
+../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
+[sam_header_read2] 2 sequences loaded.
+../samtools index ex1.bam
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
+[samopen] SAM header is present: 2 sequences.
+../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
+[samopen] SAM header is present: 2 sequences.
+(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
+../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
+make[1]: *** [ex1f.bam] Killed
+make: *** [debian/stamp-makefile-check] Error 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20121223-0456
+FAILED [dpkg-buildpackage died]
+────────────────────────────────────────────────────────────────────────────────
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-87753949-4301-408f-ad75-3e402223fe91/build/buildd-samtools_0.1.18-4-s390x-3fMAMA
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: s390x
+Build-Space: 9652
+Build-Time: 70
+Distribution: sid
+Fail-Stage: build
+Install-Time: 15
+Job: samtools_0.1.18-4
+Package: samtools
+Package-Time: 94
+Source-Version: 0.1.18-4
+Space: 9652
+Status: attempted
+Version: 0.1.18-4
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20121223-0456
+Build needed 00:01:34, 9652k disc space
diff --git a/sparc.log b/sparc.log
index 93377c3..a06fa21 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,62 +1,62 @@
-From buildd at lebrun.debian.org Fri Jul 27 15:45:27 2012
+From buildd at lebrun.debian.org Sun Dec 23 05:00:21 2012
Return-path: <buildd at lebrun.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+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 1SumjH-0005oK-6F
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:27 +0000
+ id 1Tmdfg-000816-Qb
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:00:20 +0000
Received: from [2001:b68:ff:5:203:baff:fe59:abad] (helo=lebrun.debian.org)
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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)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1SumjG-0001sq-3e
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:45:26 +0000
+ id 1Tmdff-00084R-SU
+ for logs at buildd.debian.org; Sun, 23 Dec 2012 05:00:19 +0000
Received: from buildd by lebrun.debian.org with local (Exim 4.72)
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-Message-Id: <E1SumjE-0002pT-2f at lebrun.debian.org>
+ id 1Tmdfe-0001kg-3i; Sun, 23 Dec 2012 05:00:18 +0000
+Message-Id: <E1Tmdfe-0001kg-3i at lebrun.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Fri, 27 Jul 2012 15:45:23 +0000
+Date: Sun, 23 Dec 2012 05:00:17 +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_0.1.18-3 on sparc (dist=sid)
+Subject: Log for attempted build of samtools_0.1.18-4 on sparc (dist=sid)
Key-Id: E1D842D6
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-3 (sparc) 27 Jul 2012 15:40 ║
+║ samtools 0.1.18-4 (sparc) 23 Dec 2012 04:55 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.18-4
+Source Version: 0.1.18-4
Architecture: sparc
-Get:1 http://debian.carnet.hr unstable InRelease [249 kB]
-Get:2 http://incoming.debian.org unstable InRelease [249 kB]
-Get:3 http://debian.carnet.hr unstable/main Sources [6315 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [227 kB]
+Get:2 http://incoming.debian.org unstable InRelease [227 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [6458 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 [6315 kB]
-Get:6 http://debian.carnet.hr unstable/contrib Sources [53.9 kB]
-Get:7 http://debian.carnet.hr unstable/non-free Sources [98.1 kB]
-Get:8 http://debian.carnet.hr unstable/main sparc Packages [5980 kB]
-Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [37.8 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [98.1 kB]
-Get:12 http://incoming.debian.org unstable/main sparc Packages [5980 kB]
-Get:13 http://incoming.debian.org unstable/contrib sparc Packages [37.8 kB]
-Get:14 http://incoming.debian.org Release [1601 B]
-Get:15 http://incoming.debian.org Sources [14.5 kB]
-Get:16 http://incoming.debian.org Packages [117 kB]
-Fetched 25.6 MB in 59s (431 kB/s)
+Get:5 http://incoming.debian.org unstable/main Sources [6458 kB]
+Get:6 http://debian.carnet.hr unstable/contrib Sources [53.0 kB]
+Get:7 http://debian.carnet.hr unstable/non-free Sources [101 kB]
+Get:8 http://debian.carnet.hr unstable/main sparc Packages [6099 kB]
+Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [36.6 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:12 http://incoming.debian.org unstable/main sparc Packages [6099 kB]
+Get:13 http://incoming.debian.org unstable/contrib sparc Packages [36.6 kB]
+Get:14 http://incoming.debian.org Release [1141 B]
+Get:15 http://incoming.debian.org Sources [14.0 kB]
+Get:16 http://incoming.debian.org Packages [118 kB]
+Fetched 26.1 MB in 59s (435 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -77,11 +77,11 @@ 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 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (261 kB/s)
+Need to get 391 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
+Fetched 391 kB in 1s (256 kB/s)
Download complete and in download only mode
Check arch
@@ -101,66 +101,67 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 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, quilt, 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (6.12)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-3)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2-5)
+coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
hostname: already installed (3.11)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-15)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-28)
-sysvinit: already installed (2.88dsf-28)
+sysvinit-utils: already installed (2.88dsf-34)
+sysvinit: already installed (2.88dsf-34)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-mount: already installed (2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-34)
-libc6-dev-sparc64: already installed (2.13-34)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+bsdutils: already installed (1:2.20.1-5.2)
+mount: already installed (2.20.1-5.2)
+util-linux: already installed (2.20.1-5.2)
+libc6-dev: already installed (2.13-37)
+libc6-dev-sparc64: already installed (2.13-37)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion 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 libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev 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 procmail graphviz default-mta
@@ -169,84 +170,94 @@ 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 diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 25 not upgraded.
-Need to get 10.5 MB of archives.
-After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.1-1 [35.8 kB]
-Get:2 http://debian.carnet.hr/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-9 [26.5 kB]
-Get:3 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.11-2 [197 kB]
-Get:4 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 1:8.30-5 [246 kB]
-Get:5 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-5 [826 kB]
-Get:6 http://debian.carnet.hr/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
-Get:7 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.32.3-1 [1926 kB]
-Get:8 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.5-1 [135 kB]
-Get:9 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:10 http://debian.carnet.hr/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-9 [129 kB]
-Get:11 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 9.0.3 [206 kB]
-Get:12 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-9 [1133 kB]
-Get:13 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.2-1 [1032 kB]
-Get:14 http://debian.carnet.hr/debian/ unstable/main file sparc 5.11-2 [51.1 kB]
-Get:15 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-9 [148 kB]
-Get:16 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
-Get:17 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:18 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-9 [1893 kB]
-Get:19 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:20 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:21 http://debian.carnet.hr/debian/ unstable/main debhelper all 9.20120608 [700 kB]
-Get:22 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
-Get:23 http://debian.carnet.hr/debian/ unstable/main libtinfo-dev sparc 5.9-10 [97.5 kB]
-Get:24 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-10 [204 kB]
-Get:25 http://debian.carnet.hr/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:26 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.7.dfsg-13 [211 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 20 not upgraded.
+Need to get 10.3 MB of archives.
+After this operation, 29.2 MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.2-1 [36.2 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-9 [1133 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 9.0.3 [206 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.3-3 [865 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-10 [26.9 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.11-2 [197 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 1:8.31-1 [252 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-7 [826 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.33.12+really2.32.4-3 [1645 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.6-2 [114 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-10 [130 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main file sparc 5.11-2 [51.1 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-10 [148 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:19 http://debian.carnet.hr/debian/ unstable/main libasprintf-dev sparc 0.18.1.1-10 [26.6 kB]
+Get:20 http://debian.carnet.hr/debian/ unstable/main libgettextpo-dev sparc 0.18.1.1-10 [172 kB]
+Get:21 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-10 [1745 kB]
+Get:22 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://debian.carnet.hr/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
+Get:26 http://debian.carnet.hr/debian/ unstable/main libtinfo-dev sparc 5.9-10 [97.5 kB]
+Get:27 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-10 [204 kB]
+Get:28 http://debian.carnet.hr/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.5 MB in 10s (1006 kB/s)
+Fetched 10.3 MB in 11s (876 kB/s)
Selecting previously unselected package libpipeline1:sparc.
-(Reading database ... 11055 files and directories currently installed.)
-Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.1-1_sparc.deb) ...
+(Reading database ... 11141 files and directories currently installed.)
+Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.2-1_sparc.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_sparc.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_sparc.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_sparc.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:sparc.
-Unpacking libasprintf0c2:sparc (from .../libasprintf0c2_0.18.1.1-9_sparc.deb) ...
+Unpacking libasprintf0c2:sparc (from .../libasprintf0c2_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package libmagic1:sparc.
Unpacking libmagic1:sparc (from .../libmagic1_5.11-2_sparc.deb) ...
Selecting previously unselected package libpcre3:sparc.
-Unpacking libpcre3:sparc (from .../libpcre3_1%3a8.30-5_sparc.deb) ...
+Unpacking libpcre3:sparc (from .../libpcre3_1%3a8.31-1_sparc.deb) ...
Selecting previously unselected package libxml2:sparc.
-Unpacking libxml2:sparc (from .../libxml2_2.8.0+dfsg1-5_sparc.deb) ...
+Unpacking libxml2:sparc (from .../libxml2_2.8.0+dfsg1-7_sparc.deb) ...
Selecting previously unselected package libffi5:sparc.
Unpacking libffi5:sparc (from .../libffi5_3.0.10-3_sparc.deb) ...
Selecting previously unselected package libglib2.0-0:sparc.
-Unpacking libglib2.0-0:sparc (from .../libglib2.0-0_2.32.3-1_sparc.deb) ...
+Unpacking libglib2.0-0:sparc (from .../libglib2.0-0_2.33.12+really2.32.4-3_sparc.deb) ...
Selecting previously unselected package libcroco3:sparc.
-Unpacking libcroco3:sparc (from .../libcroco3_0.6.5-1_sparc.deb) ...
+Unpacking libcroco3:sparc (from .../libcroco3_0.6.6-2_sparc.deb) ...
Selecting previously unselected package libunistring0:sparc.
Unpacking libunistring0:sparc (from .../libunistring0_0.9.3-5_sparc.deb) ...
Selecting previously unselected package libgettextpo0:sparc.
-Unpacking libgettextpo0:sparc (from .../libgettextpo0_0.18.1.1-9_sparc.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_sparc.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_sparc.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.2-1_sparc.deb) ...
+Unpacking libgettextpo0:sparc (from .../libgettextpo0_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../archives/file_5.11-2_sparc.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_sparc.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
+Selecting previously unselected package libasprintf-dev:sparc.
+Unpacking libasprintf-dev:sparc (from .../libasprintf-dev_0.18.1.1-10_sparc.deb) ...
+Selecting previously unselected package libgettextpo-dev:sparc.
+Unpacking libgettextpo-dev:sparc (from .../libgettextpo-dev_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_sparc.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_sparc.deb) ...
Selecting previously unselected package libtinfo-dev:sparc.
@@ -257,31 +268,34 @@ Selecting previously unselected package quilt.
Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
Selecting previously unselected package zlib1g-dev:sparc.
Unpacking zlib1g-dev:sparc (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_sparc.deb) ...
-Setting up libpipeline1:sparc (1.2.1-1) ...
-Setting up libasprintf0c2:sparc (0.18.1.1-9) ...
-Setting up libmagic1:sparc (5.11-2) ...
-Setting up libpcre3:sparc (1:8.30-5) ...
-Setting up libxml2:sparc (2.8.0+dfsg1-5) ...
-Setting up libffi5:sparc (3.0.10-3) ...
-Setting up libglib2.0-0:sparc (2.32.3-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:sparc (0.6.5-1) ...
-Setting up libunistring0:sparc (0.9.3-5) ...
-Setting up libgettextpo0:sparc (0.18.1.1-9) ...
+Setting up libpipeline1:sparc (1.2.2-1) ...
+Setting up groff-base (1.21-9) ...
Setting up bsdmainutils (9.0.3) ...
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 (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
+Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:sparc (0.18.1.1-10) ...
+Setting up libmagic1:sparc (5.11-2) ...
+Setting up libpcre3:sparc (1:8.31-1) ...
+Setting up libxml2:sparc (2.8.0+dfsg1-7) ...
+Setting up libffi5:sparc (3.0.10-3) ...
+Setting up libglib2.0-0:sparc (2.33.12+really2.32.4-3) ...
+No schema files found: doing nothing.
+Setting up libcroco3:sparc (0.6.6-2) ...
+Setting up libunistring0:sparc (0.9.3-5) ...
+Setting up libgettextpo0:sparc (0.18.1.1-10) ...
Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.119) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:sparc (0.18.1.1-10) ...
+Setting up libgettextpo-dev:sparc (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:sparc (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
@@ -291,11 +305,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.6_4.6.3-8 gcc-4.6_4.6.3-8 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 binutils_2.22-7 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-3 cdbs_0.4.116 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-8 dash_0.5.7-3 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.2 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.7 dpkg-dev_1.16.7 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-8 gcc_4:4.6.3-7 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.1 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libc6-dev-sparc64_2.13-34 libc6-sparc64_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-3 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-3 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libss2_1.42.4-3 libstdc++6_4.7.1-3 libstdc++6-4.6-dev_4.6.3-8 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-5 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 tzdata_2012c-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.32-1
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-14 gcc_4:4.6.3-8 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-34 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libc6-dev-sparc64_2.13-37 libc6-sparc64_2.13-37 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -306,15 +320,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
dpkg-source: info: extracting samtools in samtools-0.1.18
dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
+dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -324,7 +339,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
+dpkg-buildpackage: source version 0.1.18-4
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
@@ -332,26 +347,29 @@ test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
+Removing patch fix_float_tag.patch
+Restoring bam.h
+
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -369,11 +387,12 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
@@ -383,15 +402,18 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Now at patch fix_coverage_cap.patch
+Applying patch fix_float_tag.patch
+patching file bam.h
+
+Now at patch fix_float_tag.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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]
@@ -426,8 +448,8 @@ 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -442,10 +464,10 @@ gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=forma
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
@@ -466,24 +488,24 @@ cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -505,27 +527,27 @@ seqtk.c: In function 'stk_famask':
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
seqtk.c:546:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/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_0.1.18-3-sparc-Dzk96g/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1545
+Build finished at 20121223-0500
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-c0dfe45e-ca10-47f2-a0e7-42a63dbea57a/build/buildd-samtools_0.1.18-3-sparc-Dzk96g
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-aca2bf8d-dc86-41b0-aa8b-47a9cdd0557a/build/buildd-samtools_0.1.18-4-sparc-obycZR
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -533,18 +555,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 6800
-Build-Time: 139
+Build-Space: 6840
+Build-Time: 140
Distribution: sid
Fail-Stage: build
-Install-Time: 76
-Job: samtools_0.1.18-3
+Install-Time: 85
+Job: samtools_0.1.18-4
Package: samtools
-Package-Time: 296
-Source-Version: 0.1.18-3
-Space: 6800
+Package-Time: 307
+Source-Version: 0.1.18-4
+Space: 6840
Status: attempted
-Version: 0.1.18-3
+Version: 0.1.18-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1545
-Build needed 00:04:56, 6800k disc space
+Finished at 20121223-0500
+Build needed 00:05:07, 6840k disc space
--
Processing of sequence alignments in SAM and BAM formats.
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