[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.18-1-4-gb8d566c
Charles Plessy
plessy at debian.org
Sat Mar 30 08:54:48 UTC 2013
The following commit has been merged in the meta branch:
commit bb12be3364a534fe48c053d5b64183e52e9010de
Author: Charles Plessy <plessy at debian.org>
Date: Sat Mar 30 17:46:12 2013 +0900
Build logs for 0.1.18-2.
diff --git a/armel.log b/armel.log
index 7655088..76ddbc1 100644
--- a/armel.log
+++ b/armel.log
@@ -1,68 +1,60 @@
-From buildd at antheil.debian.org Tue Sep 06 09:33:50 2011
-Return-path: <buildd at antheil.debian.org>
+From buildd at alain.debian.org Fri Jul 27 15:14:52 2012
+Return-path: <buildd at alain.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
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CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
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- (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
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-Received: from antheil.islands.arm.com ([217.140.96.60]
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+Received: from alain.islands.arm.com ([217.140.96.58] helo=alain.debian.org)
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+ CN=alain.debian.org, EMAIL=hostmaster at alain.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at antheil.debian.org>)
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-Date: Tue, 06 Sep 2011 09:33:45 +0000
-Message-Id: <E1R0s2L-00088I-Qg at antheil.debian.org>
-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_0.1.18-1 on armel (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at alain.debian.org>)
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+Date: Fri, 27 Jul 2012 15:14:49 +0000
+Message-Id: <E1SumFd-0002ve-L1 at alain.debian.org>
+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_0.1.18-2 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 0.1.18-1 (armel) 06 Sep 2011 09:25 ║
+║ samtools 0.1.18-2 (armel) 27 Jul 2012 15:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: armel
-Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5468 kB]
+Get:1 http://incoming.debian.org unstable InRelease [249 kB]
+Get:2 http://ftp.uk.debian.org unstable InRelease [249 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 [5470 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 [94.9 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armel Packages [7494 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib armel Packages [55.6 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
-Get:13 http://incoming.debian.org unstable/main armel Packages [7495 kB]
-Get:14 http://incoming.debian.org unstable/contrib armel Packages [55.6 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [32.4 kB]
-Get:18 http://incoming.debian.org Packages [356 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 27.0 MB in 1min 6s (405 kB/s)
+Get:3 http://incoming.debian.org Release.gpg [836 B]
+Get:4 http://incoming.debian.org Release [1601 B]
+Get:5 http://ftp.uk.debian.org unstable/main Sources [6315 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:7 http://ftp.uk.debian.org unstable/contrib Sources [53.9 kB]
+Get:8 http://ftp.uk.debian.org unstable/non-free Sources [98.1 kB]
+Get:9 http://ftp.uk.debian.org unstable/main armel Packages [5978 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 armel Packages [5978 kB]
+Get:13 http://ftp.uk.debian.org unstable/contrib armel Packages [37.6 kB]
+Get:14 http://incoming.debian.org unstable/contrib armel Packages [37.6 kB]
+Get:15 http://incoming.debian.org Sources [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.6 MB in 1min 39s (256 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 1s (374 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (335 kB/s)
Download complete and in download only mode
Check arch
@@ -101,18 +93,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -121,37 +113,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-1)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-2)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-16)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-4)
+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 (1.16.8)
+e2fsprogs: already installed (1.42.4-3)
+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)
+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)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -163,126 +155,144 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ 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
+ 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 libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 41 not upgraded.
-Need to get 9838 kB of archives.
-After this operation, 29.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-3 [33.8 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-2 [990 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.04-5+b1 [235 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.04-5+b1 [49.4 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-4 [139 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-4 [815 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.6-1 [1535 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-1 [113 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-4 [409 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-4 [1984 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.54-1 [27.7 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-1 [474 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
+ 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]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9838 kB in 10s (933 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10542 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_armel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_armel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_armel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_armel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_armel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_armel.deb) ...
-Selecting previously deselected package html2text.
+Fetched 10.4 MB in 5s (1762 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) ...
+Selecting previously unselected package libasprintf0c2:armel.
+Unpacking libasprintf0c2:armel (from .../libasprintf0c2_0.18.1.1-9_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) ...
+Selecting previously unselected package libxml2:armel.
+Unpacking libxml2:armel (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:armel.
+Unpacking libcroco3:armel (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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_armel.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_armel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_armel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_armel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_armel.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_armel.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_armel.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_armel.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+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_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_armel.deb) ...
+Selecting previously unselected package libtinfo-dev:armel.
+Unpacking libtinfo-dev:armel (from .../libtinfo-dev_5.9-10_armel.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_armel.deb) ...
+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 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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:armel (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:armel (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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
-Toolchain package versions: binutils_2.21.53.20110805-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-6 gcc-4.6_4.6.1-6 libc6-dev_2.13-16 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 linux-libc-dev_3.0.0-1
-Package versions: apt_0.8.15.5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110805-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-6 dash_0.5.5.1-7.4 debconf_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_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-6 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-7 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-6 gcc-4.6-base_4.6.1-6 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 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_1.0.5-6 libc-bin_2.13-16 libc-dev-bin_2.13-16 libc6_2.13-16 libc6-dev_2.13-16 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_1:4.6.1-6 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-5 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 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-16 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-2 perl-base_5.12.4-2 perl-modules_5.12.4-2 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-5 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-7.1 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -293,13 +303,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -308,40 +320,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armel-5narhz/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
@@ -349,129 +362,135 @@ 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
+ 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_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-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_0.1.18-2-armel-5narhz/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_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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 -fstack-protector --param=ssp-buffer-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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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 `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/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_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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 `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/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_0.1.18-2-armel-5narhz/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 `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/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. 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_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/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_0.1.18-2-armel-5narhz/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_0.1.18-2-armel-5narhz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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_0.1.18-2-armel-5narhz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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]
seqtk.c: In function 'stk_subseq':
@@ -482,15 +501,15 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/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_0.1.18-2-armel-5narhz/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_0.1.18-1-armel-e_OjLd/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/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 `/build/buildd-samtools_0.1.18-1-armel-e_OjLd/samtools-0.1.18/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_0.1.18-2-armel-5narhz/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.
@@ -498,14 +517,14 @@ 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_0.1.18-1-armel-e_OjLd/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armel-5narhz/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
-dpkg-buildpackage: error: debian/rules build gave error exit status 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110906-0933
+Build finished at 20120727-1514
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-aa205354-7d1c-41d1-92e5-305c4b07ff1d/build/buildd-samtools_0.1.18-1-armel-e_OjLd
+Purging /var/lib/schroot/mount/sid-armel-sbuild-c8a6ce86-8609-468e-8b01-5d381ee6ae5e/build/buildd-samtools_0.1.18-2-armel-5narhz
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -513,19 +532,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 6420
-Build-Time: 304
+Build-Space: 6464
+Build-Time: 318
Distribution: sid
Fail-Stage: build
-Install-Time: 100
-Job: samtools_0.1.18-1
+Install-Time: 101
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 505
-Source-Version: 0.1.18-1
-Space: 6420
+Package-Time: 554
+Source-Version: 0.1.18-2
+Space: 6464
Status: attempted
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0933
-Build needed 00:08:25, 6420k disc space
+Finished at 20120727-1514
+Build needed 00:09:14, 6464k disc space
diff --git a/armhf.log b/armhf.log
new file mode 100644
index 0000000..14ec90c
--- /dev/null
+++ b/armhf.log
@@ -0,0 +1,813 @@
+From buildd at hildegard.debian.org Fri Jul 27 15:14:14 2012
+Return-path: <buildd at hildegard.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 hildegard.debian.org>)
+ id 1SumF3-0003Wp-VA
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:14:14 +0000
+Received: from hildegard.ynic.york.ac.uk ([144.32.168.74]
+ helo=hildegard.debian.org)
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=hildegard.debian.org,
+ EMAIL=hostmaster at hildegard.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 hildegard.debian.org>) id 1SumF2-0004AS-Rf
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:14:13 +0000
+Received: from buildd by hildegard.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at hildegard.debian.org>)
+ id 1SumEz-00005l-GY; Fri, 27 Jul 2012 15:14:09 +0000
+From: buildd on hildegard <buildd at hildegard.debian.org>
+To: logs at buildd.debian.org,buildd-porters at hildegard.debian.org
+Subject: Log for successful build of samtools_0.1.18-2 on armhf (dist=sid)
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+Message-Id: <E1SumEz-00005l-GY at hildegard.debian.org>
+Date: Fri, 27 Jul 2012 15:14:09 +0000
+Delivered-To: logs at buildd.debian.org
+
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hildegard.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 0.1.18-2 (armhf) 27 Jul 2012 15:04 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.18-2
+Source Version: 0.1.18-2
+Architecture: armhf
+Get:1 http://ftp.uk.debian.org unstable InRelease [249 kB]
+Get:2 http://incoming.debian.org unstable InRelease [249 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6315 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 armhf Packages [5950 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [36.1 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 armhf Packages [5950 kB]
+Get:13 http://incoming.debian.org unstable/contrib armhf Packages [36.1 kB]
+Get:14 http://incoming.debian.org Release [1601 B]
+Get:15 http://incoming.debian.org Sources [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.5 MB in 1min 29s (284 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://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 2s (185 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 43 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 43 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 (2.13-33)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.4.3 >= 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 libncurses5 libpcre3 libpipeline1 libtinfo-dev libtinfo5
+ libunistring0 libxml2 man-db ncurses-bin 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
+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:
+ libncurses5 libtinfo5 ncurses-bin
+3 upgraded, 26 newly installed, 0 to remove and 40 not upgraded.
+Need to get 10.8 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 ncurses-bin armhf 5.9-10 [329 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libtinfo5 armhf 5.9-10 [260 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libncurses5 armhf 5.9-10 [87.9 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.1-1 [33.2 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-9 [26.4 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.11-2 [199 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.30-5 [240 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-5 [785 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.32.3-1 [1896 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.5-1 [134 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-9 [122 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.3 [204 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-9 [1031 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.2-1 [1014 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.11-2 [51.5 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-9 [130 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-9 [1828 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 9.20120608 [700 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 10.8 MB in 4s (2664 kB/s)
+(Reading database ... 10757 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.9-9 (using .../ncurses-bin_5.9-10_armhf.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.9-10) ...
+(Reading database ... 10757 files and directories currently installed.)
+Preparing to replace libtinfo5:armhf 5.9-9 (using .../libtinfo5_5.9-10_armhf.deb) ...
+Unpacking replacement libtinfo5:armhf ...
+Setting up libtinfo5:armhf (5.9-10) ...
+(Reading database ... 10757 files and directories currently installed.)
+Preparing to replace libncurses5:armhf 5.9-9 (using .../libncurses5_5.9-10_armhf.deb) ...
+Unpacking replacement libncurses5:armhf ...
+Setting up libncurses5:armhf (5.9-10) ...
+Selecting previously unselected package libpipeline1:armhf.
+(Reading database ... 10757 files and directories currently installed.)
+Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ...
+Selecting previously unselected package libasprintf0c2:armhf.
+Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_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) ...
+Selecting previously unselected package libxml2:armhf.
+Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:armhf.
+Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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+b1_armhf.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_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) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_armhf.deb) ...
+Selecting previously unselected package libtinfo-dev:armhf.
+Unpacking libtinfo-dev:armhf (from .../libtinfo-dev_5.9-10_armhf.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_armhf.deb) ...
+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 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+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:armhf (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:armhf (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 40 not upgraded.
+Checking correctness of dependencies...
+Kernel: Linux 3.2.0-3-mx5 armhf (armv7l)
+Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-7 gcc-4.6_4.6.3-7 libc6-dev_2.13-33 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 linux-libc-dev_3.2.21-1
+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+b1 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_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1+b1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.4.3 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++_4:4.6.3-6 g++-4.6_4.6.3-7 gcc_4:4.6.3-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7-base_4.7.1-1 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-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+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-8+b1 libgcc1_1:4.7.1-1 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_4.7.1-1 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_2.2.4-13 libss2_1.42.4-3 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 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_3.2.21-1 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_5.9-9 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-27 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
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-2.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_0.1.18-2.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 0.1.18-2
+ dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: host architecture armhf
+ 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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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
+bam_import.c: In function 'append_text':
+bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/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]
+seqtk.c: In function 'stk_subseq':
+seqtk.c:427:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+seqtk.c: In function 'stk_mergefa':
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+seqtk.c:495:4: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+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_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/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_0.1.18-2-armhf-hZG9OI/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
+../samtools rmdup ex1f.bam ex1f-rmduppe.bam
+[bam_rmdup_core] processing reference seq1...
+[bam_rmdup_core] processing reference seq2...
+[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
+[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
+../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
+[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
+[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
+../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
+[mpileup] 1 samples in 1 input files
+<mpileup> Set max per-file depth to 8000
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
+
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/examples'
+touch debian/stamp-makefile-check
+ fakeroot debian/rules binary-arch
+test -x debian/rules
+dh_testroot
+dh_prep
+dh_installdirs -A
+mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
+Adding cdbs dependencies to debian/samtools.substvars
+dh_installdirs -psamtools
+Adding cdbs dependencies to debian/libbam-dev.substvars
+dh_installdirs -plibbam-dev
+dh_installdocs -psamtools ./NEWS ./AUTHORS
+dh_installexamples -psamtools
+dh_installman -psamtools
+dh_installinfo -psamtools
+dh_installmenu -psamtools
+dh_installcron -psamtools
+dh_installinit -psamtools
+dh_installdebconf -psamtools
+dh_installemacsen -psamtools
+dh_installcatalogs -psamtools
+dh_installpam -psamtools
+dh_installlogrotate -psamtools
+dh_installlogcheck -psamtools
+dh_installchangelogs -psamtools ./ChangeLog
+dh_installudev -psamtools
+dh_lintian -psamtools
+dh_bugfiles -psamtools
+dh_install -psamtools
+dh_link -psamtools
+dh_installmime -psamtools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
+dh_installexamples -plibbam-dev
+dh_installman -plibbam-dev
+dh_installinfo -plibbam-dev
+dh_installmenu -plibbam-dev
+dh_installcron -plibbam-dev
+dh_installinit -plibbam-dev
+dh_installdebconf -plibbam-dev
+dh_installemacsen -plibbam-dev
+dh_installcatalogs -plibbam-dev
+dh_installpam -plibbam-dev
+dh_installlogrotate -plibbam-dev
+dh_installlogcheck -plibbam-dev
+dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installudev -plibbam-dev
+dh_lintian -plibbam-dev
+dh_bugfiles -plibbam-dev
+dh_install -plibbam-dev
+dh_link -plibbam-dev
+dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
+dh_strip -psamtools
+dh_compress -psamtools
+dh_fixperms -psamtools
+dh_makeshlibs -psamtools
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-armhf-hZG9OI/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+dh_strip -plibbam-dev
+dh_compress -plibbam-dev
+dh_fixperms -plibbam-dev
+dh_makeshlibs -plibbam-dev
+dh_installdeb -psamtools
+dh_perl -psamtools
+dh_shlibdeps -psamtools
+dh_installdeb -plibbam-dev
+dh_perl -plibbam-dev
+dh_shlibdeps -plibbam-dev
+dh_gencontrol -psamtools
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+dh_md5sums -psamtools
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_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_0.1.18-2_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (hildegard) <buildd_armhf-hildegard at buildd.debian.org> >../samtools_0.1.18-2_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 20120727-1514
+
+samtools_0.1.18-2_armhf.changes:
+Format: 1.8
+Date: Thu, 26 Jul 2012 18:30:48 -0400
+Source: samtools
+Binary: samtools libbam-dev
+Architecture: armhf
+Version: 0.1.18-2
+Distribution: sid
+Urgency: low
+Maintainer: armhf Build Daemon (hildegard) <buildd_armhf-hildegard 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: 544976 671524
+Changes:
+ samtools (0.1.18-2) unstable; urgency=low
+ .
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
+Checksums-Sha1:
+ 874726fa4892b7f3c0bb1375900383b05f85ff9a 507940 samtools_0.1.18-2_armhf.deb
+ 6a27f0b89422affff54a3216792a2dbae4fd62be 144508 libbam-dev_0.1.18-2_armhf.deb
+Checksums-Sha256:
+ 8815c9c6d4112812d1afcc175aa5a71d246aacc20c3d6cbf4ddf47852eb76a20 507940 samtools_0.1.18-2_armhf.deb
+ 74e4b80a0e6ff565b98fcdf6e3df735f8fbc9e0781340ed5339a3def53e45f03 144508 libbam-dev_0.1.18-2_armhf.deb
+Files:
+ 99a0f91f8a750922081f03c4f41ea1e0 507940 science optional samtools_0.1.18-2_armhf.deb
+ 994c236405596dcd86ddc86b16cba98b 144508 libdevel optional libbam-dev_0.1.18-2_armhf.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_0.1.18-2_armhf.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 507940 bytes: control archive=1776 bytes.
+ 817 bytes, 16 lines control
+ 2453 bytes, 37 lines md5sums
+ Package: samtools
+ Version: 0.1.18-2
+ Architecture: armhf
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 828
+ 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
+ Priority: optional
+ Homepage: http://samtools.sourceforge.net
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:13 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:13 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/samtools/
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 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 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 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:13 ./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 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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:13 ./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 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
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/samtools/examples/
+-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 15:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/bin/
+-rwxr-xr-x root/root 248724 2012-07-27 15:13 ./usr/bin/samtools
+-rwxr-xr-x root/root 17620 2012-07-27 15:13 ./usr/bin/razip
+-rwxr-xr-x root/root 88388 2012-07-27 15:13 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/samtools/
+-rwxr-xr-x root/root 5892 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8480 2012-07-27 15:13 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 12900 2012-07-27 15:13 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6484 2012-07-27 15:13 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 5892 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-long
+lrwxrwxrwx root/root 0 2012-07-27 15:13 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_armhf.deb
+─────────────────────────────
+
+ new debian package, version 2.0.
+ size 144508 bytes: control archive=927 bytes.
+ 674 bytes, 15 lines control
+ 715 bytes, 11 lines md5sums
+ Package: libbam-dev
+ Source: samtools
+ Version: 0.1.18-2
+ Architecture: armhf
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 335
+ Section: libdevel
+ Priority: optional
+ Homepage: http://samtools.sourceforge.net
+ Description: manipulates nucleotide sequence alignments in BAM or SAM format
+ The BAM library provides I/O and various operations on manipulating nucleotide
+ sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
+ Alignment/Map) format. It now supports importing from or exporting to SAM,
+ sorting, merging, generating pileup, and quickly retrieval of reads overlapped
+ with a specified region.
+
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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
+-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
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./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 24720 2011-09-02 16:58 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
+-rw-r--r-- root/root 200906 2012-07-27 15:13 ./usr/lib/libbam.a
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Finished │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Built successfully
+────────────────────────────────────────────────────────────────────────────────
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-bc82cb11-d080-4070-95cb-9743779d586a/build/buildd-samtools_0.1.18-2-armhf-hZG9OI
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Architecture: armhf
+Build-Space: 9472
+Build-Time: 333
+Distribution: sid
+Install-Time: 117
+Job: samtools_0.1.18-2
+Package: samtools
+Package-Time: 575
+Source-Version: 0.1.18-2
+Space: 9472
+Status: successful
+Version: 0.1.18-2
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20120727-1514
+Build needed 00:09:35, 9472k disc space
+Signature with key '0E1957C5' requested:
+
diff --git a/i386.log b/i386.log
index f45de34..ffc4773 100644
--- a/i386.log
+++ b/i386.log
@@ -1,71 +1,61 @@
-From buildd at murphy.debian.org Tue Sep 06 09:26:25 2011
-Return-path: <buildd at murphy.debian.org>
+From buildd at biber.debian.org Fri Jul 27 15:15:41 2012
+Return-path: <buildd at biber.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
- id 1R0rvE-0000QG-PN
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:26:25 +0000
-Received: from murphy.debian.org ([70.103.162.31])
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1SumGT-0003wH-Ot
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:15:41 +0000
+Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=murphy.debian.org, EMAIL=hostmaster at murphy.debian.org (verified)
+ CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
- id 1R0rvB-00013E-W4
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:26:22 +0000
-Received: from buildd by murphy.debian.org with local (Exim 4.72)
- (envelope-from <buildd at murphy.debian.org>)
- id 1R0rvA-0008A1-Eo; Tue, 06 Sep 2011 09:26:20 +0000
-Message-Id: <E1R0rvA-0008A1-Eo at murphy.debian.org>
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1SumGS-0000Ub-LS; Fri, 27 Jul 2012 15:15:40 +0000
+Received: from buildd by biber.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at biber.debian.org>)
+ id 1SumGR-0001zm-Li; Fri, 27 Jul 2012 15:15:39 +0000
+Message-Id: <E1SumGR-0001zm-Li at biber.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Tue, 6 Sep 2011 09:26:20 +0000
-From: buildd on murphy <buildd at murphy.debian.org>
-To: logs at buildd.debian.org,buildd-admin at murphy.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on i386 (dist=sid)
-Key-Id: AC7BC9C1
+Date: Fri, 27 Jul 2012 15:15:39 +0000
+From: buildd on biber <buildd at biber.debian.org>
+To: kurt at roeckx.be,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.18-2 on i386 (dist=sid)
+Key-Id: 6EBCB100
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on murphy.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (i386) 06 Sep 2011 09:24 ║
+║ samtools 0.1.18-2 (i386) 27 Jul 2012 15:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: i386
-Hit http://ftp.us.debian.org sid InRelease
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
-Hit http://ftp.us.debian.org sid/main Sources/DiffIndex
+Get:1 http://ftp.gr.debian.org unstable InRelease [249 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [6315 kB]
+Get:3 http://incoming.debian.org unstable InRelease [249 kB]
+Get:4 http://ftp.gr.debian.org unstable/contrib Sources [53.9 kB]
+Get:5 http://ftp.gr.debian.org unstable/non-free Sources [98.1 kB]
+Get:6 http://ftp.gr.debian.org unstable/main i386 Packages [6138 kB]
+Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [46.1 kB]
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
-Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://ftp.us.debian.org sid/main i386 Packages/DiffIndex
-Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
-Ign http://ftp.us.debian.org sid/contrib TranslationIndex
-Get:4 http://ftp.us.debian.org sid/main TranslationIndex [2045 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:5 http://incoming.debian.org sid/main i386 Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:6 http://incoming.debian.org sid/main TranslationIndex [2045 B]
-Get:7 http://incoming.debian.org Release [1604 B]
-Get:8 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
-Get:9 http://incoming.debian.org sid/main i386 2011-09-06-0818.53.pdiff [2652 B]
-Get:10 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
-Get:11 http://incoming.debian.org Sources [32.4 kB]
-Ign http://ftp.us.debian.org sid/contrib Translation-en
-Get:12 http://incoming.debian.org Packages [356 kB]
-Get:13 http://incoming.debian.org sid/main i386 2011-09-06-0818.53.pdiff [2652 B]
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 553 kB in 7s (77.1 kB/s)
+Get:8 http://incoming.debian.org unstable/main Sources [6315 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 i386 Packages [6138 kB]
+Get:12 http://incoming.debian.org unstable/contrib i386 Packages [46.1 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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.9 MB in 19s (1330 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 1s (298 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (209 kB/s)
Download complete and in download only mode
Check arch
@@ -104,18 +94,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+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 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -124,37 +114,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-18)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+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 (1.16.7)
+e2fsprogs: already installed (1.42.4-3)
+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)
+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)
+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 (4:4.7.1-1 >= 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)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -166,103 +156,144 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ 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
+ 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 libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
+ 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 29 not upgraded.
+Need to get 10.8 MB of archives.
+After this operation, 28.4 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.1-1 [38.6 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main libasprintf0c2 i386 0.18.1.1-9 [26.7 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 5.11-2 [204 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 1:8.30-5 [240 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.8.0+dfsg1-5 [893 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main libffi5 i386 3.0.10-3 [21.0 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.32.3-1 [2074 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.5-1 [151 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo0 i386 0.18.1.1-9 [140 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 9.0.3 [205 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.21-9 [1131 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.2-1 [1055 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main file i386 5.11-2 [51.5 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-9 [131 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-9 [1916 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.55-3 [29.3 kB]
+Get:23 http://ftp.gr.debian.org/debian/ unstable/main libtinfo-dev i386 5.9-10 [93.2 kB]
+Get:24 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-10 [212 kB]
+Get:25 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.7.dfsg-13 [212 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/10.0 MB of archives.
-After this operation, 29.8 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10781 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_i386.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_i386.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_i386.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_i386.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_i386.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_i386.deb) ...
-Selecting previously deselected package html2text.
+Fetched 10.8 MB in 0s (11.9 MB/s)
+Selecting previously unselected package libpipeline1:i386.
+(Reading database ... 10801 files and directories currently installed.)
+Unpacking libpipeline1:i386 (from .../libpipeline1_1.2.1-1_i386.deb) ...
+Selecting previously unselected package libasprintf0c2:i386.
+Unpacking libasprintf0c2:i386 (from .../libasprintf0c2_0.18.1.1-9_i386.deb) ...
+Selecting previously unselected package libmagic1:i386.
+Unpacking libmagic1:i386 (from .../libmagic1_5.11-2_i386.deb) ...
+Selecting previously unselected package libpcre3:i386.
+Unpacking libpcre3:i386 (from .../libpcre3_1%3a8.30-5_i386.deb) ...
+Selecting previously unselected package libxml2:i386.
+Unpacking libxml2:i386 (from .../libxml2_2.8.0+dfsg1-5_i386.deb) ...
+Selecting previously unselected package libffi5:i386.
+Unpacking libffi5:i386 (from .../libffi5_3.0.10-3_i386.deb) ...
+Selecting previously unselected package libglib2.0-0:i386.
+Unpacking libglib2.0-0:i386 (from .../libglib2.0-0_2.32.3-1_i386.deb) ...
+Selecting previously unselected package libcroco3:i386.
+Unpacking libcroco3:i386 (from .../libcroco3_0.6.5-1_i386.deb) ...
+Selecting previously unselected package libunistring0:i386.
+Unpacking libunistring0:i386 (from .../libunistring0_0.9.3-5_i386.deb) ...
+Selecting previously unselected package libgettextpo0:i386.
+Unpacking libgettextpo0:i386 (from .../libgettextpo0_0.18.1.1-9_i386.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_i386.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-9_i386.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.2-1_i386.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.11-2_i386.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_i386.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_i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_i386.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_i386.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_i386.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_i386.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_i386.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_i386.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+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_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_i386.deb) ...
+Selecting previously unselected package libtinfo-dev:i386.
+Unpacking libtinfo-dev:i386 (from .../libtinfo-dev_5.9-10_i386.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_i386.deb) ...
+Selecting previously unselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Selecting previously unselected package zlib1g-dev:i386.
+Unpacking zlib1g-dev:i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_i386.deb) ...
+Setting up libpipeline1:i386 (1.2.1-1) ...
+Setting up libasprintf0c2:i386 (0.18.1.1-9) ...
+Setting up libmagic1:i386 (5.11-2) ...
+Setting up libpcre3:i386 (1:8.30-5) ...
+Setting up libxml2:i386 (2.8.0+dfsg1-5) ...
+Setting up libffi5:i386 (3.0.10-3) ...
+Setting up libglib2.0-0:i386 (2.32.3-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:i386 (0.6.5-1) ...
+Setting up libunistring0:i386 (0.9.3-5) ...
+Setting up libgettextpo0:i386 (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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:i386 (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:i386 (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 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 29 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
-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 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 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 libgomp1_4.6.1-9 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 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 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 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
+Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
+Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.7_4.7.1-3 gcc-4.7_4.7.1-3 libc6-dev_2.13-34 libstdc++6_4.7.1-3 libstdc++6-4.7-dev_4.7.1-3 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_4:4.7.1-1 cpp-4.7_4.7.1-3 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++_4:4.7.1-1 g++-4.7_4.7.1-3 gcc_4:4.7.1-1 gcc-4.7_4.7.1-3 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 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 libitm1_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 libquadmath0_4.7.1-3 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_4.7.1-3 libstdc++6-4.7-dev_4.7.1-3 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -273,13 +304,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -288,40 +321,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-i386-8lTd72/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
@@ -329,129 +363,141 @@ 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
+ 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_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-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_0.1.18-2-i386-8lTd72/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_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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 -fstack-protector --param=ssp-buffer-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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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 `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/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_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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 `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/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_0.1.18-2-i386-8lTd72/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 `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/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. 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_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/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_0.1.18-2-i386-8lTd72/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_0.1.18-2-i386-8lTd72/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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_0.1.18-2-i386-8lTd72/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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]
seqtk.c: In function 'stk_subseq':
@@ -462,15 +508,15 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/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_0.1.18-2-i386-8lTd72/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_0.1.18-1-i386-FaumRv/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/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 `/build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/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_0.1.18-2-i386-8lTd72/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 +542,7 @@ 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_0.1.18-1-i386-FaumRv/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -531,8 +577,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -558,7 +604,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-i386-FaumRv/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-i386-8lTd72/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -570,72 +616,73 @@ 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_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_i386.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_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../samtools_0.1.18-1_i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-0926
+Build finished at 20120727-1515
-samtools_0.1.18-1_i386.changes:
+samtools_0.1.18-2_i386.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: i386 Build Daemon <buildd_i386-biber 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- db4a67c1c1d94224e012f8c23cd6dd31d01a2c25 532602 samtools_0.1.18-1_i386.deb
- f16e5e8761f0bf979e1079a037888e88fac0dc32 160330 libbam-dev_0.1.18-1_i386.deb
+ dd73578b3f260e1de73b8d63c9a159884d2d911f 534640 samtools_0.1.18-2_i386.deb
+ 828b62ebc7704bb4ac7f751a3a96d80ae4f3f761 160934 libbam-dev_0.1.18-2_i386.deb
Checksums-Sha256:
- 4d72eb1b950ed9bf58d022490b850c18f445e7b8e5092d0e565622f89e24cb8e 532602 samtools_0.1.18-1_i386.deb
- 96df10e8e765e7eebe455256869db9dffc1f16c698bc15e66e160b4070691e4f 160330 libbam-dev_0.1.18-1_i386.deb
+ e26ece5bfb41a51243941c49f505b024b5cfe9980642d51d325e558508bd9088 534640 samtools_0.1.18-2_i386.deb
+ ce0841dee2ba4087dae49b6bb4a382434ce5ff533b617101f16da49e6390b135 160934 libbam-dev_0.1.18-2_i386.deb
Files:
- 2c0d7250db586536bc1f28a5381b5bf5 532602 science optional samtools_0.1.18-1_i386.deb
- 16e5bc19bcad992c877c8c60dd7b0107 160330 libdevel optional libbam-dev_0.1.18-1_i386.deb
+ d27965e80c3c3ced041c73c5ecd5707a 534640 science optional samtools_0.1.18-2_i386.deb
+ 5ed8aa277faa83b9aef3d5f79311b191 160934 libdevel optional libbam-dev_0.1.18-2_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_i386.deb
+samtools_0.1.18-2_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 532602 bytes: control archive= 1761 bytes.
- 785 bytes, 16 lines control
+ size 534640 bytes: control archive= 1768 bytes.
+ 791 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1120
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1036
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -647,71 +694,71 @@ samtools_0.1.18-1_i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/bin/
--rwxr-xr-x root/root 133752 2011-09-06 09:26 ./usr/bin/bcftools
--rwxr-xr-x root/root 24676 2011-09-06 09:26 ./usr/bin/razip
--rwxr-xr-x root/root 390696 2011-09-06 09:26 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/lib/samtools/
--rwxr-xr-x root/root 7184 2011-09-06 09:26 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6576 2011-09-06 09:26 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 16596 2011-09-06 09:26 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 10276 2011-09-06 09:26 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6576 2011-09-06 09:26 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2011-09-06 09:26 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-09-06 09:26 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/samtools/
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 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 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2011-09-06 09:26 ./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 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7484 2012-07-27 15:15 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 6860 2012-07-27 15:15 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6860 2012-07-27 15:15 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10608 2012-07-27 15:15 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 16536 2012-07-27 15:15 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/bin/
+-rwxr-xr-x root/root 134308 2012-07-27 15:15 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24740 2012-07-27 15:15 ./usr/bin/razip
+-rwxr-xr-x root/root 400020 2012-07-27 15:15 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./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 2011-09-06 09:26 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 126609 2011-09-06 09:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2012-07-27 15:15 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 1966 2011-09-06 09:26 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-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 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-lrwxrwxrwx root/root 0 2011-09-06 09:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:15 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+-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
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2012-07-27 15:15 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2012-07-27 15:15 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:15 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+lrwxrwxrwx root/root 0 2012-07-27 15:15 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.18-1_i386.deb
+libbam-dev_0.1.18-2_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 160330 bytes: control archive= 926 bytes.
+ size 160934 bytes: control archive= 926 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 456
+ Installed-Size: 432
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -722,25 +769,25 @@ libbam-dev_0.1.18-1_i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/include/samtools/
--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
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/lib/
--rw-r--r-- root/root 292326 2011-09-06 09:26 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:26 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/lib/
+-rw-r--r-- root/root 299796 2012-07-27 15:15 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./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 1676 2011-09-06 07:52 ./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 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
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:15 ./usr/include/samtools/
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 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 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -754,74 +801,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-8ffc7965-4fe7-440b-a24f-af956fb3e5cb/build/buildd-samtools_0.1.18-1-i386-FaumRv
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- bsdmainutils* cdbs* debhelper* diffstat* file* gettext* gettext-base*
- groff-base* html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
- libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
- po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded.
-After this operation, 29.8 MB disk space will be freed.
-(Reading database ... 12298 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libncurses5-dev ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Purging /var/lib/schroot/mount/sid-i386-sbuild-ad398d8d-23c5-4b5f-91a8-8eb0ec51e338/build/buildd-samtools_0.1.18-2-i386-8lTd72
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 10388
+Build-Space: 11392
Build-Time: 55
Distribution: sid
-Install-Time: 10
-Job: samtools_0.1.18-1
+Install-Time: 43
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 80
-Source-Version: 0.1.18-1
-Space: 10388
+Package-Time: 132
+Source-Version: 0.1.18-2
+Space: 11392
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0926
-Build needed 00:01:20, 10388k disc space
-Signature with key 'AC7BC9C1' requested:
+Finished at 20120727-1515
+Build needed 00:02:12, 11392k disc space
+Signature with key '6EBCB100' requested:
diff --git a/ia64.log b/ia64.log
index d401e5a..ff7d9e7 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,66 +1,60 @@
-From buildd at mundy.debian.org Tue Sep 06 11:00:20 2011
-Return-path: <buildd at mundy.debian.org>
+From buildd at alkman.debian.org Fri Jul 27 15:11:30 2012
+Return-path: <buildd at alkman.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
- id 1R0tO8-0007zP-0y
- for logs at buildd.debian.org; Tue, 06 Sep 2011 11:00:20 +0000
-Received: from mundy.debian.org ([192.25.206.62])
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1SumCQ-0002qa-JO
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:11:30 +0000
+Received: from alkman.debian.org ([192.25.206.63])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mundy.debian.org, EMAIL=hostmaster at mundy.debian.org (verified)
+ CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mundy.debian.org>)
- id 1R0tO6-00008v-2K; Tue, 06 Sep 2011 11:00:18 +0000
-Received: from buildd by mundy.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mundy.debian.org>)
- id 1R0tO2-0005zD-Fi; Tue, 06 Sep 2011 11:00:14 +0000
-Date: Tue, 06 Sep 2011 11:00:14 +0000
-Message-Id: <E1R0tO2-0005zD-Fi at mundy.debian.org>
-From: buildd on mundy <buildd at mundy.debian.org>
-To: dannf at master.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on ia64 (dist=sid)
+ (Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
+ id 1SumCO-00048K-Vx
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:11:29 +0000
+Received: from buildd by alkman.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at alkman.debian.org>)
+ id 1SumCL-00037k-Ek; Fri, 27 Jul 2012 15:11:25 +0000
+Date: Fri, 27 Jul 2012 15:11:25 +0000
+Message-Id: <E1SumCL-00037k-Ek 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_0.1.18-2 on ia64 (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 mundy.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (ia64) 06 Sep 2011 10:55 ║
+║ samtools 0.1.18-2 (ia64) 27 Jul 2012 15:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: ia64
-Get:1 http://spohr.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://spohr.debian.org unstable/main Sources [5470 kB]
+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:4 http://spohr.debian.org unstable/contrib Sources [53.9 kB]
-Get:5 http://spohr.debian.org unstable/non-free Sources [94.9 kB]
-Get:6 http://spohr.debian.org unstable/main ia64 Packages [7405 kB]
+Get:5 http://spohr.debian.org unstable/non-free Sources [98.1 kB]
+Get:6 http://spohr.debian.org unstable/main ia64 Packages [5831 kB]
Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5470 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [56.3 kB]
-Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://spohr.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [7405 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [56.3 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [32.5 kB]
-Get:18 http://incoming.debian.org Packages [331 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 26.8 MB in 17s (1539 kB/s)
+Get:7 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:8 http://spohr.debian.org unstable/contrib ia64 Packages [38.3 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 ia64 Packages [5831 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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.3 MB in 28s (873 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -81,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 0s (443 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (374 kB/s)
Download complete and in download only mode
Check arch
@@ -99,18 +93,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 50 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 50 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -119,37 +113,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-1)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-1)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-4)
-mount: already installed (2.19.1-4)
-util-linux: already installed (2.19.1-4)
-libc6.1-dev: already installed (2.13-10)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+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 (1.16.7)
+e2fsprogs: already installed (1.42.4-3)
+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)
+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)
+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)
+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 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -161,126 +155,144 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ 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
+ 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 libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 50 not upgraded.
-Need to get 12.0 MB of archives.
-After this operation, 45.6 MB of additional disk space will be used.
-Get:1 http://spohr.debian.org/debian/ unstable/main libpipeline1 ia64 1.2.0-3 [47.8 kB]
-Get:2 http://spohr.debian.org/debian/ unstable/main libpcre3 ia64 8.12-4 [272 kB]
-Get:3 http://spohr.debian.org/debian/ unstable/main bsdmainutils ia64 8.2.3 [238 kB]
-Get:4 http://spohr.debian.org/debian/ unstable/main groff-base ia64 1.21-6 [1402 kB]
-Get:5 http://spohr.debian.org/debian/ unstable/main man-db ia64 2.6.0.2-2 [1118 kB]
-Get:6 http://spohr.debian.org/debian/ unstable/main libmagic1 ia64 5.04-5+b1 [263 kB]
-Get:7 http://spohr.debian.org/debian/ unstable/main file ia64 5.04-5+b1 [52.0 kB]
-Get:8 http://spohr.debian.org/debian/ unstable/main gettext-base ia64 0.18.1.1-4 [173 kB]
-Get:9 http://spohr.debian.org/debian/ unstable/main libxml2 ia64 2.7.8.dfsg-4 [1177 kB]
-Get:10 http://spohr.debian.org/debian/ unstable/main html2text ia64 1.3.2a-15 [134 kB]
-Get:11 http://spohr.debian.org/debian/ unstable/main libglib2.0-0 ia64 2.28.6-1 [1973 kB]
-Get:12 http://spohr.debian.org/debian/ unstable/main libcroco3 ia64 0.6.2-1 [155 kB]
-Get:13 http://spohr.debian.org/debian/ unstable/main libunistring0 ia64 0.9.3-4 [467 kB]
-Get:14 http://spohr.debian.org/debian/ unstable/main gettext ia64 0.18.1.1-4 [2441 kB]
-Get:15 http://spohr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
-Get:18 http://spohr.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
-Get:19 http://spohr.debian.org/debian/ unstable/main diffstat ia64 1.54-1 [36.9 kB]
-Get:20 http://spohr.debian.org/debian/ unstable/main libncurses5-dev ia64 5.9-1 [614 kB]
-Get:21 http://spohr.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
+ 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 12.0 MB in 3s (3058 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10586 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_ia64.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_ia64.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_ia64.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_ia64.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_ia64.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_ia64.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_ia64.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_ia64.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_ia64.deb) ...
-Selecting previously deselected package html2text.
+Fetched 12.7 MB in 5s (2496 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) ...
+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 deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_ia64.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_ia64.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_ia64.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_ia64.deb) ...
-Selecting previously deselected package intltool-debian.
+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 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_ia64.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_ia64.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_ia64.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+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_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_ia64.deb) ...
+Selecting previously unselected package libtinfo-dev:ia64.
+Unpacking libtinfo-dev:ia64 (from .../libtinfo-dev_5.9-10_ia64.deb) ...
+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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+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 50 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.21.53.20110720-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-4 gcc-4.6_4.6.1-4 libc6.1-dev_2.13-10 libstdc++6_4.6.1-4 libstdc++6-4.6-dev_4.6.1-4 linux-libc-dev_2.6.39-3
-Package versions: apt_0.8.15.2 base-files_6.4 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110720-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-4 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-4 dash_0.5.5.1-7.4 debconf_1.5.40 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_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-4 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-6 gcc-4.5-base_4.5.3-3 gcc-4.6_4.6.1-4 gcc-4.6-base_4.6.1-4 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 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_2.19.1-4 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6.1_2.13-10 libc6.1-dev_2.13-10 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-4 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-4 libmpc2_0.9-3 libmpfr4_3.0.1-4 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-4 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-4 libstdc++6-4.6-dev_4.6.1-4 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-4 libxml2_2.7.8.dfsg-4 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-4 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-4 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-7 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
+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-4.4-base_4.4.7-1 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-4 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 libc6.1_2.13-34 libc6.1-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 libfile-fcntllock-perl_0.14-2 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 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 libquadmath0_4.7.1-4 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 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 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 │
@@ -291,13 +303,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -306,40 +320,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/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="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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
@@ -347,134 +362,140 @@ 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
+ 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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-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_0.1.18-2-ia64-5ePQLX/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_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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]
-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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/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_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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
+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. prob1.c -o prob1.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. 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 -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 -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 -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 -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 -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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/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_0.1.18-2-ia64-5ePQLX/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
+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_rmdup.c -o bam_rmdup.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_rmdupse.c -o bam_rmdupse.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_mate.c -o bam_mate.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_stat.c -o bam_stat.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_color.c -o bam_color.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. bamtk.c -o bamtk.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. kaln.c -o kaln.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. bam2bcf.c -o bam2bcf.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. bam2bcf_indel.c -o bam2bcf_indel.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. errmod.c -o errmod.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. sample.c -o sample.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. 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 `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/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. 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_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/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_0.1.18-2-ia64-5ePQLX/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_0.1.18-2-ia64-5ePQLX/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -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 `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/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 `/build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/examples'
+/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_0.1.18-2-ia64-5ePQLX/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.
@@ -500,7 +521,7 @@ 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_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -535,8 +556,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -562,7 +583,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-ia64-u1PcjN/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-ia64-5ePQLX/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -577,69 +598,68 @@ 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_0.1.18-1_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_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_0.1.18-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org> >../samtools_0.1.18-1_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-1100
+Build finished at 20120727-1511
-samtools_0.1.18-1_ia64.changes:
+samtools_0.1.18-2_ia64.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: ia64 Build Daemon (mundy) <buildd_ia64-mundy at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- c5702832e992687c0e3d02ff551c9572a2426926 603192 samtools_0.1.18-1_ia64.deb
- 0f9c8981134302e058ac2cacf8a99a4041ed782a 193930 libbam-dev_0.1.18-1_ia64.deb
+ ae3896cf5f6f086ed8d8fda397ee66bb8dd94712 604618 samtools_0.1.18-2_ia64.deb
+ 6b92dce40573e1c7b939593264ba0353e0ea33b1 194458 libbam-dev_0.1.18-2_ia64.deb
Checksums-Sha256:
- 87061f11c5437b1d82aae2be12f9a4bcafacdff5d389ec4eba240bf0a5521d4c 603192 samtools_0.1.18-1_ia64.deb
- 28a996a7f71bebbd88d0b14214d2051a3917328ae331e496db073d7d180760d2 193930 libbam-dev_0.1.18-1_ia64.deb
+ 9e6d5b251cc0e4f54409e9074b362472a38a6cb16092df2cae7332104614a4e9 604618 samtools_0.1.18-2_ia64.deb
+ 6393a7e2ee28f7f3b9ec8328a4cadd9d68897292f7736afb82370fa34cccbfb6 194458 libbam-dev_0.1.18-2_ia64.deb
Files:
- 4c25cf6fd0c277a9f890289958eb687a 603192 science optional samtools_0.1.18-1_ia64.deb
- 077355a1497df7e1ebd61c30b6f69937 193930 libdevel optional libbam-dev_0.1.18-1_ia64.deb
+ c842e4c8116350286a423bf5f120136e 604618 science optional samtools_0.1.18-2_ia64.deb
+ 226a9878a76be7aa84c9c6b905dc5848 194458 libdevel optional libbam-dev_0.1.18-2_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_ia64.deb
+samtools_0.1.18-2_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 603192 bytes: control archive= 1760 bytes.
- 787 bytes, 16 lines control
+ size 604618 bytes: control archive= 1762 bytes.
+ 793 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1788
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1638
+ Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -651,71 +671,71 @@ samtools_0.1.18-1_ia64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2011-09-06 10:59 ./usr/share/doc/samtools/README.bcftools
--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 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-09-06 10:59 ./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 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
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/samtools/
--rwxr-xr-x root/root 5778 2011-09-06 10:59 ./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 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
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/lib/samtools/
+-rwxr-xr-x root/root 30976 2012-07-27 15:11 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 13136 2012-07-27 15:11 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13136 2012-07-27 15:11 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 21952 2012-07-27 15:11 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 14944 2012-07-27 15:11 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/bin/
+-rwxr-xr-x root/root 303936 2012-07-27 15:11 ./usr/bin/bcftools
+-rwxr-xr-x root/root 50640 2012-07-27 15:11 ./usr/bin/razip
+-rwxr-xr-x root/root 826608 2012-07-27 15:11 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2012-07-27 15:11 ./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 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 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2011-09-06 10:59 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-09-06 10:59 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/bin/
--rwxr-xr-x root/root 826048 2011-09-06 10:59 ./usr/bin/samtools
--rwxr-xr-x root/root 50704 2011-09-06 10:59 ./usr/bin/razip
--rwxr-xr-x root/root 303872 2011-09-06 10:59 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/lib/samtools/
--rwxr-xr-x root/root 13136 2011-09-06 10:59 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13136 2011-09-06 10:59 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 14944 2011-09-06 10:59 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 30976 2011-09-06 10:59 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 21952 2011-09-06 10:59 ./usr/lib/samtools/md5fa
-lrwxrwxrwx root/root 0 2011-09-06 10:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-1_ia64.deb
+-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 15:11 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:11 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:11 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./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 1772 2012-07-27 12:17 ./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 15:11 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2012-07-27 15:10 ./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
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+lrwxrwxrwx root/root 0 2012-07-27 15:11 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 193930 bytes: control archive= 926 bytes.
+ size 194458 bytes: control archive= 925 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 736
+ Installed-Size: 672
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -726,25 +746,25 @@ libbam-dev_0.1.18-1_ia64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 11:00 ./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 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
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 10:59 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./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 24720 2011-09-02 16:58 ./usr/include/samtools/bam.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
-drwxr-xr-x root/root 0 2011-09-06 11:00 ./usr/lib/
--rw-r--r-- root/root 581210 2011-09-06 11:00 ./usr/lib/libbam.a
+-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 15:11 ./usr/lib/
+-rw-r--r-- root/root 581530 2012-07-27 15:11 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:11 ./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 1772 2012-07-27 12:17 ./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
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -758,7 +778,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-1e7e0178-a052-4b8c-9a07-72f104b43ee6/build/buildd-samtools_0.1.18-1-ia64-u1PcjN
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-bf5273e5-2a1a-43e0-98fa-fd27b951b76e/build/buildd-samtools_0.1.18-2-ia64-5ePQLX
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -766,19 +786,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 15608
-Build-Time: 144
+Build-Space: 17976
+Build-Time: 160
Distribution: sid
-Install-Time: 62
-Job: samtools_0.1.18-1
+Install-Time: 77
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 254
-Source-Version: 0.1.18-1
-Space: 15608
+Package-Time: 290
+Source-Version: 0.1.18-2
+Space: 17976
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-1100
-Build needed 00:04:14, 15608k disc space
-Signature with key '96FA48F4' requested:
+Finished at 20120727-1511
+Build needed 00:04:50, 17976k disc space
+Signature with key '94AE7BC0' requested:
diff --git a/info b/info
index 2b270f0..f1f1af5 100644
--- a/info
+++ b/info
@@ -1,11 +1,12 @@
-i386~1315301186~sid~successful
-kfreebsd-i386~1315301530~sid~successful
-powerpc~1315301629~sid~successful
-armel~1315301631~sid~failed
-kfreebsd-amd64~1315301956~sid~successful
-hurd-i386~1315302076~sid~successful
-mipsel~1315302340~sid~successful
-mips~1315302649~sid~successful
-ia64~1315306820~sid~successful
-s390~1315308404~sid~successful
-sparc~1315333538~sid~failed
+s390~1343401612~sid~successful
+powerpc~1343401854~sid~successful
+ia64~1343401891~sid~successful
+s390x~1343401918~sid~failed
+kfreebsd-i386~1343402036~sid~successful
+armhf~1343402054~sid~successful
+armel~1343402092~sid~failed
+i386~1343402142~sid~successful
+sparc~1343402299~sid~failed
+kfreebsd-amd64~1343402896~sid~successful
+mipsel~1343403117~sid~successful
+mips~1343403208~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 5ba88e4..32e912a 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,77 +1,62 @@
-From buildd at fasch.debian.org Tue Sep 06 09:39:15 2011
-Return-path: <buildd at fasch.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at fano.debian.org Fri Jul 27 15:28:16 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,
- 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 fasch.debian.org>)
- id 1R0s7f-0002vM-5V
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:39:15 +0000
-Received: from fasch.debian.org ([194.177.211.201])
+ (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
+ id 1SumSe-00009c-Aa
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:28:16 +0000
+Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
- id 1R0s7c-0001aF-Fz; Tue, 06 Sep 2011 09:39:12 +0000
-Received: from buildd by fasch.debian.org with local (Exim 4.72)
- (envelope-from <buildd at fasch.debian.org>)
- id 1R0s7b-0004VG-KM; Tue, 06 Sep 2011 09:39:11 +0000
-Message-Id: <E1R0s7b-0004VG-KM at fasch.debian.org>
+ 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 1SumSd-0004sC-2Q; Fri, 27 Jul 2012 15:28:15 +0000
+Received: from buildd by fano.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fano.debian.org>)
+ id 1SumSa-00006z-VG; Fri, 27 Jul 2012 15:28:12 +0000
+Message-Id: <E1SumSa-00006z-VG 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: Tue, 6 Sep 2011 09:39:11 +0000
-From: buildd on fasch <buildd at fasch.debian.org>
-To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on kfreebsd-amd64
+Date: Fri, 27 Jul 2012 15:28:12 +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_0.1.18-2 on kfreebsd-amd64
(dist=sid)
-Key-Id: 56BAE008
+Key-Id: 4584BE29
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (kfreebsd-amd64) 06 Sep 2011 09:36 ║
+║ samtools 0.1.18-2 (kfreebsd-amd64) 27 Jul 2012 15:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: kfreebsd-amd64
-Hit http://ftp.gr.debian.org sid InRelease
-Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org 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]
Ign http://incoming.debian.org InRelease
-Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
-Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
-Get:1 http://ftp.gr.debian.org sid/main TranslationIndex [2045 B]
-Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages
-Ign http://ftp.gr.debian.org sid/contrib Translation-en
-Ign http://ftp.gr.debian.org sid/non-free Translation-en
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:3 http://incoming.debian.org Release [1604 B]
-Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages
-Get:4 http://incoming.debian.org Sources [33.2 kB]
-Get:5 http://incoming.debian.org Packages [352 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org sid/non-free Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 389 kB in 4s (81.7 kB/s)
+Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [98.1 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5657 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: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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [114 kB]
+Fetched 25.0 MB in 23s (1052 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -92,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 2s (182 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (364 kB/s)
Download complete and in download only mode
Check arch
@@ -110,18 +95,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.17-1)
+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 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -130,70 +115,174 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.2+ds2-5)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-5)
-util-linux: already installed (2.19.1-5)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-4)
+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 (1.16.7)
+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)
+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)
+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)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
-debhelper: already installed (8.9.6 >= 8 is satisfied)
+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)
+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: already installed (0.48-7)
+quilt: missing
libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: cdbs libncurses5-dev
+Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
+The following extra packages will be installed:
+ 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
Suggested packages:
- devscripts ncurses-doc
+ 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 libncurses5-dev
+ 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]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/579 kB of archives.
-After this operation, 2003 kB of additional disk space will be used.
-Selecting previously deselected package cdbs.
-(Reading database ... 17857 files and directories currently installed.)
-Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_kfreebsd-amd64.deb) ...
-Processing triggers for man-db ...
-Setting up cdbs (0.4.96) ...
-Setting up libncurses5-dev (5.9-1) ...
+Fetched 10.4 MB in 0s (15.3 MB/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) ...
+Selecting previously unselected package libasprintf0c2:kfreebsd-amd64.
+Unpacking libasprintf0c2:kfreebsd-amd64 (from .../libasprintf0c2_0.18.1.1-9_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) ...
+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) ...
+Selecting previously unselected package libcroco3:kfreebsd-amd64.
+Unpacking libcroco3:kfreebsd-amd64 (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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_kfreebsd-amd64.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_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) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
+Unpacking libtinfo-dev:kfreebsd-amd64 (from .../libtinfo-dev_5.9-10_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_kfreebsd-amd64.deb) ...
+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 libmagic1:kfreebsd-amd64 (5.11-2) ...
+Setting up libxml2:kfreebsd-amd64 (2.8.0+dfsg1-5) ...
+Setting up libffi5:kfreebsd-amd64 (3.0.10-3) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.32.3-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:kfreebsd-amd64 (0.6.5-1) ...
+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 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) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:kfreebsd-amd64 (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:kfreebsd-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 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.4_4.4.6-10 g++-4.6_4.6.1-9 gcc-4.4_4.4.6-10 gcc-4.6_4.6.1-9 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.4-dev_4.4.6-10 libstdc++6-4.6-dev_4.6.1-9
-Package versions: apt_0.8.15.6 autoconf_2.68-1 autoconf2.64_2.64-3 autogen_1:5.12-0.1 automake_1:1.11.1-1 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bison_1:2.4.1.dfsg-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 chrpath_0.13-2 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.4_4.4.6-10 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 debian-archive-keyring_2010.08.28 debianutils_4.0.2 dejagnu_1.5-2 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 expect_5.45-1 fakeroot_1.17-1 file_5.04-5+b1 findutils_4.4.2-1 flex_2.5.35-10 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.4_4.4.6-10 g++-4.6_4.6.1-9 g++-4.6-multilib_4.6.1-9 g++-multilib_4:4.6.1-2 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-2 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gcc-4.6-multilib_4.6.1-9 gcc-multilib_4:4.6.1-2 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gperf_3.0.3-1+b1 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 guile-1.8-libs_1.8.8+1-6 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 kfreebsd-kernel-headers_0.57 lib32gcc1_1:4.6.1-9 lib32gomp1_4.6.1-9 lib32quadmath0_4.6.1-9 lib32stdc++6_4.6.1-9 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc0.1_2.13-18 libc0.1-dev_2.13-18 libc0.1-dev-i386_2.13-18 libc0.1-i386_2.13-18 libcam0_8.2+ds1-4 libcloog-ppl-dev_0.15.9-3 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb4.8_4.8.30-9 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-3 libelfg0-dev_0.8.13-3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp-dev_2:5.0.2+dfsg-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 libltdl7_2.4-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmpc-dev_0.9-3 libmpc2_0.9-3 libmpfr-dev_3.0.1-6 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libopts25_1:5.12-0.1 libopts25-dev_1:5.12-0.1 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 libppl-c4_0.11.2-4 libppl0.11-dev_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-9 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 libsigsegv2_2.9-4 libslang2_2.2.4-3 libsqlite3-0_3.7.7-2 libss2_1.42~WIP-2011-07-02-1 libssl1.0.0_1.0.0d-3 libstdc++6_4.6.1-9 libstdc++6-4.4-dev_4.4.6-10 libstdc++6-4.6-dev_4.6.1-9 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 libtool_2.4-4 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 locales_2.13-18 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lsb-release_3.2-28 lzma_4.43-14 m4_1.4.16-2 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mime-support_3.51-1 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 patchutils_0.3.2-1 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 python_2.6.7-3 python-minimal_2.6.7-3 python-support_1.0.14 python2.6_2.6.7-4 python2.6-minimal_2.6.7-4 quilt_0.48-7 readline-common_6.2-4 realpath_1.15 sed_4.2.1-9 sensible-utils_0.0.6 sharutils_1:4.11-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tcl8.5_8.5.10-1 texinfo_4.13a.dfsg.1-8 type-handling_0.2.23 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_1.16.7 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -204,13 +293,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -219,40 +310,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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
@@ -260,134 +352,146 @@ 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
+ 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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-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_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/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_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/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_0.1.18-2-kfreebsd-amd64-YYfmk3/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/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. 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_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/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_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/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_0.1.18-2-kfreebsd-amd64-YYfmk3/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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/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_0.1.18-2-kfreebsd-amd64-YYfmk3/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.
@@ -413,7 +517,7 @@ 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_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -448,8 +552,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -475,7 +579,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -490,69 +594,68 @@ 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_0.1.18-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_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_0.1.18-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../samtools_0.1.18-1_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-0938
+Build finished at 20120727-1528
-samtools_0.1.18-1_kfreebsd-amd64.changes:
+samtools_0.1.18-2_kfreebsd-amd64.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 8a39f128e0ac110ee1d45084e8243951ce3cf6aa 527722 samtools_0.1.18-1_kfreebsd-amd64.deb
- 9b59a326c91d5e85fce7e846c7d990059c6bddd5 153840 libbam-dev_0.1.18-1_kfreebsd-amd64.deb
+ 166e5a6448196b1de06d7c8d595b1342f706e8c7 532224 samtools_0.1.18-2_kfreebsd-amd64.deb
+ 3b4a76a4b48da0352866a57453199d0a936e7a3c 156374 libbam-dev_0.1.18-2_kfreebsd-amd64.deb
Checksums-Sha256:
- bf6c3f4fd9084f11801119ee989e4bf7d173a3bb2c57a79ad7f7ee9413623d57 527722 samtools_0.1.18-1_kfreebsd-amd64.deb
- 2dca0e928fb2c3f451ae07a518b083c06fc6a21fea40713b9944627bdb845ff8 153840 libbam-dev_0.1.18-1_kfreebsd-amd64.deb
+ 926a6f84e198b3368e1f35c621f7ffdd040babbcafdf9f79a23fcdbfcc21f611 532224 samtools_0.1.18-2_kfreebsd-amd64.deb
+ ee0a28ab625a8a48039c30937a457e783832a3a611e1e0ed4d23f22bad95b16e 156374 libbam-dev_0.1.18-2_kfreebsd-amd64.deb
Files:
- 8b5fc39f2c2a24d1d455126ac50a801f 527722 science optional samtools_0.1.18-1_kfreebsd-amd64.deb
- 4fa210cfabefb9fcd39c5abb0c2dc303 153840 libdevel optional libbam-dev_0.1.18-1_kfreebsd-amd64.deb
+ 44b2ad6bbf66c531a379864281b0073d 532224 science optional samtools_0.1.18-2_kfreebsd-amd64.deb
+ 0c90e18b15ac65490405229b86ad2afc 156374 libdevel optional libbam-dev_0.1.18-2_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_kfreebsd-amd64.deb
+samtools_0.1.18-2_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 527722 bytes: control archive= 1766 bytes.
- 797 bytes, 16 lines control
+ size 532224 bytes: control archive= 1767 bytes.
+ 802 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1036
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 968
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -564,31 +667,31 @@ samtools_0.1.18-1_kfreebsd-amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/doc/samtools/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 592 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 2011-09-06 09:38 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-09-06 09:38 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2012-07-27 15:27 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-09-06 09:38 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-07-27 15:27 ./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 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-09-06 09:38 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-09-06 09:38 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/samtools/
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:27 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:27 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./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
@@ -601,34 +704,34 @@ drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-09-06 09:38 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/bin/
--rwxr-xr-x root/root 130528 2011-09-06 09:38 ./usr/bin/bcftools
--rwxr-xr-x root/root 24536 2011-09-06 09:38 ./usr/bin/razip
--rwxr-xr-x root/root 363832 2011-09-06 09:38 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/samtools/
--rwxr-xr-x root/root 18000 2011-09-06 09:38 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8208 2011-09-06 09:38 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8144 2011-09-06 09:38 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11864 2011-09-06 09:38 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8736 2011-09-06 09:38 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-1_kfreebsd-amd64.deb
+-rwxr-xr-x root/root 5778 2012-07-27 15:28 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/bin/
+-rwxr-xr-x root/root 130696 2012-07-27 15:28 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24912 2012-07-27 15:28 ./usr/bin/razip
+-rwxr-xr-x root/root 372576 2012-07-27 15:28 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18208 2012-07-27 15:28 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8440 2012-07-27 15:28 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8360 2012-07-27 15:28 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 12104 2012-07-27 15:28 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 8896 2012-07-27 15:28 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 153840 bytes: control archive= 928 bytes.
+ size 156374 bytes: control archive= 934 bytes.
683 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 466
+ Installed-Size: 432
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -639,20 +742,20 @@ libbam-dev_0.1.18-1_kfreebsd-amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
-rw-r--r-- root/root 5502 2011-09-06 07:01 ./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 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/lib/
--rw-r--r-- root/root 323274 2011-09-06 09:38 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 09:38 ./usr/include/samtools/
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:28 ./usr/lib/
+-rw-r--r-- root/root 332474 2012-07-27 15:28 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:27 ./usr/include/samtools/
-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 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
@@ -671,40 +774,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1315301795-15293/build/buildd-samtools_0.1.18-1-kfreebsd-amd64-RjwLsE
-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* libncurses5-dev*
-0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded.
-After this operation, 2003 kB disk space will be freed.
-(Reading database ... 17948 files and directories currently installed.)
-Removing cdbs ...
-Removing libncurses5-dev ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1343402622-97734/build/buildd-samtools_0.1.18-2-kfreebsd-amd64-YYfmk3
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 12178
-Build-Time: 60
+Build-Space: 13452
+Build-Time: 66
Distribution: sid
-Install-Time: 35
-Job: samtools_0.1.18-1
+Install-Time: 58
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 127
-Source-Version: 0.1.18-1
-Space: 12178
+Package-Time: 268
+Source-Version: 0.1.18-2
+Space: 13452
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0938
-Build needed 00:02:07, 12178k disc space
-Signature with key '56BAE008' requested:
+Finished at 20120727-1528
+Build needed 00:04:28, 13452k disc space
+Signature with key '4584BE29' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index c1bb53a..f790c47 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,83 +1,62 @@
-From buildd at finzi.debian.org Tue Sep 06 09:32:10 2011
-Return-path: <buildd at finzi.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at fils.debian.org Fri Jul 27 15:13:56 2012
+Return-path: <buildd at fils.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 finzi.debian.org>)
- id 1R0s0n-0001sW-MP
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:32:10 +0000
-Received: from finzi.debian.org ([206.12.19.111])
+ (Exim 4.72) (envelope-from <buildd at fils.debian.org>)
+ id 1SumEm-0003SU-1o
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:13:56 +0000
+Received: from fils.debian.org ([82.195.75.89])
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)
- (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1R0s0k-0001KV-DO; Tue, 06 Sep 2011 09:32:06 +0000
-Received: from buildd by finzi.debian.org with local (Exim 4.72)
- (envelope-from <buildd at finzi.debian.org>)
- id 1R0s0i-000EQw-17; Tue, 06 Sep 2011 09:32:04 +0000
-Message-Id: <E1R0s0i-000EQw-17 at finzi.debian.org>
+ CN=fils.debian.org, EMAIL=hostmaster at fils.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at fils.debian.org>)
+ id 1SumEl-0004AH-2a; Fri, 27 Jul 2012 15:13:55 +0000
+Received: from buildd by fils.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fils.debian.org>)
+ id 1SumEj-000KwE-Vx; Fri, 27 Jul 2012 15:13:53 +0000
+Message-Id: <E1SumEj-000KwE-Vx at fils.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Tue, 6 Sep 2011 09:32:03 +0000
-From: buildd on finzi <buildd at finzi.debian.org>
-To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on kfreebsd-i386
+Date: Fri, 27 Jul 2012 15:13:53 +0000
+From: buildd on fils <buildd at fils.debian.org>
+To: logs at buildd.debian.org,christoph at debian.org
+Subject: Log for successful build of samtools_0.1.18-2 on kfreebsd-i386
(dist=sid)
-Key-Id: C1A6480B
+Key-Id: 52E1CE73
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fils.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (kfreebsd-i386) 06 Sep 2011 09:29 ║
+║ samtools 0.1.18-2 (kfreebsd-i386) 27 Jul 2012 15:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: kfreebsd-i386
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Get:1 http://debian.netcologne.de unstable InRelease [249 kB]
+Get:2 http://debian.netcologne.de unstable/main Sources [6317 kB]
+Get:3 http://incoming.debian.org unstable InRelease [249 kB]
+Get:4 http://debian.netcologne.de unstable/contrib Sources [53.9 kB]
+Get:5 http://debian.netcologne.de unstable/non-free Sources [98.1 kB]
+Get:6 http://debian.netcologne.de unstable/main kfreebsd-i386 Packages [5652 kB]
+Get:7 http://debian.netcologne.de unstable/contrib kfreebsd-i386 Packages [37.0 kB]
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:4 http://incoming.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
-Hit http://incoming.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:5 http://incoming.debian.org sid/main TranslationIndex [2045 B]
-Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:6 http://mirror-ubc.debian.org sid InRelease [146 kB]
-Get:7 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:8 http://incoming.debian.org Release [1604 B]
-Get:9 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
-Get:10 http://incoming.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Get:11 http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Get:12 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:13 http://incoming.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
-Get:14 http://mirror-ubc.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
-Get:15 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
-Get:16 http://incoming.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
-Get:17 http://incoming.debian.org Sources [32.4 kB]
-Get:18 http://incoming.debian.org Packages [356 kB]
-Get:19 http://mirror-ubc.debian.org sid/main 2011-09-06-0818.53.pdiff [5050 B]
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org sid/non-free Translation-en
-Ign http://incoming.debian.org Translation-en
-Get:20 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-09-06-0818.53.pdiff [3396 B]
-Fetched 712 kB in 9s (72.5 kB/s)
+Get:8 http://incoming.debian.org unstable/main Sources [6315 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-i386 Packages [5652 kB]
+Get:12 http://incoming.debian.org unstable/contrib kfreebsd-i386 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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 24.9 MB in 15s (1594 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -98,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 0s (397 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (287 kB/s)
Download complete and in download only mode
Check arch
@@ -116,18 +95,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.17-1)
+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 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -136,37 +115,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.2+ds2-5)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-5)
-util-linux: already installed (2.19.1-5)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-4)
+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 (1.16.7)
+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)
+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)
+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)
+tar: already installed (1.26-4)
+bsdutils: already installed (1:2.20.1-5.1)
+util-linux: already installed (2.20.1-5.1)
libc6-dev: already installed (~*=PROVIDED=*=)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -177,95 +156,145 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
+ 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:
- devscripts dh-make gettext-doc ncurses-doc groff 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:
- curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
- libmail-sendmail-perl
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1
+ 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://debian.netcologne.de/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.1-1 [38.4 kB]
+Get:2 http://debian.netcologne.de/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-9 [26.7 kB]
+Get:3 http://debian.netcologne.de/debian/ unstable/main libmagic1 kfreebsd-i386 5.11-2 [204 kB]
+Get:4 http://debian.netcologne.de/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.30-5 [241 kB]
+Get:5 http://debian.netcologne.de/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-5 [904 kB]
+Get:6 http://debian.netcologne.de/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
+Get:7 http://debian.netcologne.de/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.32.3-1 [2060 kB]
+Get:8 http://debian.netcologne.de/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.5-1 [151 kB]
+Get:9 http://debian.netcologne.de/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
+Get:10 http://debian.netcologne.de/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-9 [140 kB]
+Get:11 http://debian.netcologne.de/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.3 [204 kB]
+Get:12 http://debian.netcologne.de/debian/ unstable/main groff-base kfreebsd-i386 1.21-9 [1095 kB]
+Get:13 http://debian.netcologne.de/debian/ unstable/main man-db kfreebsd-i386 2.6.2-1 [1038 kB]
+Get:14 http://debian.netcologne.de/debian/ unstable/main file kfreebsd-i386 5.11-2 [51.5 kB]
+Get:15 http://debian.netcologne.de/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-9 [131 kB]
+Get:16 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://debian.netcologne.de/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
+Get:18 http://debian.netcologne.de/debian/ unstable/main gettext kfreebsd-i386 0.18.1.1-9 [1894 kB]
+Get:19 http://debian.netcologne.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://debian.netcologne.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://debian.netcologne.de/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://debian.netcologne.de/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
+Get:23 http://debian.netcologne.de/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9-10 [93.1 kB]
+Get:24 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9-10 [210 kB]
+Get:25 http://debian.netcologne.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://debian.netcologne.de/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
-0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/8631 kB of archives.
-After this operation, 24.1 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 12381 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_kfreebsd-i386.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_kfreebsd-i386.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_kfreebsd-i386.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_kfreebsd-i386.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package html2text.
+Fetched 10.7 MB in 1s (6041 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) ...
+Selecting previously unselected package libasprintf0c2:kfreebsd-i386.
+Unpacking libasprintf0c2:kfreebsd-i386 (from .../libasprintf0c2_0.18.1.1-9_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) ...
+Selecting previously unselected package libxml2:kfreebsd-i386.
+Unpacking libxml2:kfreebsd-i386 (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:kfreebsd-i386.
+Unpacking libcroco3:kfreebsd-i386 (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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_kfreebsd-i386.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_kfreebsd-i386.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_kfreebsd-i386.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_kfreebsd-i386.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_kfreebsd-i386.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_kfreebsd-i386.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-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_9.20120608_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.
+Unpacking libtinfo-dev:kfreebsd-i386 (from .../libtinfo-dev_5.9-10_kfreebsd-i386.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_kfreebsd-i386.deb) ...
+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 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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:kfreebsd-i386 (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:kfreebsd-i386 (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 0 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-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 kfreebsd-kernel-headers_0.57 libc0.1-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9
-Package versions: apt_0.8.15.6 autotools-dev_20110511.1 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 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-english_1.5.38 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_1.17-1 file_5.04-5+b1 findutils_4.4.2-1 freebsd-utils_8.2+ds2-5 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 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 kfreebsd-kernel-headers_0.57 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc0.1_2.13-18 libc0.1-dev_2.13-18 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libexpat1_2.0.1-7 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 libgssglue1_0.3-3 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-6 libncurses5_5.9-1 libncurses5-dev_5.9-1 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libquadmath0_4.6.1-9 libreadline6_6.2-4 libsbuf0_8.2+ds1-4 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 libtimedate-perl_1.2000-1 libtirpc1_0.2.2-5 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 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 quilt_0.48-7 readline-common_6.2-4 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 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_1.16.7 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -276,13 +305,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -291,40 +322,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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
@@ -332,129 +364,141 @@ 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
+ 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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-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_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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 -fstack-protector --param=ssp-buffer-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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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 `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/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_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/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_0.1.18-2-kfreebsd-i386-cUguNf/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/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. 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_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/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_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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]
seqtk.c: In function 'stk_subseq':
@@ -465,15 +509,15 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/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_0.1.18-2-kfreebsd-i386-cUguNf/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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/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 `/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/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_0.1.18-2-kfreebsd-i386-cUguNf/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.
@@ -499,7 +543,7 @@ 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_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -534,8 +578,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -561,7 +605,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -576,69 +620,68 @@ 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_0.1.18-1_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_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_0.1.18-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.18-1_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-0931
+Build finished at 20120727-1513
-samtools_0.1.18-1_kfreebsd-i386.changes:
+samtools_0.1.18-2_kfreebsd-i386.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: kfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- cb33cc7329b1278127faff60292add2734416ffc 532642 samtools_0.1.18-1_kfreebsd-i386.deb
- 10b014005110e5fc17890bd96bfe206df1153ff4 160694 libbam-dev_0.1.18-1_kfreebsd-i386.deb
+ e6caa849974d817e29efb83bf5e3d56e832f4769 533754 samtools_0.1.18-2_kfreebsd-i386.deb
+ e4239efcd784e9fbbadabbd3ed88d38c3997f64a 160586 libbam-dev_0.1.18-2_kfreebsd-i386.deb
Checksums-Sha256:
- 6270482bbac85ed3cb7300cdb1d516aaab254846a84dfbd036c2908ec4e69534 532642 samtools_0.1.18-1_kfreebsd-i386.deb
- 1f972e4fb50e21be809430edadadfdf744fce92591a28bdd2e5c35dfe8303191 160694 libbam-dev_0.1.18-1_kfreebsd-i386.deb
+ 66fe54b4d029aeb954eaf9da191f15b0b425fdf69ea1db2fed3f622b51aa950d 533754 samtools_0.1.18-2_kfreebsd-i386.deb
+ d1ec8eb701ab60344ba07ab5c7d3ebb26d49bb38793f4c387bde978fb7fe69e8 160586 libbam-dev_0.1.18-2_kfreebsd-i386.deb
Files:
- 717849b0b349a09f57b0a384e0bb90d2 532642 science optional samtools_0.1.18-1_kfreebsd-i386.deb
- 53394320ca5f013d7be58c182b0f8504 160694 libdevel optional libbam-dev_0.1.18-1_kfreebsd-i386.deb
+ 9592907ebb2fff8a8f42e17bd07f1aa5 533754 science optional samtools_0.1.18-2_kfreebsd-i386.deb
+ 7cf87258eb269a602a7ee4deefe1f6d9 160586 libdevel optional libbam-dev_0.1.18-2_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_kfreebsd-i386.deb
+samtools_0.1.18-2_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 532642 bytes: control archive= 1761 bytes.
- 796 bytes, 16 lines control
+ size 533754 bytes: control archive= 1769 bytes.
+ 801 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1054
- Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 990
+ Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -650,31 +693,31 @@ samtools_0.1.18-1_kfreebsd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./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 2011-09-06 09:31 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-09-06 09:31 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2012-07-27 15:13 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2011-09-06 09:31 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-07-27 15:13 ./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 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2011-09-06 09:31 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2011-09-06 09:31 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/samtools/
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:13 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:13 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./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
@@ -687,34 +730,34 @@ drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2011-09-06 09:31 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/bin/
--rwxr-xr-x root/root 133656 2011-09-06 09:31 ./usr/bin/bcftools
--rwxr-xr-x root/root 25684 2011-09-06 09:31 ./usr/bin/razip
--rwxr-xr-x root/root 391400 2011-09-06 09:31 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/lib/samtools/
--rwxr-xr-x root/root 16748 2011-09-06 09:31 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6560 2011-09-06 09:31 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6560 2011-09-06 09:31 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10244 2011-09-06 09:31 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7136 2011-09-06 09:31 ./usr/lib/samtools/md5sum-lite
-lrwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-1_kfreebsd-i386.deb
+-rwxr-xr-x root/root 5778 2012-07-27 15:13 ./usr/share/samtools/varfilter.py
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/bin/
+-rwxr-xr-x root/root 134212 2012-07-27 15:13 ./usr/bin/bcftools
+-rwxr-xr-x root/root 24676 2012-07-27 15:13 ./usr/bin/razip
+-rwxr-xr-x root/root 399924 2012-07-27 15:13 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/samtools/
+-rwxr-xr-x root/root 16472 2012-07-27 15:13 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 6844 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 6844 2012-07-27 15:13 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10576 2012-07-27 15:13 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7452 2012-07-27 15:13 ./usr/lib/samtools/md5sum-lite
+lrwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 160694 bytes: control archive= 929 bytes.
+ size 160586 bytes: control archive= 929 bytes.
682 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 434
+ Installed-Size: 400
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -725,20 +768,20 @@ libbam-dev_0.1.18-1_kfreebsd-i386.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./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 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 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/lib/
--rw-r--r-- root/root 293418 2011-09-06 09:31 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 09:31 ./usr/include/samtools/
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/lib/
+-rw-r--r-- root/root 299796 2012-07-27 15:13 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:13 ./usr/include/samtools/
-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 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
@@ -757,70 +800,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1315301373-52721/build/buildd-samtools_0.1.18-1-kfreebsd-i386-uGxhWm
-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* html2text*
- intltool-debian* libcroco3* libglib2.0-0* libmagic1* libncurses5-dev*
- libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 20 to remove and 0 not upgraded.
-After this operation, 24.1 MB disk space will be freed.
-(Reading database ... 13608 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing 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 man-db ...
-Purging configuration files for man-db ...
-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-ki-sbuild-1343401937-78235/build/buildd-samtools_0.1.18-2-kfreebsd-i386-cUguNf
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 10056
-Build-Time: 67
+Build-Space: 11026
+Build-Time: 49
Distribution: sid
-Install-Time: 41
-Job: samtools_0.1.18-1
+Install-Time: 8
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 129
-Source-Version: 0.1.18-1
-Space: 10056
+Package-Time: 94
+Source-Version: 0.1.18-2
+Space: 11026
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0931
-Build needed 00:02:09, 10056k disc space
-Signature with key 'C1A6480B' requested:
+Finished at 20120727-1513
+Build needed 00:01:34, 11026k disc space
+Signature with key '52E1CE73' requested:
diff --git a/mips.log b/mips.log
index eb49adf..d192cd8 100644
--- a/mips.log
+++ b/mips.log
@@ -1,67 +1,60 @@
-From buildd2 at corelli.debian.org Tue Sep 06 09:50:49 2011
+From buildd2 at corelli.debian.org Fri Jul 27 15:33:27 2012
Return-path: <buildd2 at corelli.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 <buildd2 at corelli.debian.org>)
- id 1R0sIq-0005Hf-N7
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:50:49 +0000
+ id 1SumXf-0002B0-FW
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:33:27 +0000
Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=corelli.debian.org, EMAIL=hostmaster at corelli.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 <buildd2 at corelli.debian.org>)
- id 1R0sIn-0002DM-QB
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:50:46 +0000
-Received: from buildd2 by corelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd2 at corelli.debian.org>) id 1R0sIl-0005Rp-Hc
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:50:43 +0000
+ id 1SumXd-00055o-QE
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:33:26 +0000
+Received: from buildd2 by corelli.debian.org with local (Exim 4.72)
+ (envelope-from <buildd2 at corelli.debian.org>) id 1SumXa-0005ZD-OG
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:33:22 +0000
+Date: Fri, 27 Jul 2012 15:33:22 +0000
+Message-Id: <E1SumXa-0005ZD-OG at corelli.debian.org>
From: buildd on corelli <buildd2 at corelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on mips (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-2 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1R0sIl-0005Rp-Hc at corelli.debian.org>
-Date: Tue, 06 Sep 2011 09:50:43 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on corelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (mips) 06 Sep 2011 09:27 ║
+║ samtools 0.1.18-2 (mips) 27 Jul 2012 15:07 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5470 kB]
+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]
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 [5470 kB]
+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 [94.9 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7462 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib mips Packages [56.2 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:10 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
-Get:13 http://incoming.debian.org unstable/main mips Packages [7462 kB]
-Get:14 http://incoming.debian.org unstable/contrib mips Packages [56.2 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [32.4 kB]
-Get:18 http://incoming.debian.org Packages [356 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 27.0 MB in 1min 12s (372 kB/s)
+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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.6 MB in 1min 36s (264 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 0s (432 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (361 kB/s)
Download complete and in download only mode
Check arch
@@ -100,24 +93,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 69 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 69 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -126,37 +113,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-18)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.10)
+base-passwd: already installed (3.5.24)
+bash: already installed (4.2-2)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.1)
+diffutils: already installed (1:3.2-6)
+dpkg: already installed (1.16.4.2)
+e2fsprogs: already installed (1.42.2-2)
+findutils: already installed (4.4.2-4)
+grep: already installed (2.12-2)
+gzip: already installed (1.4-5)
+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)
+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)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.4.2 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -166,134 +153,169 @@ Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-de
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
+ liblzma5 libmagic1 libncurses5 libpipeline1 libtinfo-dev libtinfo5
+ libunistring0 libxml2 man-db ncurses-bin po-debconf zlib1g
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz
+ 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
+ libgpm2 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 libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 13 not upgraded.
-Need to get 10.0 MB of archives.
-After this operation, 31.5 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-3 [35.6 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 8.12-4 [227 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 8.2.3 [206 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-6 [1152 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.0.2-2 [990 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.04-5+b1 [239 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.04-5+b1 [49.9 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-4 [142 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.7.8.dfsg-4 [858 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.28.6-1 [1509 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.2-1 [110 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-4 [415 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-4 [2025 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.54-1 [28.8 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-1 [509 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
+ 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
+The following packages will be upgraded:
+ liblzma5 libncurses5 libtinfo5 ncurses-bin zlib1g
+5 upgraded, 25 newly installed, 0 to remove and 64 not upgraded.
+Need to get 11.4 MB of archives.
+After this operation, 28.9 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 libxml2 mips 2.8.0+dfsg1-5 [869 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 2.32.3-1 [1991 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.5-1 [140 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 0.18.1.1-9 [139 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.3 [208 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-9 [1156 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.2-1 [1029 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.11-2 [51.5 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-9 [141 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-9 [1918 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev mips 5.9-10 [104 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-10 [223 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:30 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 10.0 MB in 1s (5927 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10686 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mips.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mips.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mips.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mips.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mips.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_mips.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mips.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mips.deb) ...
-Selecting previously deselected package html2text.
+Fetched 11.4 MB in 5s (2267 kB/s)
+(Reading database ... 10730 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 ... 10730 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 ... 10730 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 ... 10730 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 ... 10730 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) ...
+Selecting previously unselected package libpipeline1:mips.
+(Reading database ... 10730 files and directories currently installed.)
+Unpacking libpipeline1:mips (from .../libpipeline1_1.2.1-1_mips.deb) ...
+Selecting previously unselected package libasprintf0c2:mips.
+Unpacking libasprintf0c2:mips (from .../libasprintf0c2_0.18.1.1-9_mips.deb) ...
+Selecting previously unselected package libmagic1:mips.
+Unpacking libmagic1:mips (from .../libmagic1_5.11-2_mips.deb) ...
+Selecting previously unselected package libxml2:mips.
+Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:mips.
+Unpacking libcroco3:mips (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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_mips.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mips.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mips.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mips.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_mips.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_mips.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_mips.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mips.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
+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_mips.deb) ...
+Selecting previously unselected package libtinfo-dev:mips.
+Unpacking libtinfo-dev:mips (from .../libtinfo-dev_5.9-10_mips.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_mips.deb) ...
+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 libmagic1:mips (5.11-2) ...
+Setting up libxml2:mips (2.8.0+dfsg1-5) ...
+Setting up libffi5:mips (3.0.10-3) ...
+Setting up libglib2.0-0:mips (2.32.3-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:mips (0.6.5-1) ...
+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 (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:mips (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:mips (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libppl9 libpwl5 libcloog-ppl0 libgmpxx4ldbl libppl-c4
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-8 gcc-4.6_4.6.1-8 libc6-dev_2.13-18 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 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_2.21.52.20110606-2 binutils-dev_2.21.52.20110606-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-8 dash_0.5.7-1 debconf_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_4.6.1-8 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-10 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-8 gcc-4.6-base_4.6.1-8 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_1.0.5-6 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 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_1:4.6.1-8 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_4.6.1-8 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 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 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_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 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 netbase_4.46 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-1 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
+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_2.1.6-6 libsemanage1_2.1.6-2 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 netbase_5.0 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-27 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -304,13 +326,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -319,40 +343,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/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" -k clean
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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
@@ -360,129 +385,135 @@ 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
+ 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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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]
-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 -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 -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 -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 -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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+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.c -o sam.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_index.c -o bam_index.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_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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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
+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. prob1.c -o prob1.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. 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 -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 -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 -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 -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 -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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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
+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_rmdup.c -o bam_rmdup.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_rmdupse.c -o bam_rmdupse.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_mate.c -o bam_mate.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_stat.c -o bam_stat.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_color.c -o bam_color.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. bamtk.c -o bamtk.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. kaln.c -o kaln.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. bam2bcf.c -o bam2bcf.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. bam2bcf_indel.c -o bam2bcf_indel.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. errmod.c -o errmod.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. sample.c -o sample.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. 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 `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/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. 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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -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]
seqtk.c: In function 'stk_subseq':
@@ -493,15 +524,15 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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 `/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/examples'
+/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/buildd2-samtools_0.1.18-2-mips-5Yrc8L/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.
@@ -527,7 +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/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -562,8 +593,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -589,7 +620,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.18-2-mips-5Yrc8L/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -604,69 +635,68 @@ 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_0.1.18-1_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_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_0.1.18-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../samtools_0.1.18-1_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-0950
+Build finished at 20120727-1533
-samtools_0.1.18-1_mips.changes:
+samtools_0.1.18-2_mips.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli2 at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 0556db815f6ab9c75d000c38d220bcd6e51d6ff2 524810 samtools_0.1.18-1_mips.deb
- 0cbc630a407d999d3d18b06334ded7f86c8f8a73 163634 libbam-dev_0.1.18-1_mips.deb
+ 1e6f2e7d1256c1f20d62b8c1dc2aa88284687f8a 525022 samtools_0.1.18-2_mips.deb
+ 2103520b2fa9f1081a0452fc08da309a9b12942f 162998 libbam-dev_0.1.18-2_mips.deb
Checksums-Sha256:
- 1db408c1fe42dfeaea2128756b51366a2817e6a17c1ed94cf3457908a1188d2d 524810 samtools_0.1.18-1_mips.deb
- a20ffd308f29f865fa66d0a17d7940b5083c7bb767dac8f082b35536b219d69c 163634 libbam-dev_0.1.18-1_mips.deb
+ 254fc1e9ddfd18395a50c6c89c8241431afa69a43f2f069ba6a8428af051a290 525022 samtools_0.1.18-2_mips.deb
+ 9632d34be16163f57274720135c8b437c64653ccde8f3e8c396f6339275b8ce4 162998 libbam-dev_0.1.18-2_mips.deb
Files:
- 1db4db366036e5ce0a5ef3881d36a986 524810 science optional samtools_0.1.18-1_mips.deb
- b88be612247af99b9f5af291ad89566b 163634 libdevel optional libbam-dev_0.1.18-1_mips.deb
+ ac982ec5b317b07ea294b16e52de99d8 525022 science optional samtools_0.1.18-2_mips.deb
+ aff061d43305d6b844a16026ddc09eae 162998 libdevel optional libbam-dev_0.1.18-2_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_mips.deb
+samtools_0.1.18-2_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 524810 bytes: control archive= 1769 bytes.
- 785 bytes, 16 lines control
+ size 525022 bytes: control archive= 1765 bytes.
+ 791 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1200
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1106
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -678,22 +708,71 @@ samtools_0.1.18-1_mips.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-380d3c0f-13d1-414c-ac3d-217f99a29cfc/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/samtools_0.1.18-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
-
-
-libbam-dev_0.1.18-1_mips.deb
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/samtools/
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:32 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 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 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:31 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:31 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 126609 2012-07-27 15:19 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 592 2011-09-06 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
+-rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:32 ./usr/share/doc/samtools/README.bcftools
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/lib/samtools/
+-rwxr-xr-x root/root 12432 2012-07-27 15:32 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2012-07-27 15:32 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 7472 2012-07-27 15:32 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9252 2012-07-27 15:32 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 17692 2012-07-27 15:32 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/bin/
+-rwxr-xr-x root/root 155204 2012-07-27 15:32 ./usr/bin/bcftools
+-rwxr-xr-x root/root 440320 2012-07-27 15:32 ./usr/bin/samtools
+-rwxr-xr-x root/root 29296 2012-07-27 15:32 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2012-07-27 15:32 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 163634 bytes: control archive= 930 bytes.
+ size 162998 bytes: control archive= 930 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 496
+ Installed-Size: 467
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -704,7 +783,25 @@ libbam-dev_0.1.18-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mips-sbuild-380d3c0f-13d1-414c-ac3d-217f99a29cfc/build/buildd2-samtools_0.1.18-1-mips-etBaIQ/libbam-dev_0.1.18-1_mips.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/include/samtools/
+-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 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 15:32 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2012-07-27 15:32 ./usr/lib/
+-rw-r--r-- root/root 335554 2012-07-27 15:32 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -718,7 +815,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-380d3c0f-13d1-414c-ac3d-217f99a29cfc/build/buildd2-samtools_0.1.18-1-mips-etBaIQ
+Purging /var/lib/schroot/mount/sid-mips-sbuild-e0fa827d-2930-47ab-919a-e891a4214d2f/build/buildd2-samtools_0.1.18-2-mips-5Yrc8L
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
@@ -728,83 +825,79 @@ Can't open average space db /var/lib/sbuild/avg-build-space
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 10920
-Build-Time: 1176
+Build-Space: 10956
+Build-Time: 1307
Distribution: sid
-Install-Time: 75
-Job: samtools_0.1.18-1
+Install-Time: 81
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 1366
-Source-Version: 0.1.18-1
-Space: 10920
+Package-Time: 1532
+Source-Version: 0.1.18-2
+Space: 10956
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0950
-Build needed 00:22:46, 10920k disc space
-Signature with key '4D9CC026' requested:
+Finished at 20120727-1533
+Build needed 00:25:32, 10956k disc space
+Signature with key 'B5319330' requested:
-From buildd at mayer.debian.org Tue Sep 06 09:45:40 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at rem.debian.org Fri Jul 27 15:31:57 2012
+Return-path: <buildd at rem.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1R0sDr-0004bB-Fy
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:40 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1SumWC-0001kx-Kx
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:56 +0000
+Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
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- CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1R0sDo-0001wh-HQ
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:37 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
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- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:32 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1SumWB-00054a-Ja
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:55 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>) id 1SumWA-0000eV-1l
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:54 +0000
+Date: Fri, 27 Jul 2012 15:31:54 +0000
+Message-Id: <E1SumWA-0000eV-1l at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-2 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1R0sDk-00042i-2R at mayer.debian.org>
-Date: Tue, 06 Sep 2011 09:45:32 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (mipsel) 06 Sep 2011 09:39 ║
+║ samtools 0.1.18-2 (mipsel) 27 Jul 2012 15:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: mipsel
-Hit http://debian.oregonstate.edu sid InRelease
-Hit http://debian.oregonstate.edu sid/main Sources
-Hit http://debian.oregonstate.edu sid/contrib Sources
-Hit http://debian.oregonstate.edu sid/main mipsel Packages
-Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://mirror.ayous.org unstable InRelease [249 kB]
+Get:2 http://incoming.debian.org unstable InRelease [249 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [6317 kB]
Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
+Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:5 http://mirror.ayous.org unstable/contrib Sources [53.9 kB]
+Get:6 http://mirror.ayous.org unstable/non-free Sources [98.1 kB]
+Get:7 http://mirror.ayous.org unstable/main mipsel Packages [5970 kB]
+Get:8 http://mirror.ayous.org unstable/contrib mipsel Packages [38.3 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 mipsel Packages [5971 kB]
+Get:12 http://incoming.debian.org unstable/contrib mipsel 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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [114 kB]
+Fetched 25.6 MB in 1min 10s (361 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -825,11 +918,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 0s (467 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (285 kB/s)
Download complete and in download only mode
Check arch
@@ -843,18 +936,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+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 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -863,37 +956,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-18)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+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 (1.16.7)
+e2fsprogs: already installed (1.42.4-3)
+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)
+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)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -904,98 +997,145 @@ 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
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ 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:
- 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 zlib1g-dev
+ 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 18 not upgraded.
+Need to get 10.6 MB of archives.
+After this operation, 29.3 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.1-1 [36.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libasprintf0c2 mipsel 0.18.1.1-9 [26.8 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.11-2 [202 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 1:8.30-5 [245 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.8.0+dfsg1-5 [868 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libffi5 mipsel 3.0.10-3 [22.8 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.32.3-1 [1985 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.5-1 [139 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libgettextpo0 mipsel 0.18.1.1-9 [139 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 9.0.3 [207 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-9 [1143 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.2-1 [1029 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.11-2 [51.5 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-9 [140 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-9 [1918 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.55-3 [28.8 kB]
+Get:23 http://mirror.ayous.org/debian/ unstable/main libtinfo-dev mipsel 5.9-10 [102 kB]
+Get:24 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.9-10 [221 kB]
+Get:25 http://mirror.ayous.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 4 not upgraded.
-Need to get 0 B/9778 kB of archives.
-After this operation, 30.7 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 11131 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_mipsel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
-Selecting previously deselected package html2text.
+Fetched 10.6 MB in 6s (1600 kB/s)
+Selecting previously unselected package libpipeline1:mipsel.
+(Reading database ... 10726 files and directories currently installed.)
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
+Selecting previously unselected package libasprintf0c2:mipsel.
+Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
+Selecting previously unselected package libmagic1:mipsel.
+Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
+Selecting previously unselected package libpcre3:mipsel.
+Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.30-5_mipsel.deb) ...
+Selecting previously unselected package libxml2:mipsel.
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:mipsel.
+Unpacking libcroco3:mipsel (from .../libcroco3_0.6.5-1_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 bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_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) ...
+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) ...
+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_mipsel.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mipsel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_mipsel.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_mipsel.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mipsel.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-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_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
+Selecting previously unselected package libtinfo-dev:mipsel.
+Unpacking libtinfo-dev:mipsel (from .../libtinfo-dev_5.9-10_mipsel.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_mipsel.deb) ...
+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 libmagic1:mipsel (5.11-2) ...
+Setting up libpcre3:mipsel (1:8.30-5) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-5) ...
+Setting up libffi5:mipsel (3.0.10-3) ...
+Setting up libglib2.0-0:mipsel (2.32.3-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:mipsel (0.6.5-1) ...
+Setting up libunistring0:mipsel (0.9.3-5) ...
+Setting up libgettextpo0:mipsel (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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:mipsel (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:mipsel (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 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-7 gcc-4.6_4.6.1-7 libc6-dev_2.13-18 libstdc++6_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 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_2.21.52.20110606-2 binutils-dev_2.21.52.20110606-2 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 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-7 dash_0.5.7-1 debconf_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 dmsetup_2:1.02.65-1 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_4.6.1-7 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-8 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-7 gcc-4.6-base_4.6.1-7 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 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-7 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_4.6.1-7 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 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 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_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 libtimedate-perl_1.2000-1 libudev0_172-1 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 module-init-tools_3.16-1 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 procps_1:3.2.8-11 quilt_0.48-7 readline-common_6.2-4 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-1 udev_172-1 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 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 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 libfile-fcntllock-perl_0.14-2 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 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_4.7.1-4 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1006,13 +1146,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -1021,40 +1163,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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
@@ -1062,129 +1205,135 @@ 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
+ 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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-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_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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]
-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 -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 -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 -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 -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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+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.c -o sam.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_index.c -o bam_index.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_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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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
+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. prob1.c -o prob1.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. 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 -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 -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 -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 -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 -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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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_0.1.18-2-mipsel-gTK9Kz/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
+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_rmdup.c -o bam_rmdup.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_rmdupse.c -o bam_rmdupse.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_mate.c -o bam_mate.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_stat.c -o bam_stat.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_color.c -o bam_color.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. bamtk.c -o bamtk.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. kaln.c -o kaln.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. bam2bcf.c -o bam2bcf.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. bam2bcf_indel.c -o bam2bcf_indel.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. errmod.c -o errmod.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. sample.c -o sample.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. 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 `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/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. 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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -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]
seqtk.c: In function 'stk_subseq':
@@ -1195,15 +1344,15 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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 `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
+/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_0.1.18-2-mipsel-gTK9Kz/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.
@@ -1229,7 +1378,7 @@ 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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -1264,8 +1413,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -1291,7 +1440,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -1306,69 +1455,68 @@ 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_0.1.18-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-0945
+Build finished at 20120727-1531
-samtools_0.1.18-1_mipsel.changes:
+samtools_0.1.18-2_mipsel.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
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- c3a6dab5622d5c2fd0578f13e2b4149a801b3ead 165668 libbam-dev_0.1.18-1_mipsel.deb
+ a504d15f054ac891b1ba7284434385f36055c933 528714 samtools_0.1.18-2_mipsel.deb
+ c66e727d2352afe7ef3951ed955346b8b00545c0 165552 libbam-dev_0.1.18-2_mipsel.deb
Checksums-Sha256:
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- a49d72fe4def41845d68a5e769800c8eb0bb06162e8f1d6a33d1061257e4dd32 165668 libbam-dev_0.1.18-1_mipsel.deb
+ 04d6a9bd7c5cd26399e5f857a9926d84e9bf8129e5fff69a8050f7bbfce89503 528714 samtools_0.1.18-2_mipsel.deb
+ 9cac6f06e69744fb5e0d00a5ec86244df335296c8f0a9aac5b1a3c8156dd41ec 165552 libbam-dev_0.1.18-2_mipsel.deb
Files:
- 4deeb6454e957327454c23815fba395d 527834 science optional samtools_0.1.18-1_mipsel.deb
- 34d65a3d9781feaa3681e21a80b13191 165668 libdevel optional libbam-dev_0.1.18-1_mipsel.deb
+ c813d9138d332a5252f94c369916b746 528714 science optional samtools_0.1.18-2_mipsel.deb
+ 4529f73dd815a7c74c6b207ac6d3a174 165552 libdevel optional libbam-dev_0.1.18-2_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_mipsel.deb
+samtools_0.1.18-2_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 527834 bytes: control archive= 1766 bytes.
- 787 bytes, 16 lines control
+ size 528714 bytes: control archive= 1765 bytes.
+ 793 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1200
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1106
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -1380,22 +1528,71 @@ samtools_0.1.18-1_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
-
-
-libbam-dev_0.1.18-1_mipsel.deb
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9252 2012-07-27 15:31 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 17692 2012-07-27 15:31 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 12432 2012-07-27 15:31 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:31 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:31 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2012-07-27 15:31 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2012-07-27 15:30 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:31 ./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 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+-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
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/bin/
+-rwxr-xr-x root/root 440320 2012-07-27 15:31 ./usr/bin/samtools
+-rwxr-xr-x root/root 155204 2012-07-27 15:31 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29168 2012-07-27 15:31 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2012-07-27 15:31 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165668 bytes: control archive= 923 bytes.
+ size 165552 bytes: control archive= 927 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 496
+ Installed-Size: 467
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -1406,7 +1603,25 @@ libbam-dev_0.1.18-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/libbam-dev_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./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
+-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 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
+-rw-r--r-- root/root 335626 2012-07-27 15:31 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./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 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1420,73 +1635,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 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* zlib1g-dev*
-0 upgraded, 0 newly installed, 21 to remove and 4 not upgraded.
-After this operation, 30.7 MB disk space will be freed.
-(Reading database ... 12540 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-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-mipsel-sbuild-a7bf88ef-1513-4495-9eba-fbb46666b629/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10932
-Build-Time: 290
+Build-Space: 10952
+Build-Time: 295
Distribution: sid
-Install-Time: 46
-Job: samtools_0.1.18-1
+Install-Time: 72
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 351
-Source-Version: 0.1.18-1
-Space: 10932
+Package-Time: 471
+Source-Version: 0.1.18-2
+Space: 10952
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0945
-Build needed 00:05:51, 10932k disc space
-Signature with key 'A5633F94' requested:
+Finished at 20120727-1531
+Build needed 00:07:51, 10952k disc space
+Signature with key 'BDA682F0' requested:
diff --git a/mipsel.log b/mipsel.log
index b40c66a..994c654 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,64 +1,60 @@
-From buildd at mayer.debian.org Tue Sep 06 09:45:40 2011
-Return-path: <buildd at mayer.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at rem.debian.org Fri Jul 27 15:31:57 2012
+Return-path: <buildd at rem.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1R0sDr-0004bB-Fy
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:40 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1SumWC-0001kx-Kx
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:56 +0000
+Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1R0sDo-0001wh-HQ
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:37 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1R0sDk-00042i-2R
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:45:32 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1SumWB-00054a-Ja
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:55 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>) id 1SumWA-0000eV-1l
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:31:54 +0000
+Date: Fri, 27 Jul 2012 15:31:54 +0000
+Message-Id: <E1SumWA-0000eV-1l at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.18-2 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1R0sDk-00042i-2R at mayer.debian.org>
-Date: Tue, 06 Sep 2011 09:45:32 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (mipsel) 06 Sep 2011 09:39 ║
+║ samtools 0.1.18-2 (mipsel) 27 Jul 2012 15:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: mipsel
-Hit http://debian.oregonstate.edu sid InRelease
-Hit http://debian.oregonstate.edu sid/main Sources
-Hit http://debian.oregonstate.edu sid/contrib Sources
-Hit http://debian.oregonstate.edu sid/main mipsel Packages
-Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Hit http://debian.oregonstate.edu sid/main TranslationIndex
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://mirror.ayous.org unstable InRelease [249 kB]
+Get:2 http://incoming.debian.org unstable InRelease [249 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [6317 kB]
Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org Release.gpg
-Hit http://incoming.debian.org sid/main Sources
-Hit http://incoming.debian.org sid/contrib Sources
-Hit http://incoming.debian.org sid/main mipsel Packages
-Hit http://incoming.debian.org sid/contrib mipsel Packages
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org Release
-Hit http://incoming.debian.org Sources
-Hit http://incoming.debian.org Packages
-Ign http://incoming.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
+Get:4 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:5 http://mirror.ayous.org unstable/contrib Sources [53.9 kB]
+Get:6 http://mirror.ayous.org unstable/non-free Sources [98.1 kB]
+Get:7 http://mirror.ayous.org unstable/main mipsel Packages [5970 kB]
+Get:8 http://mirror.ayous.org unstable/contrib mipsel Packages [38.3 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 mipsel Packages [5971 kB]
+Get:12 http://incoming.debian.org unstable/contrib mipsel 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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [114 kB]
+Fetched 25.6 MB in 1min 10s (361 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -79,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 0s (467 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (285 kB/s)
Download complete and in download only mode
Check arch
@@ -97,18 +93,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+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 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -117,37 +113,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-18)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+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 (1.16.7)
+e2fsprogs: already installed (1.42.4-3)
+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)
+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)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -158,98 +154,145 @@ 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
- libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf
+ 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:
- 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 zlib1g-dev
+ 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 18 not upgraded.
+Need to get 10.6 MB of archives.
+After this operation, 29.3 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.1-1 [36.7 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libasprintf0c2 mipsel 0.18.1.1-9 [26.8 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.11-2 [202 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 1:8.30-5 [245 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.8.0+dfsg1-5 [868 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libffi5 mipsel 3.0.10-3 [22.8 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.32.3-1 [1985 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.5-1 [139 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libgettextpo0 mipsel 0.18.1.1-9 [139 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 9.0.3 [207 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-9 [1143 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.2-1 [1029 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.11-2 [51.5 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-9 [140 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-9 [1918 kB]
+Get:19 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://mirror.ayous.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://mirror.ayous.org/debian/ unstable/main diffstat mipsel 1.55-3 [28.8 kB]
+Get:23 http://mirror.ayous.org/debian/ unstable/main libtinfo-dev mipsel 5.9-10 [102 kB]
+Get:24 http://mirror.ayous.org/debian/ unstable/main libncurses5-dev mipsel 5.9-10 [221 kB]
+Get:25 http://mirror.ayous.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 4 not upgraded.
-Need to get 0 B/9778 kB of archives.
-After this operation, 30.7 MB of additional disk space will be used.
-Selecting previously deselected package libpipeline1.
-(Reading database ... 11131 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_mipsel.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_mipsel.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_mipsel.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_mipsel.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_mipsel.deb) ...
-Selecting previously deselected package html2text.
+Fetched 10.6 MB in 6s (1600 kB/s)
+Selecting previously unselected package libpipeline1:mipsel.
+(Reading database ... 10726 files and directories currently installed.)
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.1-1_mipsel.deb) ...
+Selecting previously unselected package libasprintf0c2:mipsel.
+Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-9_mipsel.deb) ...
+Selecting previously unselected package libmagic1:mipsel.
+Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
+Selecting previously unselected package libpcre3:mipsel.
+Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.30-5_mipsel.deb) ...
+Selecting previously unselected package libxml2:mipsel.
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:mipsel.
+Unpacking libcroco3:mipsel (from .../libcroco3_0.6.5-1_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 bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_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) ...
+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) ...
+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_mipsel.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_mipsel.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_mipsel.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_mipsel.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_mipsel.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_mipsel.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_mipsel.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_mipsel.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-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_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
+Selecting previously unselected package libtinfo-dev:mipsel.
+Unpacking libtinfo-dev:mipsel (from .../libtinfo-dev_5.9-10_mipsel.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_mipsel.deb) ...
+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 libmagic1:mipsel (5.11-2) ...
+Setting up libpcre3:mipsel (1:8.30-5) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-5) ...
+Setting up libffi5:mipsel (3.0.10-3) ...
+Setting up libglib2.0-0:mipsel (2.32.3-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:mipsel (0.6.5-1) ...
+Setting up libunistring0:mipsel (0.9.3-5) ...
+Setting up libgettextpo0:mipsel (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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:mipsel (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:mipsel (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 4 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.52.20110606-2 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-7 gcc-4.6_4.6.1-7 libc6-dev_2.13-18 libstdc++6_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 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_2.21.52.20110606-2 binutils-dev_2.21.52.20110606-2 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 cpio_2.11-7 cpp_4:4.6.1-2 cpp-4.6_4.6.1-7 dash_0.5.7-1 debconf_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 dmsetup_2:1.02.65-1 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_4.6.1-7 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-8 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-7 gcc-4.6-base_4.6.1-7 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 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.65-1 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-7 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_4.6.1-7 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 libncursesw5_5.9-1 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-2 libpcre3_8.12-4 libpipeline1_1.2.0-3 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 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_4.6.1-7 libstdc++6-4.6-dev_4.6.1-7 libtimedate-perl_1.2000-1 libudev0_172-1 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 module-init-tools_3.16-1 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 procps_1:3.2.8-11 quilt_0.48-7 readline-common_6.2-4 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-1 udev_172-1 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 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 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 libfile-fcntllock-perl_0.14-2 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 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_4.7.1-4 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -260,13 +303,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -275,40 +320,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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
@@ -316,129 +362,135 @@ 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
+ 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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-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_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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]
-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 -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 -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 -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 -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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+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.c -o sam.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_index.c -o bam_index.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_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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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
+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. prob1.c -o prob1.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. 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 -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 -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 -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 -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 -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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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_0.1.18-2-mipsel-gTK9Kz/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
+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_rmdup.c -o bam_rmdup.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_rmdupse.c -o bam_rmdupse.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_mate.c -o bam_mate.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_stat.c -o bam_stat.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_color.c -o bam_color.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. bamtk.c -o bamtk.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. kaln.c -o kaln.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. bam2bcf.c -o bam2bcf.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. bam2bcf_indel.c -o bam2bcf_indel.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. errmod.c -o errmod.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. sample.c -o sample.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. 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 `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/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. 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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -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]
seqtk.c: In function 'stk_subseq':
@@ -449,15 +501,15 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/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 `/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
+/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_0.1.18-2-mipsel-gTK9Kz/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.
@@ -483,7 +535,7 @@ 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_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -518,8 +570,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -545,7 +597,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -560,69 +612,68 @@ 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_0.1.18-1_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-1_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (rem) <buildd_mipsel-rem at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-0945
+Build finished at 20120727-1531
-samtools_0.1.18-1_mipsel.changes:
+samtools_0.1.18-2_mipsel.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: mipsel Build Daemon (rem) <buildd_mipsel-rem 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- 246b8af54b8e4f52d6d4dc8a408a431878aef7c7 527834 samtools_0.1.18-1_mipsel.deb
- c3a6dab5622d5c2fd0578f13e2b4149a801b3ead 165668 libbam-dev_0.1.18-1_mipsel.deb
+ a504d15f054ac891b1ba7284434385f36055c933 528714 samtools_0.1.18-2_mipsel.deb
+ c66e727d2352afe7ef3951ed955346b8b00545c0 165552 libbam-dev_0.1.18-2_mipsel.deb
Checksums-Sha256:
- ef734da95a9d183c7603141f20ce78dfe1c036044704f648e6c48e0b38e88840 527834 samtools_0.1.18-1_mipsel.deb
- a49d72fe4def41845d68a5e769800c8eb0bb06162e8f1d6a33d1061257e4dd32 165668 libbam-dev_0.1.18-1_mipsel.deb
+ 04d6a9bd7c5cd26399e5f857a9926d84e9bf8129e5fff69a8050f7bbfce89503 528714 samtools_0.1.18-2_mipsel.deb
+ 9cac6f06e69744fb5e0d00a5ec86244df335296c8f0a9aac5b1a3c8156dd41ec 165552 libbam-dev_0.1.18-2_mipsel.deb
Files:
- 4deeb6454e957327454c23815fba395d 527834 science optional samtools_0.1.18-1_mipsel.deb
- 34d65a3d9781feaa3681e21a80b13191 165668 libdevel optional libbam-dev_0.1.18-1_mipsel.deb
+ c813d9138d332a5252f94c369916b746 528714 science optional samtools_0.1.18-2_mipsel.deb
+ 4529f73dd815a7c74c6b207ac6d3a174 165552 libdevel optional libbam-dev_0.1.18-2_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_mipsel.deb
+samtools_0.1.18-2_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 527834 bytes: control archive= 1766 bytes.
- 787 bytes, 16 lines control
+ size 528714 bytes: control archive= 1765 bytes.
+ 793 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1200
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1106
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -634,22 +685,71 @@ samtools_0.1.18-1_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/samtools_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
-
-
-libbam-dev_0.1.18-1_mipsel.deb
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9252 2012-07-27 15:31 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 17692 2012-07-27 15:31 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 12432 2012-07-27 15:31 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7472 2012-07-27 15:31 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2012-07-27 15:31 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2012-07-27 15:31 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/samtools/
+-rwxr-xr-x root/root 5778 2012-07-27 15:31 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 126609 2012-07-27 15:30 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 1966 2012-07-27 15:31 ./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 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./usr/share/doc/samtools/changelog.Debian.gz
+-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
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/bin/
+-rwxr-xr-x root/root 440320 2012-07-27 15:31 ./usr/bin/samtools
+-rwxr-xr-x root/root 155204 2012-07-27 15:31 ./usr/bin/bcftools
+-rwxr-xr-x root/root 29168 2012-07-27 15:31 ./usr/bin/razip
+lrwxrwxrwx root/root 0 2012-07-27 15:31 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165668 bytes: control archive= 923 bytes.
+ size 165552 bytes: control archive= 927 bytes.
675 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 496
+ Installed-Size: 467
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -660,7 +760,25 @@ libbam-dev_0.1.18-1_mipsel.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-dpkg-deb: file `/var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu/libbam-dev_0.1.18-1_mipsel.deb' contains ununderstood data member data.tar.xz , giving up
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./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
+-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 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/lib/
+-rw-r--r-- root/root 335626 2012-07-27 15:31 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:31 ./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 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -674,73 +792,27 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-b2bddbbb-bf0e-4be4-a302-020e24fbfb7f/build/buildd-samtools_0.1.18-1-mipsel-YYhVbu
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 4 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* zlib1g-dev*
-0 upgraded, 0 newly installed, 21 to remove and 4 not upgraded.
-After this operation, 30.7 MB disk space will be freed.
-(Reading database ... 12540 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-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-mipsel-sbuild-a7bf88ef-1513-4495-9eba-fbb46666b629/build/buildd-samtools_0.1.18-2-mipsel-gTK9Kz
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 10932
-Build-Time: 290
+Build-Space: 10952
+Build-Time: 295
Distribution: sid
-Install-Time: 46
-Job: samtools_0.1.18-1
+Install-Time: 72
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 351
-Source-Version: 0.1.18-1
-Space: 10932
+Package-Time: 471
+Source-Version: 0.1.18-2
+Space: 10952
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0945
-Build needed 00:05:51, 10932k disc space
-Signature with key 'A5633F94' requested:
+Finished at 20120727-1531
+Build needed 00:07:51, 10952k disc space
+Signature with key 'BDA682F0' requested:
diff --git a/powerpc.log b/powerpc.log
index 0f8bfb4..a9a9be8 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,61 @@
-From buildd at poulenc.debian.org Tue Sep 06 09:33:42 2011
-Return-path: <buildd at poulenc.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at praetorius.debian.org Fri Jul 27 15:10:54 2012
+Return-path: <buildd at praetorius.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 1R0s2H-00024n-Fg
- for logs at buildd.debian.org; Tue, 06 Sep 2011 09:33:41 +0000
-Received: from poulenc.ynic.york.ac.uk ([144.32.168.77]
- helo=poulenc.debian.org)
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1SumBp-0002aq-Tf
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:10:54 +0000
+Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
+ (helo=praetorius.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 1R0s2E-0001LO-Vh; Tue, 06 Sep 2011 09:33:39 +0000
-Received: from buildd by poulenc.debian.org with local (Exim 4.72)
- (envelope-from <buildd at poulenc.debian.org>)
- id 1R0s2E-0006DP-Ik; Tue, 06 Sep 2011 09:33:38 +0000
-Message-Id: <E1R0s2E-0006DP-Ik at poulenc.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Tue, 6 Sep 2011 09:33:38 +0000
-From: buildd on poulenc <buildd at poulenc.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on powerpc (dist=sid)
-Key-Id: 779E1DD6
+ CN=praetorius.debian.org,
+ EMAIL=hostmaster at praetorius.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1SumBo-00043a-7w; Fri, 27 Jul 2012 15:10:52 +0000
+Received: from buildd by praetorius.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at praetorius.debian.org>)
+ id 1SumBm-0003zD-Ln; Fri, 27 Jul 2012 15:10:50 +0000
+Date: Fri, 27 Jul 2012 15:10:50 +0000
+Message-Id: <E1SumBm-0003zD-Ln at praetorius.debian.org>
+From: buildd on praetorius <buildd at praetorius.debian.org>
+To: wouter at debian.org,logs at buildd.debian.org
+Subject: Log for successful build of samtools_0.1.18-2 on powerpc (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 poulenc.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (powerpc) 06 Sep 2011 09:30 ║
+║ samtools 0.1.18-2 (powerpc) 27 Jul 2012 15:07 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5468 kB]
+Get:1 http://ftp.se.debian.org unstable InRelease [249 kB]
+Get:2 http://ftp.se.debian.org unstable/main Sources [6317 kB]
+Get:3 http://incoming.debian.org unstable InRelease [249 kB]
+Get:4 http://ftp.se.debian.org unstable/contrib Sources [53.9 kB]
+Get:5 http://ftp.se.debian.org unstable/non-free Sources [98.1 kB]
+Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [6016 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 [5470 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 [94.9 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7561 kB]
+Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [37.7 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6315 kB]
Get:9 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
-Get:11 http://incoming.debian.org unstable/main powerpc Packages [7562 kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.8 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:13 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
-Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.8 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [32.4 kB]
-Get:18 http://incoming.debian.org Packages [356 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 27.2 MB in 23s (1177 kB/s)
+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: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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.7 MB in 21s (1178 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 1s (362 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (234 kB/s)
Download complete and in download only mode
Check arch
@@ -102,18 +94,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+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 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 34 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 34 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,37 +114,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-18)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-2)
+coreutils: already installed (8.13-3.2)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.1)
+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)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.11)
+ncurses-base: already installed (5.9-9)
+ncurses-bin: already installed (5.9-9)
+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)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.4.3 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -164,126 +156,161 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5 libpcre3 libpipeline1 libtinfo-dev libtinfo5
+ libunistring0 libxml2 man-db ncurses-bin po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz
+ 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
+ libgpm2 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 libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 12 not upgraded.
-Need to get 10.2 MB of archives.
-After this operation, 30.9 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-3 [37.2 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-2 [1013 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.04-5+b1 [240 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.04-5+b1 [49.9 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-4 [134 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-4 [837 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.6-1 [1611 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-1 [128 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-4 [422 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-4 [2032 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.54-1 [28.4 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-1 [489 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+ 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:
+ libncurses5 libtinfo5 ncurses-bin
+3 upgraded, 26 newly installed, 0 to remove and 31 not upgraded.
+Need to get 11.5 MB of archives.
+After this operation, 28.9 MB of additional disk space will be used.
+Get:1 http://ftp.se.debian.org/debian/ unstable/main ncurses-bin powerpc 5.9-10 [333 kB]
+Get:2 http://ftp.se.debian.org/debian/ unstable/main libtinfo5 powerpc 5.9-10 [272 kB]
+Get:3 http://ftp.se.debian.org/debian/ unstable/main libncurses5 powerpc 5.9-10 [104 kB]
+Get:4 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.1-1 [38.5 kB]
+Get:5 http://ftp.se.debian.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-9 [27.0 kB]
+Get:6 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.11-2 [201 kB]
+Get:7 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 1:8.30-5 [240 kB]
+Get:8 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-5 [851 kB]
+Get:9 http://ftp.se.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
+Get:10 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.32.3-1 [2044 kB]
+Get:11 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.5-1 [143 kB]
+Get:12 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:13 http://ftp.se.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-9 [137 kB]
+Get:14 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.3 [208 kB]
+Get:15 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-9 [1179 kB]
+Get:16 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.2-1 [1062 kB]
+Get:17 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.11-2 [51.7 kB]
+Get:18 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-9 [131 kB]
+Get:19 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:20 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:21 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-9 [1929 kB]
+Get:22 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp.se.debian.org/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:25 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
+Get:26 http://ftp.se.debian.org/debian/ unstable/main libtinfo-dev powerpc 5.9-10 [105 kB]
+Get:27 http://ftp.se.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-10 [211 kB]
+Get:28 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:29 http://ftp.se.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 10.2 MB in 2s (3391 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10610 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_powerpc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_powerpc.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_powerpc.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_powerpc.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_powerpc.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_powerpc.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_powerpc.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_powerpc.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_powerpc.deb) ...
-Selecting previously deselected package html2text.
+Fetched 11.5 MB in 2s (5676 kB/s)
+(Reading database ... 10745 files and directories currently installed.)
+Preparing to replace ncurses-bin 5.9-9 (using .../ncurses-bin_5.9-10_powerpc.deb) ...
+Unpacking replacement ncurses-bin ...
+Setting up ncurses-bin (5.9-10) ...
+(Reading database ... 10745 files and directories currently installed.)
+Preparing to replace libtinfo5:powerpc 5.9-9 (using .../libtinfo5_5.9-10_powerpc.deb) ...
+Unpacking replacement libtinfo5:powerpc ...
+Setting up libtinfo5:powerpc (5.9-10) ...
+(Reading database ... 10745 files and directories currently installed.)
+Preparing to replace libncurses5:powerpc 5.9-9 (using .../libncurses5_5.9-10_powerpc.deb) ...
+Unpacking replacement libncurses5:powerpc ...
+Setting up libncurses5:powerpc (5.9-10) ...
+Selecting previously unselected package libpipeline1:powerpc.
+(Reading database ... 10745 files and directories currently installed.)
+Unpacking libpipeline1:powerpc (from .../libpipeline1_1.2.1-1_powerpc.deb) ...
+Selecting previously unselected package libasprintf0c2:powerpc.
+Unpacking libasprintf0c2:powerpc (from .../libasprintf0c2_0.18.1.1-9_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) ...
+Selecting previously unselected package libxml2:powerpc.
+Unpacking libxml2:powerpc (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:powerpc.
+Unpacking libcroco3:powerpc (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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_powerpc.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_powerpc.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_powerpc.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_powerpc.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_powerpc.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_powerpc.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_powerpc.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_powerpc.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_powerpc.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
+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_powerpc.deb) ...
+Selecting previously unselected package libtinfo-dev:powerpc.
+Unpacking libtinfo-dev:powerpc (from .../libtinfo-dev_5.9-10_powerpc.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_powerpc.deb) ...
+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 libmagic1:powerpc (5.11-2) ...
+Setting up libpcre3:powerpc (1:8.30-5) ...
+Setting up libxml2:powerpc (2.8.0+dfsg1-5) ...
+Setting up libffi5:powerpc (3.0.10-3) ...
+Setting up libglib2.0-0:powerpc (2.32.3-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:powerpc (0.6.5-1) ...
+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 (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+Setting up groff-base (1.21-9) ...
+Setting up man-db (2.6.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5+b1) ...
-Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-4) ...
-Setting up libxml2 (2.7.8.dfsg-4) ...
+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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:powerpc (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:powerpc (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 12 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 31 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-8 gcc-4.6_4.6.1-8 libc6-dev_2.13-18 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 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_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-8 dash_0.5.7-1 debconf_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_4.6.1-8 gcc_4:4.6.1-2 gcc-4.6_4.6.1-8 gcc-4.6-base_4.6.1-8 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_1.0.5-6 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-8 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-8 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 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_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011h-4 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_2.22-6.1 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_4.3.1 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-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 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 libfile-fcntllock-perl_0.14-2 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 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_2.2.4-13 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_5.9-9 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-27 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -294,13 +321,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -309,40 +338,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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
@@ -350,129 +380,135 @@ 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
+ 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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-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_0.1.18-2-powerpc-gR0dcB/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_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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 -fstack-protector --param=ssp-buffer-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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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 `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/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_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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 `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/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_0.1.18-2-powerpc-gR0dcB/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 `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/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. 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_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/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_0.1.18-2-powerpc-gR0dcB/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_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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]
seqtk.c: In function 'stk_subseq':
@@ -483,15 +519,15 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/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_0.1.18-2-powerpc-gR0dcB/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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/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 `/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/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_0.1.18-2-powerpc-gR0dcB/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 +553,7 @@ 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_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -552,8 +588,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -579,7 +615,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-powerpc-fXFcA6/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-powerpc-gR0dcB/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -594,69 +630,68 @@ 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_0.1.18-1_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_powerpc.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org> >../samtools_0.1.18-1_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-0933
+Build finished at 20120727-1510
-samtools_0.1.18-1_powerpc.changes:
+samtools_0.1.18-2_powerpc.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (poulenc) <buildd_powerpc-poulenc at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- f7ed545f582aa2efadee0d55422588213ad4d5db 512292 samtools_0.1.18-1_powerpc.deb
- 2c43474da868b56256ca0acc5a5080e01f5d9579 149584 libbam-dev_0.1.18-1_powerpc.deb
+ 526e893c91a8c60e7379b4bb2ead4c2371a49812 513788 samtools_0.1.18-2_powerpc.deb
+ a1d4325586bf89cbc9e97e1be73bd0ae128c36a5 150414 libbam-dev_0.1.18-2_powerpc.deb
Checksums-Sha256:
- c48b3ca656154208361b4d13fb6897eeff47a6189e1f197cc3bc36c01c280143 512292 samtools_0.1.18-1_powerpc.deb
- e204784b09aa88f9f999d5e0364d134ac7c682230099168bd868149ad7b3386d 149584 libbam-dev_0.1.18-1_powerpc.deb
+ 24e3c29d3ae4f99efb75dee2648f1990e2b704d2c8bfcb832fe94cc01e987c17 513788 samtools_0.1.18-2_powerpc.deb
+ 03a4fb47ea65f56b8358f36590aea108c1129e0892bb80d4bd03876b243b2185 150414 libbam-dev_0.1.18-2_powerpc.deb
Files:
- 338eb3e991fcdea95207ba74a922fade 512292 science optional samtools_0.1.18-1_powerpc.deb
- 8d976b9703d653b65f3e75bcad81b7d4 149584 libdevel optional libbam-dev_0.1.18-1_powerpc.deb
+ 60a3c941233db871ec58cb293307936d 513788 science optional samtools_0.1.18-2_powerpc.deb
+ ace1b0d9145133516849a955abc2dd39 150414 libdevel optional libbam-dev_0.1.18-2_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_powerpc.deb
+samtools_0.1.18-2_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 512292 bytes: control archive= 1767 bytes.
- 788 bytes, 16 lines control
+ size 513788 bytes: control archive= 1763 bytes.
+ 794 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1100
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1013
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -668,71 +703,71 @@ samtools_0.1.18-1_powerpc.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2011-09-06 09:33 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-09-06 09:33 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./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 2011-09-06 09:33 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/samtools/
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/bin/
+-rwxr-xr-x root/root 130976 2012-07-27 15:10 ./usr/bin/bcftools
+-rwxr-xr-x root/root 25484 2012-07-27 15:10 ./usr/bin/razip
+-rwxr-xr-x root/root 375080 2012-07-27 15:10 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/lib/samtools/
+-rwxr-xr-x root/root 7348 2012-07-27 15:10 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 11080 2012-07-27 15:10 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 18528 2012-07-27 15:10 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 7348 2012-07-27 15:10 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8036 2012-07-27 15:10 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2012-07-27 15:10 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2012-07-27 15:10 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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 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 2011-09-06 09:33 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./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 2011-09-06 09:33 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126609 2012-07-27 15:10 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 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 126609 2011-09-06 09:33 ./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 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
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/lib/samtools/
--rwxr-xr-x root/root 7168 2011-09-06 09:33 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10916 2011-09-06 09:33 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7872 2011-09-06 09:33 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7152 2011-09-06 09:33 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 18528 2011-09-06 09:33 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/bin/
--rwxr-xr-x root/root 373860 2011-09-06 09:33 ./usr/bin/samtools
--rwxr-xr-x root/root 25336 2011-09-06 09:33 ./usr/bin/razip
--rwxr-xr-x root/root 130168 2011-09-06 09:33 ./usr/bin/bcftools
-lrwxrwxrwx root/root 0 2011-09-06 09:33 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-1_powerpc.deb
+-rw-r--r-- root/root 1966 2012-07-27 15:10 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/samtools/
+-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 5778 2012-07-27 15:10 ./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 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
+lrwxrwxrwx root/root 0 2012-07-27 15:10 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.18-2_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 149584 bytes: control archive= 927 bytes.
+ size 150414 bytes: control archive= 926 bytes.
676 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 440
+ Installed-Size: 409
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -743,25 +778,25 @@ libbam-dev_0.1.18-1_powerpc.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./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 2011-09-06 09:33 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/lib/
+-rw-r--r-- root/root 276222 2012-07-27 15:10 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./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 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-drwxr-xr-x root/root 0 2011-09-06 09:33 ./usr/lib/
--rw-r--r-- root/root 275254 2011-09-06 09:33 ./usr/lib/libbam.a
+-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 15:10 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:10 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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 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
+-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -775,7 +810,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-d8c0c76c-2697-4d52-b93a-866cdd0ed93f/build/buildd-samtools_0.1.18-1-powerpc-fXFcA6
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-105a1aa5-a0a8-46f0-a2ca-b14adcdb81dc/build/buildd-samtools_0.1.18-2-powerpc-gR0dcB
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -783,18 +818,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 10444
-Build-Time: 76
+Build-Space: 10504
+Build-Time: 86
Distribution: sid
-Install-Time: 46
-Job: samtools_0.1.18-1
+Install-Time: 79
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 159
-Source-Version: 0.1.18-1
-Space: 10444
+Package-Time: 207
+Source-Version: 0.1.18-2
+Space: 10504
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-0933
-Build needed 00:02:39, 10444k disc space
-Signature with key '779E1DD6' requested:
+Finished at 20120727-1510
+Build needed 00:03:27, 10504k disc space
+
diff --git a/s390.log b/s390.log
index 57e298e..127fbd5 100644
--- a/s390.log
+++ b/s390.log
@@ -1,4 +1,4 @@
-From buildd at zandonai.debian.org Tue Sep 06 11:26:39 2011
+From buildd at zandonai.debian.org Fri Jul 27 15:06:52 2012
Return-path: <buildd at zandonai.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,64 +6,57 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1R0tnb-0002G0-8u
- for logs at buildd.debian.org; Tue, 06 Sep 2011 11:26:39 +0000
+ id 1Sum7w-0001fy-9h
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:06:52 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1R0tnY-0006rD-Ou; Tue, 06 Sep 2011 11:26:36 +0000
+ id 1Sum7v-00008M-8I; Fri, 27 Jul 2012 15:06:51 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1R0tnY-0007wU-Df; Tue, 06 Sep 2011 11:26:36 +0000
-Message-Id: <E1R0tnY-0007wU-Df at zandonai.debian.org>
+ id 1Sum7u-0003mU-9i; Fri, 27 Jul 2012 15:06:50 +0000
+Message-Id: <E1Sum7u-0003mU-9i 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: Tue, 6 Sep 2011 11:26:36 +0000
+Date: Fri, 27 Jul 2012 15:06:50 +0000
From: buildd on zandonai <buildd at zandonai.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-1 on s390 (dist=sid)
-Key-Id: 2D941D26
+Subject: Log for successful build of samtools_0.1.18-2 on s390 (dist=sid)
+Key-Id: E7C67939
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (s390) 06 Sep 2011 11:24 ║
+║ samtools 0.1.18-2 (s390) 27 Jul 2012 15:05 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: s390
-Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.de.debian.org unstable/main Sources [5470 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Hit http://ftp.de.debian.org unstable InRelease
+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 s390 Packages
+Hit http://ftp.de.debian.org unstable/contrib s390 Packages
+Hit http://incoming.debian.org unstable InRelease
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 [5470 kB]
-Get:6 http://ftp.de.debian.org unstable/contrib Sources [53.9 kB]
-Get:7 http://ftp.de.debian.org unstable/non-free Sources [94.9 kB]
-Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7467 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib s390 Packages [54.8 kB]
-Ign http://ftp.de.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.de.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.de.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [94.9 kB]
-Get:13 http://incoming.debian.org unstable/main s390 Packages [7467 kB]
-Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.8 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [34.4 kB]
-Get:18 http://incoming.debian.org Packages [324 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Ign http://incoming.debian.org Translation-en
-Fetched 26.9 MB in 27s (982 kB/s)
+Hit http://incoming.debian.org unstable/main Sources
+Hit http://incoming.debian.org unstable/contrib Sources
+Hit http://incoming.debian.org unstable/non-free Sources
+Hit http://incoming.debian.org unstable/main s390 Packages
+Hit http://incoming.debian.org unstable/contrib s390 Packages
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:2 http://incoming.debian.org Release [1601 B]
+Get:3 http://incoming.debian.org Sources [14.3 kB]
+Get:4 http://incoming.debian.org Packages [113 kB]
+Fetched 129 kB in 2s (55.0 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +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 389 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 1s (311 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (287 kB/s)
Download complete and in download only mode
Check arch
@@ -102,18 +95,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.16-1)
+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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -122,37 +115,37 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-1)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-2)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.25-3)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-15)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+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 (1.16.7)
+e2fsprogs: already installed (1.42.4-3)
+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)
+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)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -164,126 +157,144 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ 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
+ 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 libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 41 not upgraded.
-Need to get 10.3 MB of archives.
-After this operation, 30.8 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.0-3 [39.0 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 8.12-4 [228 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 8.2.3 [209 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-6 [1156 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.0.2-2 [1029 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.04-5+b1 [243 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main file s390 5.04-5+b1 [50.1 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-4 [143 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.7.8.dfsg-4 [879 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.28.6-1 [1639 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.2-1 [128 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-4 [431 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-4 [2073 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.54-1 [28.4 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-1 [504 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
+ 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 11.0 MB of archives.
+After this operation, 29.1 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.1-1 [40.0 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-9 [26.8 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 5.11-2 [205 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 1:8.30-5 [248 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-5 [892 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.32.3-1 [2122 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.5-1 [150 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390 0.18.1.1-9 [146 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 9.0.3 [213 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.21-9 [1148 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.2-1 [1074 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main file s390 5.11-2 [52.0 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-9 [152 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 s390 1.3.2a-15 [101 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-9 [1959 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 s390 1.55-3 [29.8 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 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 s390 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.3 MB in 4s (2199 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10583 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_s390.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_s390.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_s390.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_s390.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_s390.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_s390.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_s390.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_s390.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_s390.deb) ...
-Selecting previously deselected package html2text.
+Fetched 11.0 MB in 5s (2080 kB/s)
+Selecting previously unselected package libpipeline1:s390.
+(Reading database ... 10663 files and directories currently installed.)
+Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.1-1_s390.deb) ...
+Selecting previously unselected package libasprintf0c2:s390.
+Unpacking libasprintf0c2:s390 (from .../libasprintf0c2_0.18.1.1-9_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) ...
+Selecting previously unselected package libxml2:s390.
+Unpacking libxml2:s390 (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:s390.
+Unpacking libcroco3:s390 (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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_s390.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_s390.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_s390.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_s390.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_s390.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_s390.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_s390.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_s390.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_s390.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+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_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_s390.deb) ...
+Selecting previously unselected package libtinfo-dev:s390.
+Unpacking libtinfo-dev:s390 (from .../libtinfo-dev_5.9-10_s390.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_s390.deb) ...
+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 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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:s390 (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:s390 (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 41 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.21.53.20110805-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-6 gcc-4.6_4.6.1-6 libc6-dev_2.13-15 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 linux-libc-dev_3.0.0-1
-Package versions: apt_0.8.15.5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110805-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-6 dash_0.5.5.1-7.4 debconf_1.5.41 debconf-english_1.5.38 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_1.16-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-6 gcc_4:4.6.1-2 gcc-4.4-base_4.4.6-7 gcc-4.5-base_4.5.3-5 gcc-4.6_4.6.1-6 gcc-4.6-base_4.6.1-6 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 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_1.0.5-6 libc-bin_2.13-15 libc-dev-bin_2.13-15 libc6_2.13-15 libc6-dev_2.13-15 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_1:4.6.1-6 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-6 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-5 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 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-6 libstdc++6-4.6-dev_4.6.1-6 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-18 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-15 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-2 perl-base_5.12.4-2 perl-modules_5.12.4-2 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.7.4p6-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-5 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.22-7 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-4.4-base_4.4.7-1 gcc-4.6_4.6.3-8 gcc-4.6-base_4.6.3-8 gcc-4.7-base_4.7.1-3 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 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 libfile-fcntllock-perl_0.14-2 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 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_4.7.1-3 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -294,13 +305,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -309,40 +322,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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
@@ -350,134 +364,140 @@ 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
+ 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_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-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_0.1.18-2-s390-QXGKh8/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_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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 `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/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_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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 `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/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_0.1.18-2-s390-QXGKh8/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 `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/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. 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_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/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_0.1.18-2-s390-QXGKh8/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_0.1.18-2-s390-QXGKh8/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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_0.1.18-2-s390-QXGKh8/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/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_0.1.18-2-s390-QXGKh8/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_0.1.18-1-s390-u0rVt9/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/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 `/build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/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_0.1.18-2-s390-QXGKh8/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.
@@ -503,7 +523,7 @@ 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_0.1.18-1-s390-u0rVt9/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -538,8 +558,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -565,7 +585,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-1-s390-u0rVt9/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-2-s390-QXGKh8/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -580,69 +600,68 @@ 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_0.1.18-1_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-2_s390.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.18-1_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-2_s390.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.18-2_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 20110906-1126
+Build finished at 20120727-1506
-samtools_0.1.18-1_s390.changes:
+samtools_0.1.18-2_s390.changes:
Format: 1.8
-Date: Tue, 06 Sep 2011 16:52:04 +0900
+Date: Thu, 26 Jul 2012 18:30:48 -0400
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.18-1
+Version: 0.1.18-2
Distribution: sid
Urgency: low
-Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Maintainer: s390/s390x Build Daemon (zandonai) <buildd_s390-zandonai 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: 544976 671524
Changes:
- samtools (0.1.18-1) unstable; urgency=low
+ samtools (0.1.18-2) unstable; urgency=low
.
- [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.
+ * added patch to fix segfault in mpileup (Closes: #544976)
+ * added patch to fix coverage cap (Closes: #671524)
Checksums-Sha1:
- ad01740b1f0b6eeb8ae20d3bfc6d1715d235dff2 528480 samtools_0.1.18-1_s390.deb
- daff8ba29c9e4dc4a474bb75b0574028503e6541 156202 libbam-dev_0.1.18-1_s390.deb
+ 76f21c3aa163dae86db10c87248a6e3cefa425cf 529036 samtools_0.1.18-2_s390.deb
+ 6d62763947814acc48fa0d228b35a2f95bc77ae6 156454 libbam-dev_0.1.18-2_s390.deb
Checksums-Sha256:
- 7b524fc82bf4a5bed7567ae0fcb2d309bf4796452dd57fb6b48a0e162101d1f5 528480 samtools_0.1.18-1_s390.deb
- c8f9a97601fbf99c8c3bbab4408e077eacdb6e9c09aad60165c847c0f3075cc3 156202 libbam-dev_0.1.18-1_s390.deb
+ 230fcce76704d86173deab1a84cb78e18611e1754887ec9b2daf3b549b6d2047 529036 samtools_0.1.18-2_s390.deb
+ 030cdbfdaf16e414a85a8964304a707e1e08cfa430d2ba837066eced8acd0e64 156454 libbam-dev_0.1.18-2_s390.deb
Files:
- bf41bbb8305379ab1d388bb9f3253210 528480 science optional samtools_0.1.18-1_s390.deb
- 8fc2b46e29bbd9fd20cd994b200765f6 156202 libdevel optional libbam-dev_0.1.18-1_s390.deb
+ 965800e9f5c5a9738b63dc7097a12951 529036 science optional samtools_0.1.18-2_s390.deb
+ b0304fea00da983af8345be33bef5ee0 156454 libdevel optional libbam-dev_0.1.18-2_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-1_s390.deb
+samtools_0.1.18-2_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 528480 bytes: control archive= 1759 bytes.
- 785 bytes, 16 lines control
+ size 529036 bytes: control archive= 1759 bytes.
+ 791 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1156
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
+ Installed-Size: 1066
+ Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -654,25 +673,25 @@ samtools_0.1.18-1_s390.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/bin/
--rwxr-xr-x root/root 141448 2011-09-06 11:26 ./usr/bin/bcftools
--rwxr-xr-x root/root 415908 2011-09-06 11:26 ./usr/bin/samtools
--rwxr-xr-x root/root 27452 2011-09-06 11:26 ./usr/bin/razip
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/lib/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/lib/samtools/
--rwxr-xr-x root/root 11364 2011-09-06 11:26 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7416 2011-09-06 11:26 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7416 2011-09-06 11:26 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8276 2011-09-06 11:26 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 17340 2011-09-06 11:26 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2011-09-06 11:26 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2011-09-06 11:26 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/bin/
+-rwxr-xr-x root/root 141452 2012-07-27 15:06 ./usr/bin/bcftools
+-rwxr-xr-x root/root 416680 2012-07-27 15:06 ./usr/bin/samtools
+-rwxr-xr-x root/root 27584 2012-07-27 15:06 ./usr/bin/razip
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/lib/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11488 2012-07-27 15:06 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7596 2012-07-27 15:06 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 7596 2012-07-27 15:06 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 8424 2012-07-27 15:06 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 17340 2012-07-27 15:06 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/man/man1/
+-rw-r--r-- root/root 9890 2012-07-27 15:06 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2012-07-27 15:06 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/samtools/
-rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
@@ -682,43 +701,43 @@ drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/samtools/
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2011-09-06 11:26 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2012-07-27 15:06 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./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 1031 2011-09-06 07:01 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 592 2011-09-06 07:01 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2011-09-06 11:26 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1966 2012-07-27 15:06 ./usr/share/doc/samtools/README.bcftools
-rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1676 2011-09-06 07:52 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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 2011-09-06 11:26 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2011-09-06 11:26 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2012-07-27 15:06 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
-lrwxrwxrwx root/root 0 2011-09-06 11:26 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+lrwxrwxrwx root/root 0 2012-07-27 15:06 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.18-1_s390.deb
+libbam-dev_0.1.18-2_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 156202 bytes: control archive= 922 bytes.
+ size 156454 bytes: control archive= 922 bytes.
673 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-1
+ Version: 0.1.18-2
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 452
+ Installed-Size: 421
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -729,24 +748,24 @@ libbam-dev_0.1.18-1_s390.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/include/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/include/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/include/samtools/
-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 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
-rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/lib/
--rw-r--r-- root/root 288314 2011-09-06 11:26 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-09-06 11:26 ./usr/share/doc/libbam-dev/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/lib/
+-rw-r--r-- root/root 288978 2012-07-27 15:06 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-07-27 15:06 ./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 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 1676 2011-09-06 07:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 1772 2012-07-27 12:17 ./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
@@ -761,7 +780,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-9c6ebf4f-c0d8-40a3-b578-aee78824964f/build/buildd-samtools_0.1.18-1-s390-u0rVt9
+Purging /var/lib/schroot/mount/sid-s390-sbuild-f8862312-c6fc-4cdf-9518-200305394bf9/build/buildd-samtools_0.1.18-2-s390-QXGKh8
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -769,18 +788,504 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 11232
-Build-Time: 66
+Build-Space: 11272
+Build-Time: 33
Distribution: sid
-Install-Time: 14
-Job: samtools_0.1.18-1
+Install-Time: 10
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 123
-Source-Version: 0.1.18-1
-Space: 11232
+Package-Time: 57
+Source-Version: 0.1.18-2
+Space: 11272
Status: successful
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-1126
-Build needed 00:02:03, 11232k disc space
-Signature with key '2D941D26' requested:
+Finished at 20120727-1506
+Build needed 00:00:57, 11272k disc space
+Signature with key 'E7C67939' requested:
+From buildd at zandonai.debian.org Fri Jul 27 15:11:58 2012
+Return-path: <buildd at zandonai.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 zandonai.debian.org>)
+ id 1SumCr-0002yt-TQ
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:11:58 +0000
+Received: from zandonai.debian.org ([80.245.147.46])
+ from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
+ CN=zandonai.debian.org,
+ EMAIL=hostmaster at zandonai.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1SumCq-000498-VX; Fri, 27 Jul 2012 15:11:57 +0000
+Received: from buildd by zandonai.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zandonai.debian.org>)
+ id 1SumCq-0005Vc-IP; Fri, 27 Jul 2012 15:11:56 +0000
+Message-Id: <E1SumCq-0005Vc-IP 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: Fri, 27 Jul 2012 15:11:56 +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_0.1.18-2 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 0.1.18-2 (s390x) 27 Jul 2012 15:09 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.18-2
+Source Version: 0.1.18-2
+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]
+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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.4 MB in 24s (1028 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://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (286 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 23 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: 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 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]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.1 MB in 5s (2157 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_0.4.116_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 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 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+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 13:09:06 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_0.1.18-2.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_0.1.18-2.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 0.1.18-2
+ 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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/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
diff --git a/s390x.log b/s390x.log
new file mode 100644
index 0000000..759d351
--- /dev/null
+++ b/s390x.log
@@ -0,0 +1,486 @@
+From buildd at zandonai.debian.org Fri Jul 27 15:11:58 2012
+Return-path: <buildd at zandonai.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 zandonai.debian.org>)
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+ EMAIL=hostmaster at zandonai.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
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+Date: Fri, 27 Jul 2012 15:11:56 +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_0.1.18-2 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 0.1.18-2 (s390x) 27 Jul 2012 15:09 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 0.1.18-2
+Source Version: 0.1.18-2
+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]
+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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.4 MB in 24s (1028 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://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (286 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 23 not upgraded.
+Removing negative dependencies:
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 23 not upgraded.
+Checking correctness of dependencies...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (internal resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build-Depends: 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 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]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 11.1 MB in 5s (2157 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_0.4.116_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 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 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+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 13:09:06 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_0.1.18-2.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_0.1.18-2.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 0.1.18-2
+ 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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[2]: Nothing to be done for `lib'.
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/samtools-0.1.18/misc'
+make[3]: Nothing to be done for `lib'.
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/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_0.1.18-2-s390x-oetGYg/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
diff --git a/sparc.log b/sparc.log
index c54bdaf..8bacb06 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,62 @@
-From buildd at spontini.debian.org Tue Sep 06 18:25:37 2011
-Return-path: <buildd at spontini.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at stadler.debian.org Fri Jul 27 15:18:18 2012
+Return-path: <buildd at stadler.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 spontini.debian.org>)
- id 1R10L3-0004DW-5z
- for logs at buildd.debian.org; Tue, 06 Sep 2011 18:25:37 +0000
-Received: from spontini.debian.org ([2607:f8f0:610:4000:a00:20ff:fea0:918b])
+ (Exim 4.72) (envelope-from <buildd at stadler.debian.org>)
+ id 1SumJ0-0004ng-D1
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:18:18 +0000
+Received: from stadler.debian.org ([2a02:16a8:dc41:100::ffff])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=spontini.debian.org,
- EMAIL=hostmaster at spontini.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at spontini.debian.org>)
- id 1R10Kr-0003Ih-Dv
- for logs at buildd.debian.org; Tue, 06 Sep 2011 18:25:25 +0000
-Received: from buildd by spontini.debian.org with local (Exim 4.72)
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- id 1R10Ke-0006ZI-U6; Tue, 06 Sep 2011 18:25:13 +0000
-Message-Id: <E1R10Ke-0006ZI-U6 at spontini.debian.org>
+ CN=stadler.debian.org, EMAIL=hostmaster at stadler.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at stadler.debian.org>)
+ id 1SumIz-0004O4-FU
+ for logs at buildd.debian.org; Fri, 27 Jul 2012 15:18:17 +0000
+Received: from buildd by stadler.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at stadler.debian.org>)
+ id 1SumIx-0008Bn-Jr; Fri, 27 Jul 2012 15:18:15 +0000
+Message-Id: <E1SumIx-0008Bn-Jr at stadler.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Tue, 6 Sep 2011 18:25:12 +0000
-From: buildd on spontini <buildd at spontini.debian.org>
-To: logs at buildd.debian.org,buildd-admin at spontini.debian.org
-Subject: Log for attempted build of samtools_0.1.18-1 on sparc (dist=sid)
-Key-Id: 4B280692
+Date: Fri, 27 Jul 2012 15:18:15 +0000
+From: buildd on stadler <buildd at stadler.debian.org>
+To: logs at buildd.debian.org,buildd-admin at stadler.debian.org
+Subject: Log for attempted build of samtools_0.1.18-2 on sparc (dist=sid)
+Key-Id: F53143B2
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on spontini.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on stadler.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-1 (sparc) 06 Sep 2011 18:16 ║
+║ samtools 0.1.18-2 (sparc) 27 Jul 2012 15:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-1
-Source Version: 0.1.18-1
+Version: 0.1.18-2
+Source Version: 0.1.18-2
Architecture: sparc
-Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5481 kB]
+Get:1 http://debian.inode.at unstable InRelease [249 kB]
+Get:2 http://incoming.debian.org unstable InRelease [249 kB]
+Get:3 http://debian.inode.at unstable/main Sources [6317 kB]
Ign http://incoming.debian.org InRelease
Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://incoming.debian.org unstable/main Sources [5481 kB]
-Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [53.9 kB]
-Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [95.2 kB]
-Get:9 http://mirror-ubc.debian.org unstable/main sparc Packages [7513 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib sparc Packages [55.8 kB]
-Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
-Get:11 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://mirror-ubc.debian.org unstable/contrib Translation-en
-Get:12 http://incoming.debian.org unstable/contrib Sources [53.9 kB]
-Get:13 http://incoming.debian.org unstable/non-free Sources [95.2 kB]
-Get:14 http://incoming.debian.org unstable/main sparc Packages [7513 kB]
-Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.8 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:17 http://incoming.debian.org Sources [53.9 kB]
-Get:18 http://incoming.debian.org Packages [387 kB]
-Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org unstable/contrib Translation-en
-Fetched 27.1 MB in 1min 1s (443 kB/s)
+Get:5 http://incoming.debian.org unstable/main Sources [6315 kB]
+Get:6 http://debian.inode.at unstable/contrib Sources [53.9 kB]
+Get:7 http://debian.inode.at unstable/non-free Sources [98.1 kB]
+Get:8 http://debian.inode.at unstable/main sparc Packages [5980 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 sparc Packages [5980 kB]
+Get:12 http://debian.inode.at unstable/contrib sparc Packages [37.8 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 [14.3 kB]
+Get:16 http://incoming.debian.org Packages [113 kB]
+Fetched 25.6 MB in 2min 36s (163 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,11 +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 389 kB of source archives.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.18-1 (dsc) [1946 B]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.18-1 (tar) [379 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main samtools 0.1.18-1 (diff) [7593 B]
-Fetched 389 kB in 0s (898 kB/s)
+Need to get 390 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (dsc) [1429 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (tar) [379 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-2 (diff) [8901 B]
+Fetched 390 kB in 1s (297 kB/s)
Download complete and in download only mode
Check arch
@@ -103,18 +95,18 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.18-1)
+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 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,38 +115,38 @@ Checking correctness of dependencies...
Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.5)
-base-passwd: already installed (3.5.23)
-bash: already installed (4.1-3)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.7-1)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
-findutils: already installed (4.4.2-1+b2)
-grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
-hostname: already installed (3.06)
-ncurses-base: already installed (5.9-1)
-ncurses-bin: already installed (5.9-1)
-perl-base: already installed (5.12.4-4)
-sed: already installed (4.2.1-9)
-login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
-bsdutils: already installed (1:2.19.1-5)
-mount: already installed (2.19.1-5)
-util-linux: already installed (2.19.1-5)
-libc6-dev: already installed (2.13-18)
-libc6-dev-sparc64: already installed (2.13-18)
-gcc: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.1-2 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.0.3 >= 1.13.5 is satisfied)
+base-files: already installed (6.11)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2-3)
+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 (1.16.7)
+e2fsprogs: already installed (1.42.4-3)
+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)
+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)
+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)
+make: already installed (3.81-8.2)
+dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 8.9.6
+Using default version 9.20120608
cdbs: missing
quilt: missing
libncurses5-dev: missing
@@ -166,126 +158,144 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libunistring0 libxml2 man-db po-debconf
+ 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
+ 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 libcroco3 libglib2.0-0 libmagic1 libncurses5-dev
- libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 22 newly installed, 0 to remove and 9 not upgraded.
-Need to get 9998 kB of archives.
-After this operation, 30.4 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-3 [36.0 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-2 [1005 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 sparc 5.04-5+b1 [239 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main file sparc 5.04-5+b1 [49.6 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-4 [132 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-4 [816 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.6-1 [1556 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-1 [119 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-4 [424 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-4 [1985 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.6 [562 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.96 [75.8 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main diffstat sparc 1.54-1 [28.3 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev sparc 5.9-1 [481 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.48-7 [354 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+ 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.inode.at/debian/ unstable/main libpipeline1 sparc 1.2.1-1 [35.8 kB]
+Get:2 http://debian.inode.at/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-9 [26.5 kB]
+Get:3 http://debian.inode.at/debian/ unstable/main libmagic1 sparc 5.11-2 [197 kB]
+Get:4 http://debian.inode.at/debian/ unstable/main libpcre3 sparc 1:8.30-5 [246 kB]
+Get:5 http://debian.inode.at/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-5 [826 kB]
+Get:6 http://debian.inode.at/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
+Get:7 http://debian.inode.at/debian/ unstable/main libglib2.0-0 sparc 2.32.3-1 [1926 kB]
+Get:8 http://debian.inode.at/debian/ unstable/main libcroco3 sparc 0.6.5-1 [135 kB]
+Get:9 http://debian.inode.at/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:10 http://debian.inode.at/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-9 [129 kB]
+Get:11 http://debian.inode.at/debian/ unstable/main bsdmainutils sparc 9.0.3 [206 kB]
+Get:12 http://debian.inode.at/debian/ unstable/main groff-base sparc 1.21-9 [1133 kB]
+Get:13 http://debian.inode.at/debian/ unstable/main man-db sparc 2.6.2-1 [1032 kB]
+Get:14 http://debian.inode.at/debian/ unstable/main file sparc 5.11-2 [51.1 kB]
+Get:15 http://debian.inode.at/debian/ unstable/main gettext-base sparc 0.18.1.1-9 [148 kB]
+Get:16 http://debian.inode.at/debian/ unstable/main cdbs all 0.4.116 [79.9 kB]
+Get:17 http://debian.inode.at/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:18 http://debian.inode.at/debian/ unstable/main gettext sparc 0.18.1.1-9 [1893 kB]
+Get:19 http://debian.inode.at/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:20 http://debian.inode.at/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:21 http://debian.inode.at/debian/ unstable/main debhelper all 9.20120608 [700 kB]
+Get:22 http://debian.inode.at/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
+Get:23 http://debian.inode.at/debian/ unstable/main libtinfo-dev sparc 5.9-10 [97.5 kB]
+Get:24 http://debian.inode.at/debian/ unstable/main libncurses5-dev sparc 5.9-10 [204 kB]
+Get:25 http://debian.inode.at/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:26 http://debian.inode.at/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 9998 kB in 3s (3005 kB/s)
-Selecting previously deselected package libpipeline1.
-(Reading database ... 10977 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_sparc.deb) ...
-Selecting previously deselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_sparc.deb) ...
-Selecting previously deselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_sparc.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_sparc.deb) ...
-Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-2_sparc.deb) ...
-Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_sparc.deb) ...
-Selecting previously deselected package file.
-Unpacking file (from .../file_5.04-5+b1_sparc.deb) ...
-Selecting previously deselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_sparc.deb) ...
-Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_sparc.deb) ...
-Selecting previously deselected package html2text.
+Fetched 10.5 MB in 10s (979 kB/s)
+Selecting previously unselected package libpipeline1:sparc.
+(Reading database ... 11051 files and directories currently installed.)
+Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.1-1_sparc.deb) ...
+Selecting previously unselected package libasprintf0c2:sparc.
+Unpacking libasprintf0c2:sparc (from .../libasprintf0c2_0.18.1.1-9_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) ...
+Selecting previously unselected package libxml2:sparc.
+Unpacking libxml2:sparc (from .../libxml2_2.8.0+dfsg1-5_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) ...
+Selecting previously unselected package libcroco3:sparc.
+Unpacking libcroco3:sparc (from .../libcroco3_0.6.5-1_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) ...
+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) ...
+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_sparc.deb) ...
-Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_sparc.deb) ...
-Selecting previously deselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-1_sparc.deb) ...
-Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-4_sparc.deb) ...
-Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-4_sparc.deb) ...
-Selecting previously deselected package intltool-debian.
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-9_sparc.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_sparc.deb) ...
-Selecting previously deselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_sparc.deb) ...
-Selecting previously deselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
-Selecting previously deselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_sparc.deb) ...
-Setting up libpipeline1 (1.2.0-3) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up bsdmainutils (8.2.3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
-Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-2) ...
+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_9.20120608_all.deb) ...
+Selecting previously unselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.55-3_sparc.deb) ...
+Selecting previously unselected package libtinfo-dev:sparc.
+Unpacking libtinfo-dev:sparc (from .../libtinfo-dev_5.9-10_sparc.deb) ...
+Selecting previously unselected package libncurses5-dev.
+Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_sparc.deb) ...
+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 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 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 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 libglib2.0-0 (2.28.6-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3 (0.6.2-1) ...
-Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-4) ...
+Setting up gettext (0.18.1.1-9) ...
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 po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120608) ...
+Setting up diffstat (1.55-3) ...
+Setting up libtinfo-dev:sparc (5.9-10) ...
+Setting up libncurses5-dev (5.9-10) ...
+Setting up quilt (0.60-2) ...
+Setting up zlib1g-dev:sparc (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 9 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 25 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-8 gcc-4.6_4.6.1-8 libc6-dev_2.13-18 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 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_4.6.1-8 dash_0.5.7-1 debconf_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+b2 g++_4:4.6.1-2 g++-4.6_4.6.1-8 gcc_4:4.6.1-2 gcc-4.6_4.6.1-8 gcc-4.6-base_4.6.1-8 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 libc6-dev-sparc64_2.13-18 libc6-sparc64_2.13-18 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_1:4.6.1-8 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-8 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 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-8 libstdc++6-4.6-dev_4.6.1-8 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+b1 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 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-1 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-1 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 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -296,13 +306,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 6 08:31:29 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Jul 27 13:09:06 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_0.1.18-1.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-2.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_0.1.18-2.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
────────────────
@@ -311,40 +323,41 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor):
-dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
-dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor):
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-1
+dpkg-buildpackage: source version 0.1.18-2
dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/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" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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
@@ -352,129 +365,135 @@ 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
+ 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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
Applying patch no-pileup-tests.patch
patching file examples/Makefile
-Now at patch no-pileup-tests.patch
+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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-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_0.1.18-2-sparc-HSj7IP/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_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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 -fstack-protector --param=ssp-buffer-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
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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 `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/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_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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 `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/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_0.1.18-2-sparc-HSj7IP/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 `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/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. 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_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/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_0.1.18-2-sparc-HSj7IP/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_0.1.18-2-sparc-HSj7IP/samtools-0.1.18'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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]
seqtk.c: In function 'stk_subseq':
@@ -485,28 +504,28 @@ 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 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/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_0.1.18-2-sparc-HSj7IP/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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/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 `/build/buildd-samtools_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/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_0.1.18-2-sparc-HSj7IP/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_0.1.18-1-sparc-NEkTE7/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.18-2-sparc-HSj7IP/samtools-0.1.18/examples'
make: *** [debian/stamp-makefile-check] Error 2
-dpkg-buildpackage: error: debian/rules build gave error exit status 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110906-1825
+Build finished at 20120727-1518
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-9fa16328-83bf-4bcd-9f01-67b63bcd622e/build/buildd-samtools_0.1.18-1-sparc-NEkTE7
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-6973a6e3-efb0-4bfc-ba6f-7c96b1af3c3a/build/buildd-samtools_0.1.18-2-sparc-HSj7IP
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -514,18 +533,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 6748
-Build-Time: 334
+Build-Space: 6704
+Build-Time: 267
Distribution: sid
Fail-Stage: build
-Install-Time: 82
-Job: samtools_0.1.18-1
+Install-Time: 87
+Job: samtools_0.1.18-2
Package: samtools
-Package-Time: 519
-Source-Version: 0.1.18-1
-Space: 6748
+Package-Time: 542
+Source-Version: 0.1.18-2
+Space: 6704
Status: attempted
-Version: 0.1.18-1
+Version: 0.1.18-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110906-1825
-Build needed 00:08:39, 6748k disc space
+Finished at 20120727-1518
+Build needed 00:09:02, 6704k disc space
--
Processing of sequence alignments in SAM and BAM formats.
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