[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.19-1-1-g139f347
Charles Plessy
plessy at debian.org
Sun Mar 31 08:45:01 UTC 2013
The following commit has been merged in the meta branch:
commit 139f347693915e1ecda6e7dbd562f4b978193ec9
Author: Charles Plessy <plessy at debian.org>
Date: Sun Mar 31 17:44:39 2013 +0900
Build logs for 0.1.19-1.
diff --git a/armel.log b/armel.log
index 7e8e21e..6d3e382 100644
--- a/armel.log
+++ b/armel.log
@@ -1,60 +1,60 @@
-From buildd at alain.debian.org Sun Dec 23 05:02:49 2012
-Return-path: <buildd at alain.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at alwyn.debian.org Sat Mar 30 09:39:54 2013
+Return-path: <buildd at alwyn.debian.org>
+Received: from mailly.debian.org ([82.195.75.114])
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 alain.debian.org>)
- id 1Tmdi5-0008Km-In
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:02:49 +0000
-Received: from alain.islands.arm.com ([217.140.96.58] helo=alain.debian.org)
+ CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
+ (Exim 4.72) (envelope-from <buildd at alwyn.debian.org>)
+ id 1ULsGQ-0006To-8J
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:39:54 +0000
+Received: from alwyn.islands.arm.com ([217.140.96.59] helo=alwyn.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=alain.debian.org, EMAIL=hostmaster at alain.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at alain.debian.org>)
- id 1Tmdi4-0008Iu-F7
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:02:48 +0000
-Received: from buildd by alain.debian.org with local (Exim 4.72)
- (envelope-from <buildd at alain.debian.org>)
- id 1Tmdi2-0001tj-Fb; Sun, 23 Dec 2012 05:02:46 +0000
-Date: Sun, 23 Dec 2012 05:02:46 +0000
-Message-Id: <E1Tmdi2-0001tj-Fb 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_0.1.18-4 on armel (dist=sid)
+ CN=alwyn.debian.org, EMAIL=hostmaster at alwyn.debian.org (verified)
+ by mailly.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at alwyn.debian.org>)
+ id 1ULsGP-0004Ob-4I
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:39:53 +0000
+Received: from buildd by alwyn.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at alwyn.debian.org>)
+ id 1ULsGO-0003bY-7L; Sat, 30 Mar 2013 09:39:52 +0000
+Date: Sat, 30 Mar 2013 09:39:52 +0000
+Message-Id: <E1ULsGO-0003bY-7L at alwyn.debian.org>
+From: buildd on alwyn <buildd at alwyn.debian.org>
+To: buildd-porters at alwyn.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of samtools_0.1.19-1 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 alain.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alwyn.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (armel) 23 Dec 2012 04:53 ║
+║ samtools 0.1.19-1 (armel) 30 Mar 2013 09:29 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: armel
-Get:1 http://incoming.debian.org unstable InRelease [227 kB]
-Get:2 http://ftp.uk.debian.org unstable InRelease [227 kB]
-Ign http://incoming.debian.org InRelease
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://incoming.debian.org Release [1141 B]
-Get:5 http://ftp.uk.debian.org unstable/main Sources [6458 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:7 http://ftp.uk.debian.org unstable/contrib Sources [53.0 kB]
-Get:8 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
-Get:9 http://ftp.uk.debian.org unstable/main armel Packages [6097 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:12 http://incoming.debian.org unstable/main armel Packages [6097 kB]
-Get:13 http://ftp.uk.debian.org unstable/contrib armel Packages [36.7 kB]
-Get:14 http://incoming.debian.org unstable/contrib armel Packages [36.7 kB]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 26.1 MB in 1min 39s (261 kB/s)
+Get:1 http://ftp.uk.debian.org unstable InRelease [236 kB]
+Get:2 http://incoming.debian.org unstable InRelease [236 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6484 kB]
+Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [51.0 kB]
+Get:7 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
+Get:8 http://ftp.uk.debian.org unstable/main armel Packages [6113 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://incoming.debian.org unstable/main armel Packages [6113 kB]
+Get:12 http://ftp.uk.debian.org unstable/contrib armel Packages [35.7 kB]
+Get:13 http://incoming.debian.org unstable/contrib armel Packages [35.7 kB]
+Get:14 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:15 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:16 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:17 http://incoming.debian.org buildd-unstable/main armel Packages [13.1 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib armel Packages [14 B]
+Fetched 26.2 MB in 1min 43s (253 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,12 +74,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (311 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (399 kB/s)
Download complete and in download only mode
Check arch
@@ -99,12 +99,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 63 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 63 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -172,26 +172,26 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 37 not upgraded.
-Need to get 10.2 MB of archives.
+0 upgraded, 29 newly installed, 0 to remove and 63 not upgraded.
+Need to get 9834 kB of archives.
After this operation, 28.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.2-1 [35.1 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-9 [1079 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.3 [208 kB]
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.2-2 [35.4 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.22.2-1 [674 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.4 [212 kB]
Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.3-3 [868 kB]
Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armel 0.18.1.1-10 [26.6 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.11-2 [200 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 1:8.31-1 [247 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.8.0+dfsg1-7 [825 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 1:5.11-2.1 [200 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 1:8.31-2 [246 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.8.0+dfsg1-7+nmu1 [825 kB]
Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armel 3.0.10-3 [22.8 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.33.12+really2.32.4-3 [1694 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.33.12+really2.32.4-5 [1694 kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.6-2 [120 kB]
Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armel 0.18.1.1-10 [132 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.11-2 [51.4 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armel 1:5.11-2.1 [51.5 kB]
Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-10 [138 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev armel 0.18.1.1-10 [26.5 kB]
Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev armel 0.18.1.1-10 [163 kB]
@@ -202,17 +202,17 @@ Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [
Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat armel 1.55-3 [28.6 kB]
Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armel 5.9-10 [90.3 kB]
Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 5.9-10 [205 kB]
-Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.2 MB in 5s (1995 kB/s)
+Fetched 9834 kB in 5s (1841 kB/s)
Selecting previously unselected package libpipeline1:armel.
(Reading database ... 10693 files and directories currently installed.)
-Unpacking libpipeline1:armel (from .../libpipeline1_1.2.2-1_armel.deb) ...
+Unpacking libpipeline1:armel (from .../libpipeline1_1.2.2-2_armel.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_armel.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_armel.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armel.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_armel.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_armel.deb) ...
Selecting previously unselected package bash-completion.
@@ -220,15 +220,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:armel.
Unpacking libasprintf0c2:armel (from .../libasprintf0c2_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package libmagic1:armel.
-Unpacking libmagic1:armel (from .../libmagic1_5.11-2_armel.deb) ...
+Unpacking libmagic1:armel (from .../libmagic1_1%3a5.11-2.1_armel.deb) ...
Selecting previously unselected package libpcre3:armel.
-Unpacking libpcre3:armel (from .../libpcre3_1%3a8.31-1_armel.deb) ...
+Unpacking libpcre3:armel (from .../libpcre3_1%3a8.31-2_armel.deb) ...
Selecting previously unselected package libxml2:armel.
-Unpacking libxml2:armel (from .../libxml2_2.8.0+dfsg1-7_armel.deb) ...
+Unpacking libxml2:armel (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_armel.deb) ...
+Unpacking libglib2.0-0:armel (from .../libglib2.0-0_2.33.12+really2.32.4-5_armel.deb) ...
Selecting previously unselected package libcroco3:armel.
Unpacking libcroco3:armel (from .../libcroco3_0.6.6-2_armel.deb) ...
Selecting previously unselected package libunistring0:armel.
@@ -236,11 +236,11 @@ Unpacking libunistring0:armel (from .../libunistring0_0.9.3-5_armel.deb) ...
Selecting previously unselected package libgettextpo0:armel.
Unpacking libgettextpo0:armel (from .../libgettextpo0_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_armel.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_armel.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_armel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
Selecting previously unselected package libasprintf-dev:armel.
@@ -262,30 +262,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:armel (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:armel (0.18.1.1-10) ...
-Setting up libmagic1:armel (5.11-2) ...
-Setting up libpcre3:armel (1:8.31-1) ...
-Setting up libxml2:armel (2.8.0+dfsg1-7) ...
+Setting up libmagic1:armel (1:5.11-2.1) ...
+Setting up libpcre3:armel (1:8.31-2) ...
+Setting up libxml2:armel (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:armel (3.0.10-3) ...
-Setting up libglib2.0-0:armel (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:armel (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:armel (0.6.6-2) ...
Setting up libunistring0:armel (0.9.3-5) ...
Setting up libgettextpo0:armel (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:armel (0.18.1.1-10) ...
Setting up libgettextpo-dev:armel (0.18.1.1-10) ...
@@ -296,17 +296,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:armel (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 37 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 63 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32 armel (armv5tel)
Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-4 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-4 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -317,16 +317,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -336,44 +335,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -386,11 +382,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -399,139 +395,176 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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_0.1.18-4-armel-E7vUyT/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armel-E7vUyT/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-armel-DBqlzN/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -539,14 +572,14 @@ 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_0.1.18-4-armel-E7vUyT/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armel-DBqlzN/samtools-0.1.19/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0502
+Build finished at 20130330-0939
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-armel-sbuild-eb1bd0de-67fc-4971-b540-486b400c689e/build/buildd-samtools_0.1.18-4-armel-E7vUyT
+Purging /var/lib/schroot/mount/sid-armel-sbuild-34e2c03c-0d4b-40b8-90e6-24a2760cc633/build/buildd-samtools_0.1.19-1-armel-DBqlzN
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -554,19 +587,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 6504
-Build-Time: 316
+Build-Space: 7864
+Build-Time: 341
Distribution: sid
Fail-Stage: build
-Install-Time: 113
-Job: samtools_0.1.18-4
+Install-Time: 110
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 565
-Source-Version: 0.1.18-4
-Space: 6504
+Package-Time: 590
+Source-Version: 0.1.19-1
+Space: 7864
Status: attempted
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0502
-Build needed 00:09:25, 6504k disc space
+Finished at 20130330-0939
+Build needed 00:09:50, 7864k disc space
diff --git a/armhf.log b/armhf.log
index 14b380f..f1ffbb6 100644
--- a/armhf.log
+++ b/armhf.log
@@ -1,60 +1,60 @@
-From buildd at hasse.debian.org Sun Dec 23 05:02:50 2012
-Return-path: <buildd at hasse.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at hummel.debian.org Sat Mar 30 09:23:12 2013
+Return-path: <buildd at hummel.debian.org>
+Received: from mailly.debian.org ([82.195.75.114])
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 hasse.debian.org>)
- id 1Tmdi6-0008Kt-9D
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:02:50 +0000
-Received: from [217.140.96.68] (helo=hasse.debian.org)
+ CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
+ (Exim 4.72) (envelope-from <buildd at hummel.debian.org>)
+ id 1ULs0G-0003ZL-28
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:23:12 +0000
+Received: from hummel.ynic.york.ac.uk ([144.32.168.76] helo=hummel.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=hasse.debian.org, EMAIL=hostmaster at hasse.debian.org (verified)
- by merikanto.debian.org with esmtps
- (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.72)
- (envelope-from <buildd at hasse.debian.org>) id 1Tmdi5-0008Is-6X
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:02:49 +0000
-Received: from buildd by hasse.debian.org with local (Exim 4.80)
- (envelope-from <buildd at hasse.debian.org>)
- id 1Tmdhz-0000jb-Pj; Sun, 23 Dec 2012 05:02:43 +0000
-From: buildd on hasse <buildd at hasse.debian.org>
-To: logs at buildd.debian.org,buildd-porters at hasse.debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on armhf (dist=sid)
+ CN=hummel.debian.org, EMAIL=hostmaster at hummel.debian.org (verified)
+ by mailly.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
+ (Exim 4.80) (envelope-from <buildd at hummel.debian.org>)
+ id 1ULs0F-0003N1-4a
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:23:11 +0000
+Received: from buildd by hummel.debian.org with local (Exim 4.80)
+ (envelope-from <buildd at hummel.debian.org>)
+ id 1ULs0B-0003dF-Qb; Sat, 30 Mar 2013 09:23:08 +0000
+From: buildd on hummel <buildd at hummel.debian.org>
+To: logs at buildd.debian.org,buildd-porters at hummel.debian.org
+Subject: Log for successful build of samtools_0.1.19-1 on armhf (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1Tmdhz-0000jb-Pj at hasse.debian.org>
-Date: Sun, 23 Dec 2012 05:02:43 +0000
+Message-Id: <E1ULs0B-0003dF-Qb at hummel.debian.org>
+Date: Sat, 30 Mar 2013 09:23:07 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hasse.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hummel.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (armhf) 23 Dec 2012 04:53 ║
+║ samtools 0.1.19-1 (armhf) 30 Mar 2013 09:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: armhf
-Get:1 http://ftp.uk.debian.org unstable InRelease [227 kB]
-Get:2 http://incoming.debian.org unstable InRelease [227 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6458 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [53.0 kB]
+Get:1 http://ftp.uk.debian.org unstable InRelease [236 kB]
+Get:2 http://incoming.debian.org unstable InRelease [236 kB]
+Get:3 http://ftp.uk.debian.org unstable/main Sources [6484 kB]
+Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:6 http://ftp.uk.debian.org unstable/contrib Sources [51.0 kB]
Get:7 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [6061 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://incoming.debian.org unstable/main armhf Packages [6061 kB]
-Get:12 http://ftp.uk.debian.org unstable/contrib armhf Packages [35.8 kB]
-Get:13 http://incoming.debian.org unstable/contrib armhf Packages [35.8 kB]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 26.0 MB in 1min 27s (297 kB/s)
+Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [6081 kB]
+Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [34.8 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:12 http://incoming.debian.org unstable/main armhf Packages [6081 kB]
+Get:13 http://incoming.debian.org unstable/contrib armhf Packages [34.8 kB]
+Get:14 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:15 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:16 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:17 http://incoming.debian.org buildd-unstable/main armhf Packages [13.1 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib armhf Packages [14 B]
+Fetched 26.1 MB in 1min 33s (279 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,12 +74,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (286 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (328 kB/s)
Download complete and in download only mode
Check arch
@@ -92,28 +92,53 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5+b1)
+build-essential: already installed (11.6)
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 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-36)
+base-files: already installed (7.1)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.20-3)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-17)
+sed: already installed (4.2.1-10)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
@@ -148,26 +173,26 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 40 not upgraded.
-Need to get 10.0 MB of archives.
+0 upgraded, 29 newly installed, 0 to remove and 22 not upgraded.
+Need to get 9700 kB of archives.
After this operation, 26.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.2-1 [33.7 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.21-9 [1031 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.3 [204 kB]
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.2-2 [33.7 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.22.2-1 [678 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.4 [205 kB]
Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.3-3 [870 kB]
Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-10 [26.8 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 5.11-2 [199 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.31-1 [246 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-7 [786 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 1:5.11-2.1 [199 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.31-2 [246 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-7+nmu1 [785 kB]
Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.33.12+really2.32.4-3 [1708 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.33.12+really2.32.4-5 [1709 kB]
Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.6-2 [120 kB]
Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-10 [123 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armhf 5.11-2 [51.5 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armhf 1:5.11-2.1 [51.5 kB]
Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-10 [129 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev armhf 0.18.1.1-10 [27.1 kB]
Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev armhf 0.18.1.1-10 [143 kB]
@@ -178,17 +203,17 @@ Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [
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:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-8 [381 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 10.0 MB in 4s (2408 kB/s)
+Fetched 9700 kB in 3s (2577 kB/s)
Selecting previously unselected package libpipeline1:armhf.
-(Reading database ... 12862 files and directories currently installed.)
-Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.2-1_armhf.deb) ...
+(Reading database ... 10833 files and directories currently installed.)
+Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.2-2_armhf.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_armhf.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armhf.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_armhf.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_armhf.deb) ...
Selecting previously unselected package bash-completion.
@@ -196,15 +221,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
-Unpacking libmagic1:armhf (from .../libmagic1_5.11-2_armhf.deb) ...
+Unpacking libmagic1:armhf (from .../libmagic1_1%3a5.11-2.1_armhf.deb) ...
Selecting previously unselected package libpcre3:armhf.
-Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.31-1_armhf.deb) ...
+Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.31-2_armhf.deb) ...
Selecting previously unselected package libxml2:armhf.
-Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-7_armhf.deb) ...
+Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_armhf.deb) ...
+Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.33.12+really2.32.4-5_armhf.deb) ...
Selecting previously unselected package libcroco3:armhf.
Unpacking libcroco3:armhf (from .../libcroco3_0.6.6-2_armhf.deb) ...
Selecting previously unselected package libunistring0:armhf.
@@ -212,11 +237,11 @@ Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5+b1_armhf.deb) ...
Selecting previously unselected package libgettextpo0:armhf.
Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_armhf.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_armhf.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_armhf.deb) ...
Selecting previously unselected package libasprintf-dev:armhf.
@@ -238,30 +263,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:armhf (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:armhf (0.18.1.1-10) ...
-Setting up libmagic1:armhf (5.11-2) ...
-Setting up libpcre3:armhf (1:8.31-1) ...
-Setting up libxml2:armhf (2.8.0+dfsg1-7) ...
+Setting up libmagic1:armhf (1:5.11-2.1) ...
+Setting up libpcre3:armhf (1:8.31-2) ...
+Setting up libxml2:armhf (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:armhf (3.0.10-3+b1) ...
-Setting up libglib2.0-0:armhf (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:armhf (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.6-2) ...
Setting up libunistring0:armhf (0.9.3-5+b1) ...
Setting up libgettextpo0:armhf (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15+b1) ...
Setting up libasprintf-dev:armhf (0.18.1.1-10) ...
Setting up libgettextpo-dev:armhf (0.18.1.1-10) ...
@@ -272,17 +297,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:armhf (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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.
+0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 3.2.0-4-mx5 armhf (armv7l)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.01.08 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libalgorithm-diff-perl_1.19.02-3 libalgorithm-merge-perl_0.08-2 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-4 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8 make_3.81-8.2 man-db_2.6.3-3 manpages_3.42-1 manpages-dev_3.42-1 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.35-2
+Package versions: apt_0.9.7.7 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15+b1 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.7 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.35-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-17 perl-base_5.14.2-17 perl-modules_5.14.2-17 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2012j-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -293,16 +318,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -312,44 +336,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -362,11 +383,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -375,139 +396,176 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-armhf-D4t91G/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -529,11 +587,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtoo
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -561,7 +619,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -569,8 +627,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -586,7 +644,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -598,7 +656,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-armhf-OvDkY3/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -613,79 +671,78 @@ 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_0.1.18-4_armhf.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_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_0.1.18-4_armhf.deb'.
- dpkg-genchanges -B -marmhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org> >../samtools_0.1.18-4_armhf.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_armhf.deb'.
+ dpkg-genchanges -B -marmhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org> >../samtools_0.1.19-1_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-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0502
+Build finished at 20130330-0923
-samtools_0.1.18-4_armhf.changes:
+samtools_0.1.19-1_armhf.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: armhf
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
-Maintainer: armhf Build Daemon (hasse) <buildd_armhf-hasse at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Maintainer: armhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
- .
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- ea1fbb66f93218a136ebd1be2a9ef4f27d3b1b18 509328 samtools_0.1.18-4_armhf.deb
- df42fb0fd5de5c3da45b3e272d28f44242cbe470 145006 libbam-dev_0.1.18-4_armhf.deb
+ e2e44ecdbc2a81cfe3ee7ce42a0114ff22990ded 531712 samtools_0.1.19-1_armhf.deb
+ 1f686b97cdc388ea1733e335acf545a3ea858c2b 112002 libbam-dev_0.1.19-1_armhf.deb
Checksums-Sha256:
- e72a183123fdb6ce8bb30cac6d100eec433dc1422f4a486cdccf6573fb3172e2 509328 samtools_0.1.18-4_armhf.deb
- 1d0bc38fcc3935555aa5290629b5a454c8988c401e6c224da256dcf7bf8a11bb 145006 libbam-dev_0.1.18-4_armhf.deb
+ 9e901f8398ac191356eca7f608fb27a308aefdf4389610f866eccc25e81e140f 531712 samtools_0.1.19-1_armhf.deb
+ b77b5c68c4cb39d7dd053299a0fb27e5401edee46ee1bd39be580b5f8bd36bfa 112002 libbam-dev_0.1.19-1_armhf.deb
Files:
- e930890b5de1b5d0ea580195913a3e61 509328 science optional samtools_0.1.18-4_armhf.deb
- 2e6f18b585bc19c181b45bf0df1d3e7c 145006 libdevel optional libbam-dev_0.1.18-4_armhf.deb
+ 1562af621276816eecd35a1f9f48b77c 531712 science optional samtools_0.1.19-1_armhf.deb
+ 4ebb46893751e2c220950fb1a7d739c2 112002 libdevel optional libbam-dev_0.1.19-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_armhf.deb
+samtools_0.1.19-1_armhf.deb
───────────────────────────
new debian package, version 2.0.
- size 509328 bytes: control archive=1819 bytes.
+ size 531712 bytes: control archive=1947 bytes.
32 bytes, 1 lines conffiles
- 817 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 818 bytes, 16 lines control
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 837
+ Installed-Size: 1047
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
@@ -698,74 +755,79 @@ samtools_0.1.18-4_armhf.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/bin/
--rwxr-xr-x root/root 17620 2012-12-23 05:02 ./usr/bin/razip
--rwxr-xr-x root/root 88388 2012-12-23 05:02 ./usr/bin/bcftools
--rwxr-xr-x root/root 248876 2012-12-23 05:02 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:01 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2012-12-23 05:01 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126583 2012-12-23 05:01 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2012-12-23 05:02 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 05:01 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 05:01 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 05:01 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/samtools/
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 5778 2012-12-23 05:02 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/lib/samtools/
--rwxr-xr-x root/root 5892 2012-12-23 05:02 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 6484 2012-12-23 05:02 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 12900 2012-12-23 05:02 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 5892 2012-12-23 05:02 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8480 2012-12-23 05:02 ./usr/lib/samtools/md5fa
-lrwxrwxrwx root/root 0 2012-12-23 05:02 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_armhf.deb
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/lib/samtools/
+-rwxr-xr-x root/root 13832 2013-03-30 09:22 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 117880 2013-03-30 09:22 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 9688 2013-03-30 09:22 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 9716 2013-03-30 09:22 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9720 2013-03-30 09:22 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13892 2013-03-30 09:22 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9720 2013-03-30 09:22 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/bin/
+-rwxr-xr-x root/root 275848 2013-03-30 09:22 ./usr/bin/samtools
+-rwxr-xr-x root/root 100460 2013-03-30 09:22 ./usr/bin/bcftools
+-rwxr-xr-x root/root 18064 2013-03-30 09:22 ./usr/bin/razip
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/samtools/
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 5778 2013-03-30 09:22 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126580 2013-03-30 09:22 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 1966 2013-03-30 09:22 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/man/man1/
+-rw-r--r-- root/root 10654 2013-03-30 09:22 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2013-03-30 09:22 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_armhf.deb
─────────────────────────────
new debian package, version 2.0.
- size 145006 bytes: control archive=937 bytes.
+ size 112002 bytes: control archive=930 bytes.
712 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 336
+ Installed-Size: 311
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -778,25 +840,25 @@ libbam-dev_0.1.18-4_armhf.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/include/samtools/
--rw-r--r-- root/root 24732 2012-12-23 04:57 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 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
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
-drwxr-xr-x root/root 0 2012-12-23 05:02 ./usr/lib/
--rw-r--r-- root/root 201058 2012-12-23 05:02 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/include/samtools/
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/lib/
+-rw-r--r-- root/root 196386 2013-03-30 09:22 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -810,7 +872,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-6d05ad6f-19a9-4623-b5e3-70d3193a6028/build/buildd-samtools_0.1.18-4-armhf-OvDkY3
+Purging /var/lib/schroot/mount/sid-armhf-sbuild-fe467231-1b43-413f-a5bb-24c4c3455418/build/buildd-samtools_0.1.19-1-armhf-D4t91G
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -818,19 +880,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armhf
-Build-Space: 9404
-Build-Time: 338
+Build-Space: 11024
+Build-Time: 372
Distribution: sid
-Install-Time: 85
-Job: samtools_0.1.18-4
+Install-Time: 114
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 539
-Source-Version: 0.1.18-4
-Space: 9404
+Package-Time: 612
+Source-Version: 0.1.19-1
+Space: 11024
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0502
-Build needed 00:08:59, 9404k disc space
-Signature with key '0B213A80' requested:
+Finished at 20130330-0923
+Build needed 00:10:12, 11024k disc space
+Signature with key '630B2C7A' requested:
diff --git a/hurd-i386.log b/hurd-i386.log
index 6c6cc89..39f3b8a 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,85 +1,101 @@
-From buildd at ironforge.sceen.net Sun Dec 23 05:24:57 2012
+From buildd at ironforge.sceen.net Sat Mar 30 09:19:59 2013
Return-path: <buildd at ironforge.sceen.net>
Received: from ironforge.sceen.net ([46.105.42.111])
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
(Exim 4.72) (envelope-from <buildd at ironforge.sceen.net>)
- id 1Tme3U-0004ox-Mu
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:24:57 +0000
-Received: from buildd by ironforge.sceen.net with local (Exim 4.77)
+ id 1ULrx9-0002xO-FI
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:59 +0000
+Received: from buildd by ironforge.sceen.net with local (Exim 4.80)
(envelope-from <buildd at ironforge.sceen.net>)
- id 1TmdfK-0006lO-5U; Sun, 23 Dec 2012 05:59:58 +0100
+ id 1ULrxD-0003sk-CG; Sat, 30 Mar 2013 10:20:03 +0100
Content-Transfer-Encoding: binary
MIME-Version: 1.0
X-Mailer: MIME::Lite 3.027 (F2.82; B3.13; Q3.13)
-Date: Sun, 23 Dec 2012 05:59:58 +0100
+Date: Sat, 30 Mar 2013 10:20:03 +0100
From: Build Daemon <buildd at ironforge.sceen.net>
To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian.org,
debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on hurd-i386 (dist=sid)
-Message-Id: <E1TmdfK-0006lO-5U at ironforge.sceen.net>
+Subject: Log for successful build of samtools_0.1.19-1 on hurd-i386 (dist=sid)
+Message-Id: <E1ULrxD-0003sk-CG at ironforge.sceen.net>
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ironforge.sceen.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (hurd-i386) 23 Dec 2012 05:56 ║
+║ samtools 0.1.19-1 (hurd-i386) 30 Mar 2013 10:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: hurd-i386
-Ign file: ./ InRelease
Ign file: ./ Release.gpg
Ign file: ./ Release
Ign file: ./ Translation-en
-Get:1 http://ftp.fr.debian.org sid InRelease [227 kB]
-Get:2 http://ftp.fr.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:3 http://incoming.debian.org sid InRelease [227 kB]
-Ign http://incoming.debian.org InRelease
-Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
+Get:1 http://ftp.fr.debian.org sid Release.gpg [836 B]
+Get:2 http://ftp.fr.debian.org sid Release [235 kB]
+Get:3 http://incoming.debian.org sid Release.gpg [836 B]
+Get:4 http://ftp.fr.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:5 http://incoming.debian.org buildd-sid Release.gpg [836 B]
+Get:6 http://ftp.fr.debian.org sid/contrib Sources/DiffIndex [7819 B]
Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
-Get:4 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
+Get:7 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
+Get:8 http://incoming.debian.org sid Release [235 kB]
Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
Hit http://ftp.fr.debian.org sid/contrib Translation-en/DiffIndex
-Get:5 http://ftp.fr.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:6 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:9 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:10 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
-Get:11 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
+Get:9 http://ftp.fr.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:10 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:11 http://ftp.fr.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:12 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:13 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
+Get:14 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:15 http://incoming.debian.org buildd-sid Release [109 kB]
+Get:16 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:17 http://incoming.debian.org sid/contrib Sources/DiffIndex [7819 B]
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:12 http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
+Get:18 http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
Hit http://incoming.debian.org sid/contrib hurd-i386 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
-Get:13 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:16 http://incoming.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
-Get:17 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
-Get:18 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Get:19 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:20 http://incoming.debian.org Sources [14.0 kB]
-Get:21 http://incoming.debian.org Packages [118 kB]
-Get:22 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
-Get:23 http://ftp.fr.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Ign http://incoming.debian.org Translation-en
-Get:24 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:25 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Get:26 http://incoming.debian.org sid/main hurd-i386 2012-12-22-2010.30.pdiff [1469 B]
-Get:27 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:28 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Get:29 http://incoming.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
-Get:30 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:31 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Get:32 http://ftp.fr.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
-Get:33 http://ftp.fr.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Get:34 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:35 http://incoming.debian.org sid/main hurd-i386 2012-12-23-0210.55.pdiff [580 B]
-Get:36 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Fetched 657 kB in 59s (10.9 kB/s)
+Get:19 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:20 http://incoming.debian.org buildd-sid/main Sources [11.2 kB]
+Get:21 http://incoming.debian.org buildd-sid/contrib Sources [761 B]
+Get:22 http://incoming.debian.org buildd-sid/non-free Sources [14 B]
+Get:23 http://incoming.debian.org buildd-sid/main hurd-i386 Packages [13.9 kB]
+Get:24 http://incoming.debian.org buildd-sid/contrib hurd-i386 Packages [14 B]
+Get:25 http://ftp.fr.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:26 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
+Get:27 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:28 http://incoming.debian.org buildd-sid/contrib Translation-en [402 B]
+Get:29 http://incoming.debian.org buildd-sid/main Translation-en [13.6 kB]
+Get:30 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:31 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:32 http://incoming.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
+Get:33 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:34 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:35 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
+Get:36 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:37 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:38 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:39 http://ftp.fr.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:40 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:41 http://incoming.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
+Get:42 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:43 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:44 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
+Get:45 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
+Get:46 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:47 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:48 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
+Get:49 http://ftp.fr.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:50 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:51 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
+Get:52 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:53 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:54 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
+Get:55 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
+Get:56 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:57 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
+Fetched 716 kB in 1min 15s (9441 B/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -99,12 +115,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 3s (106 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-sid/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-sid/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-sid/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 2s (244 kB/s)
Download complete and in download only mode
Check arch
@@ -117,7 +133,7 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5+b1)
+build-essential: already installed (11.6)
fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
@@ -129,7 +145,7 @@ The following packages were automatically installed and are no longer required:
libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
@@ -139,41 +155,42 @@ The following packages were automatically installed and are no longer required:
libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
man-db
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, libc-bin, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3+b1)
-debianutils: already installed (4.3.3)
-diffutils: already installed (1:3.2-6+b1)
-dpkg: already installed (1.16.8)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.9)
e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-4+b1)
-grep: already installed (2.12-2)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11+b1)
+hostname: already installed (3.12)
hurd: already installed (20120710-3)
+libc-bin: already installed (2.13-37)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-15)
+perl-base: already installed (5.14.2-18)
sed: already installed (4.2.1-10)
-sysvinit-utils: already installed (2.88dsf-22)
sysvinit: already installed (2.88dsf-22)
-tar: already installed (1.26-4+b1)
-bsdutils: already installed (1:2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
+sysvinit-utils: already installed (2.88dsf-22)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
libc0.3-dev: already installed (2.13-37)
gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.7.1-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2+b1)
dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
hurd-dev: already installed (20120710-3)
@@ -202,14 +219,14 @@ Suggested packages:
graphviz default-mta mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libmail-sendmail-perl
+ libmail-sendmail-perl less
The following NEW packages will be installed:
cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
libasprintf-dev libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo-dev
libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev libtinfo-dev
libunistring0 libxml2 po-debconf quilt zlib1g-dev
-0 upgraded, 24 newly installed, 0 to remove and 36 not upgraded.
-Need to get 0 B/8011 kB of archives.
+0 upgraded, 24 newly installed, 0 to remove and 20 not upgraded.
+Need to get 0 B/8015 kB of archives.
After this operation, 22.7 MB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
libasprintf0c2 libmagic1 libxml2 libffi5 libglib2.0-0 libcroco3 libexpat1
@@ -218,16 +235,16 @@ WARNING: The following packages cannot be authenticated!
libtinfo-dev libncurses5-dev quilt zlib1g-dev
Authentication warning overridden.
Selecting previously unselected package libasprintf0c2:hurd-i386.
-(Reading database ... 15363 files and directories currently installed.)
+(Reading database ... 15400 files and directories currently installed.)
Unpacking libasprintf0c2:hurd-i386 (from .../libasprintf0c2_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package libmagic1:hurd-i386.
-Unpacking libmagic1:hurd-i386 (from .../libmagic1_5.11-2_hurd-i386.deb) ...
+Unpacking libmagic1:hurd-i386 (from .../libmagic1_1%3a5.11-2.1_hurd-i386.deb) ...
Selecting previously unselected package libxml2:hurd-i386.
-Unpacking libxml2:hurd-i386 (from .../libxml2_2.8.0+dfsg1-7_hurd-i386.deb) ...
+Unpacking libxml2:hurd-i386 (from .../libxml2_2.8.0+dfsg1-7+nmu1_hurd-i386.deb) ...
Selecting previously unselected package libffi5:hurd-i386.
Unpacking libffi5:hurd-i386 (from .../libffi5_3.0.10-3+b1_hurd-i386.deb) ...
Selecting previously unselected package libglib2.0-0:hurd-i386.
-Unpacking libglib2.0-0:hurd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-3_hurd-i386.deb) ...
+Unpacking libglib2.0-0:hurd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-5_hurd-i386.deb) ...
Selecting previously unselected package libcroco3:hurd-i386.
Unpacking libcroco3:hurd-i386 (from .../libcroco3_0.6.6-2_hurd-i386.deb) ...
Selecting previously unselected package libexpat1:hurd-i386.
@@ -237,11 +254,11 @@ Unpacking libunistring0:hurd-i386 (from .../libunistring0_0.9.3-5+b1_hurd-i386.d
Selecting previously unselected package libgettextpo0:hurd-i386.
Unpacking libgettextpo0:hurd-i386 (from .../libgettextpo0_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.11-2_hurd-i386.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_hurd-i386.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_hurd-i386.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b2_hurd-i386.deb) ...
Selecting previously unselected package libasprintf-dev:hurd-i386.
@@ -263,23 +280,23 @@ Unpacking libtinfo-dev:hurd-i386 (from .../libtinfo-dev_5.9-10_hurd-i386.deb) ..
Selecting previously unselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_hurd-i386.deb) ...
Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
Selecting previously unselected package zlib1g-dev:hurd-i386.
Unpacking zlib1g-dev:hurd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_hurd-i386.deb) ...
Processing triggers for man-db ...
Setting up libasprintf0c2:hurd-i386 (0.18.1.1-10) ...
-Setting up libmagic1:hurd-i386 (5.11-2) ...
-Setting up libxml2:hurd-i386 (2.8.0+dfsg1-7) ...
+Setting up libmagic1:hurd-i386 (1:5.11-2.1) ...
+Setting up libxml2:hurd-i386 (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:hurd-i386 (3.0.10-3+b1) ...
-Setting up libglib2.0-0:hurd-i386 (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:hurd-i386 (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:hurd-i386 (0.6.6-2) ...
Setting up libexpat1:hurd-i386 (2.1.0-1+b1) ...
Setting up libunistring0:hurd-i386 (0.9.3-5+b1) ...
Setting up libgettextpo0:hurd-i386 (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15+b2) ...
Setting up libasprintf-dev:hurd-i386 (0.18.1.1-10) ...
Setting up libgettextpo-dev:hurd-i386 (0.18.1.1-10) ...
@@ -290,7 +307,7 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:hurd-i386 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
Setting up zlib1g-dev:hurd-i386 (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
@@ -300,11 +317,11 @@ The following packages were automatically installed and are no longer required:
adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 gnumach-dev_2:1.3.99.dfsg.git20120923-1 hurd-dev_20120710-3 libc0.3-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
-Package versions: adduser_3.113+nmu3 apt_0.9.7.4 apt-utils_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpio_2.11-8 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3+b1 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.01.08 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6+b1 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4+b1 g++_4:4.7.1-1 g++-4.7_4.7.2-4 gawk_1:4.0.1+dfsg-2 gcc_4:4.7.2-1 gcc-4.5-base_4.5.4-1 gcc-4.6-base_4.6.3-14 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnumach-dev_2:1.3.99.dfsg.git20120923-1 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11+b1 html2text_1.3.2a-15+b2 hurd_20120710-3 hurd-dev_20120710-3 initscripts_2.88dsf-22 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-inst1.5_0.9.7.5 libapt-pkg4.12_0.9.7.5 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libboost-iostreams1.46.1_1.46.1-8+b1 libboost-iostreams1.48.0_1.48.0-3+b1 libboost-iostreams1.49.0_1.49.0-3.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc0.3_2.13-37 libc0.3-dev_2.13-37 libc0.3-i686_2.13-37 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libcwidget3_0.5.16-3.4 libdb5.1_5.1.29-5+b1 libdpkg-perl_1.16.9 libexpat1_2.1.0-1+b1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgcrypt11_1.5.0-3+b1 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.20-2 libgomp1_4.7.2-4 libgpg-error0_1.10-3.1 libldap-2.4-2_2.4.28-1.3+b2 liblocale-gettext-perl_1.05-7+b2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libncursesw5_5.9-10 libp11-kit0_0.12-3+b1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libparted0debian1_2.3-11 libpciaccess0_0.13.1-2+b2 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libpng12-0_1.2.49-3 libpopt0_1.16-7 libprocps0_1:3.3.3-2 libpthread-stubs0_0.3-3 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsasl2-2_2.1.25.dfsg1-6 libsigc++-2.0-0c2a_2.2.10-0.2 libsigsegv2_2.9-4+b1 libslang2_2.2.4-15 libss2_1.42.5-1 libssl1.0.0_1.0.1c-4 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1.2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libuuid1_2.20.1-5.3 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxapian22_1.2.8-1 libxau6_1:1.0.7-1+b1 libxcb1_1.8.1-2 libxdmcp6_1:1.1.1-1+b1 libxml2_2.8.0+dfsg1-7 lsb-base_4.1+Debian7 make_3.81-8.2+b1 man-db_2.6.2-1 mawk_1.3.3-17+b1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 netbase_5.0 netcat-traditional_1.10-40 netdde_0.0.20120710-1 passwd_1:4.1.5.1-1 patch_2.6.1-3+b1 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 procps_1:3.3.3-2 psmisc_22.19-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sgml-base_1.26+nmu4 sudo_1.8.5p2-1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26-4+b1 tzdata_2012e-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 xkb-data_2.5.1-2 xml-core_0.13+nmu1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.9 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 gnumach-dev_2:1.3.99.dfsg.git20130311-1 hurd-dev_20120710-3 libc0.3-dev_2.13-37 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5
+Package versions: adduser_3.113+nmu3 apt_0.9.7.8 apt-utils_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.2 cpio_2.11+dfsg-0.1 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3+b1 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.12.30 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.7.2-1 g++-4.7_4.7.2-5 gawk_1:4.0.1+dfsg-2.1 gcc_4:4.7.2-1 gcc-4.5-base_4.5.4-1 gcc-4.6-base_4.6.3-15 gcc-4.7_4.7.2-5 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnumach-dev_2:1.3.99.dfsg.git20130311-1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15+b2 hurd_20120710-3 hurd-dev_20120710-3 initscripts_2.88dsf-22 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-inst1.5_0.9.7.8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libboost-iostreams1.46.1_1.46.1-8+b1 libboost-iostreams1.48.0_1.48.0-3+b1 libboost-iostreams1.49.0_1.49.0-3.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc0.3_2.13-37 libc0.3-dev_2.13-37 libc0.3-i686_2.13-37 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libcwidget3_0.5.16-3.4 libdb5.1_5.1.29-5+b1 libdpkg-perl_1.16.9 libexpat1_2.1.0-1+b1 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgcrypt11_1.5.0-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.20-4 libgomp1_4.7.2-5 libgpg-error0_1.10-3.1 libldap-2.4-2_2.4.31-1 liblocale-gettext-perl_1.05-7+b2 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmpc2_0.9-4+b1 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libncursesw5_5.9-10 libp11-kit0_0.12-3+b1 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libparted0debian1_2.3-12 libpciaccess0_0.13.1-2+b2 libpcre3_1:8.31-2 libpipeline1_1.2.2-1 libpng12-0_1.2.49-3 libpopt0_1.16-7 libprocps0_1:3.3.4-2 libpthread-stubs0_0.3-3 libquadmath0_4.7.2-5 libreadline6_6.2+dfsg-0.1 libsasl2-2_2.1.25.dfsg1-6 libsigc++-2.0-0c2a_2.2.10-0.2 libsigsegv2_2.9-4+b1 libslang2_2.2.4-15 libss2_1.42.5-1 libssl1.0.0_1.0.1e-2 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libuuid1_2.20.1-5.3 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxapian22_1.2.12-2 libxau6_1:1.0.7-1+b1 libxcb1_1.8.1-2 libxdmcp6_1:1.1.1-1+b1 libxml2_2.8.0+dfsg1-7+nmu1 lsb-base_4.1+Debian9 make_3.81-8.2+b1 man-db_2.6.3-3 mawk_1.3.3-17+b1 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 netbase_5.0 netcat-traditional_1.10-40 netdde_0.0.20121127-2 passwd_1:4.1.5.1-1 patch_2.6.1-3+b1 perl_5.14.2-18 perl-base_5.14.2-18 perl-modules_5.14.2-18 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 psmisc_22.20-1 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sgml-base_1.26+nmu4 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-22 sysvinit_2.88dsf-22 sysvinit-utils_2.88dsf-22 tar_1.26+dfsg-0.1 tzdata_2013b-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.3 xkb-data_2.5.1-3 xml-core_0.13+nmu2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -315,16 +332,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -334,44 +350,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -379,16 +392,16 @@ 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
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -397,171 +410,208 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
bam_import.c: In function 'append_text':
bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_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. 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
em.c: In function 'bcf_em1':
em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.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. 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
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
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]
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]
-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 md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
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
-[sam_header_read2] 2 sequences loaded.
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/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...
-../samtools index ex1.bam
[bam_rmdup_core] processing reference seq2...
[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
+../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-[mpileup] 1 samples in 1 input files
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -589,7 +639,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -597,8 +647,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -614,7 +664,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -626,7 +676,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -641,80 +691,79 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_hurd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_hurd-i386.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../samtools_0.1.18-4_hurd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_hurd-i386.deb'.
+ dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../samtools_0.1.19-1_hurd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0559
+Build finished at 20130330-1019
-samtools_0.1.18-4_hurd-i386.changes:
+samtools_0.1.19-1_hurd-i386.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: hurd-i386
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
- .
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- 74250d587f2dd74b74c42b7719bd1e8dfdc9362f 535120 samtools_0.1.18-4_hurd-i386.deb
- a14e60c2064d1cc9e52d9ba45d2910b0e315f9b9 161108 libbam-dev_0.1.18-4_hurd-i386.deb
+ b08658b3ebb58880b3f2e0fe86f4a0279da4e7da 564414 samtools_0.1.19-1_hurd-i386.deb
+ 3320893118fbf04bfb6a1b61dd8487d1c795868d 127000 libbam-dev_0.1.19-1_hurd-i386.deb
Checksums-Sha256:
- 4a0742873f65bae405f701ac4552bf07cc778ce6069241930e198c18ca3f5d36 535120 samtools_0.1.18-4_hurd-i386.deb
- e90cab8dc79b9af30fed0f84be9fdc603820a54981f4aa23c97b36a4d2793786 161108 libbam-dev_0.1.18-4_hurd-i386.deb
+ 6bb0ab2f96636cd91d57be13c4c6f46e4a2b4a38c294d9fe8cd94b0fe837db0b 564414 samtools_0.1.19-1_hurd-i386.deb
+ 6d688ddc590c100fda7a17206b556490645fcd6fb79cb7f4e4fd58c0f61abbcd 127000 libbam-dev_0.1.19-1_hurd-i386.deb
Files:
- 5d49505b36a598f3fc19c23853bcc2ab 535120 science optional samtools_0.1.18-4_hurd-i386.deb
- c81412b0eae985be76b3b6f07548344a 161108 libdevel optional libbam-dev_0.1.18-4_hurd-i386.deb
+ 8dfb78cd74823389be6e73ee9a9fa3c3 564414 science optional samtools_0.1.19-1_hurd-i386.deb
+ eed5c18c1ca603a33a80c6a5ff08b1f5 127000 libdevel optional libbam-dev_0.1.19-1_hurd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_hurd-i386.deb
+samtools_0.1.19-1_hurd-i386.deb
───────────────────────────────
new debian package, version 2.0.
- size 535120 bytes: control archive= 1815 bytes.
+ size 564414 bytes: control archive= 1942 bytes.
32 bytes, 1 lines conffiles
- 798 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 802 bytes, 16 lines control
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1050
- Depends: libc0.3 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 1351
+ Depends: libc0.3 (>= 2.13-37), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
Priority: optional
@@ -726,74 +775,79 @@ samtools_0.1.18-4_hurd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-12-23 04:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-12-23 04:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5522 2012-12-23 04:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126583 2012-12-23 05:58 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 05:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 05:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 05:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 05:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 33578 2011-03-01 20:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-12-23 05:59 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 18:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 04:33 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 05:59 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 05:59 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 04:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 05:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 05:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 04:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 05:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 05:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 05:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 05:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 05:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 05:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 05:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 05:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 05:59 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/bin/
--rwxr-xr-x root/root 137508 2012-12-23 05:59 ./usr/bin/bcftools
--rwxr-xr-x root/root 25104 2012-12-23 05:59 ./usr/bin/razip
--rwxr-xr-x root/root 400148 2012-12-23 05:59 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/lib/samtools/
--rwxr-xr-x root/root 16696 2012-12-23 05:59 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7128 2012-12-23 05:59 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7128 2012-12-23 05:59 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10876 2012-12-23 05:59 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7816 2012-12-23 05:59 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 04:33 ./etc/bash_completion.d/samtools
-lrwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_hurd-i386.deb
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2013-03-18 15:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 03:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-01-09 03:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5012 2013-03-30 08:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 10:19 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 15:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2013-03-18 15:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2013-03-18 15:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2013-03-18 15:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 15:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2013-03-30 10:19 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 09:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 10:19 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 10:19 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 15:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2013-03-18 15:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2013-03-18 15:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 15:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 15:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2013-03-18 15:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 15:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 15:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2013-03-18 15:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2013-03-18 15:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 15:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 15:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 10:19 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2685 2013-03-18 15:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 21028 2013-03-18 15:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 29649 2013-03-18 15:43 ./usr/share/samtools/plot-bamcheck
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/bin/
+-rwxr-xr-x root/root 157732 2013-03-30 10:19 ./usr/bin/bcftools
+-rwxr-xr-x root/root 26152 2013-03-30 10:19 ./usr/bin/razip
+-rwxr-xr-x root/root 439700 2013-03-30 10:19 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17896 2013-03-30 10:19 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 17840 2013-03-30 10:19 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 187448 2013-03-30 10:19 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 9628 2013-03-30 10:19 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 9628 2013-03-30 10:19 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13728 2013-03-30 10:19 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9604 2013-03-30 10:19 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 23:52 ./etc/bash_completion.d/samtools
+lrwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_hurd-i386.deb
─────────────────────────────────
new debian package, version 2.0.
- size 161108 bytes: control archive= 943 bytes.
+ size 127000 bytes: control archive= 927 bytes.
716 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: hurd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 432
+ Installed-Size: 405
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -806,25 +860,25 @@ libbam-dev_0.1.18-4_hurd-i386.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 05:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 04:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 20:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 18:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 04:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/lib/
--rw-r--r-- root/root 300292 2012-12-23 05:59 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 05:59 ./usr/include/samtools/
--rw-r--r-- root/root 24732 2012-12-23 05:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-11 00:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 20:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 05:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 05:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2013-03-18 15:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 08:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 09:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/lib/
+-rw-r--r-- root/root 292396 2013-03-30 10:19 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/include/samtools/
+-rw-r--r-- root/root 25788 2013-03-18 15:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 15:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2013-03-18 15:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2013-03-18 15:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 15:43 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -838,7 +892,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.18-4-hurd-i386-Oja8q_
+Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS
Reading package lists...
Building dependency tree...
Reading state information...
@@ -846,7 +900,7 @@ The following packages were automatically installed and are no longer required:
adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
@@ -860,9 +914,9 @@ The following packages will be REMOVED:
libffi5* libgettextpo-dev* libgettextpo0* libglib2.0-0* libmagic1*
libncurses5-dev* libtinfo-dev* libunistring0* libxml2* po-debconf* quilt*
zlib1g-dev*
-0 upgraded, 0 newly installed, 24 to remove and 36 not upgraded.
+0 upgraded, 0 newly installed, 24 to remove and 20 not upgraded.
After this operation, 22.7 MB disk space will be freed.
-(Reading database ... 16465 files and directories currently installed.)
+(Reading database ... 16504 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing quilt ...
@@ -903,17 +957,17 @@ Processing triggers for man-db ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 11460
-Build-Time: 114
+Build-Space: 13640
+Build-Time: 88
Distribution: sid
-Install-Time: 12
-Job: samtools_0.1.18-4
+Install-Time: 18
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 199
-Source-Version: 0.1.18-4
-Space: 11460
+Package-Time: 194
+Source-Version: 0.1.19-1
+Space: 13640
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0559
-Build needed 00:03:19, 11460k disc space
+Finished at 20130330-1019
+Build needed 00:03:14, 13640k disc space
diff --git a/i386.log b/i386.log
index 5c5c025..7e6e73c 100644
--- a/i386.log
+++ b/i386.log
@@ -1,64 +1,65 @@
-From buildd at murphy.debian.org Fri Jul 27 15:40:39 2012
-Return-path: <buildd at murphy.debian.org>
+From buildd at biber.debian.org Sat Mar 30 09:18:53 2013
+Return-path: <buildd at biber.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 murphy.debian.org>)
- id 1Sumed-0004QP-Ap
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:40:39 +0000
-Received: from murphy.debian.org ([70.103.162.31])
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1ULrw4-0002p3-U6
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:18:53 +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 merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at murphy.debian.org>)
- id 1Sumec-0005YU-0h
- for logs at buildd.debian.org; Fri, 27 Jul 2012 15:40:38 +0000
-Received: from buildd by murphy.debian.org with local (Exim 4.72)
- (envelope-from <buildd at murphy.debian.org>)
- id 1Sumea-00029k-Kg; Fri, 27 Jul 2012 15:40:36 +0000
-Message-Id: <E1Sumea-00029k-Kg at murphy.debian.org>
+ (Exim 4.72) (envelope-from <buildd at biber.debian.org>)
+ id 1ULrw3-0001as-KD; Sat, 30 Mar 2013 09:18:51 +0000
+Received: from buildd by biber.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at biber.debian.org>)
+ id 1ULrw2-0001be-CE; Sat, 30 Mar 2013 09:18:50 +0000
+Message-Id: <E1ULrw2-0001be-CE 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: Fri, 27 Jul 2012 15:40:36 +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_0.1.18-3 on i386 (dist=sid)
-Key-Id: 2B54027C
+Date: Sat, 30 Mar 2013 09:18:50 +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_0.1.19-1 on i386 (dist=sid)
+Key-Id: DFABA12A
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 0.1.18-3 (i386) 27 Jul 2012 15:39 ║
+║ samtools 0.1.19-1 (i386) 30 Mar 2013 09:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-3
-Source Version: 0.1.18-3
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: i386
-Hit http://incoming.debian.org sid InRelease
-Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Get:1 http://ftp.us.debian.org sid InRelease [249 kB]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib i386 Packages/DiffIndex
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org Release [1601 B]
-Get:4 http://ftp.us.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:5 http://incoming.debian.org Sources [14.5 kB]
-Get:6 http://incoming.debian.org Packages [117 kB]
-Hit http://ftp.us.debian.org sid/contrib Sources/DiffIndex
-Get:7 http://ftp.us.debian.org sid/main i386 Packages/DiffIndex [7876 B]
-Hit http://ftp.us.debian.org sid/contrib i386 Packages/DiffIndex
-Get:8 http://ftp.us.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
-Get:9 http://ftp.us.debian.org sid/main 2012-07-27-1414.10.pdiff [1291 B]
-Get:10 http://ftp.us.debian.org sid/main i386 2012-07-27-1414.10.pdiff [1837 B]
-Get:11 http://ftp.us.debian.org sid/main i386 2012-07-27-1414.10.pdiff [1837 B]
-Fetched 402 kB in 8s (48.6 kB/s)
+Get:1 http://ftp.gr.debian.org unstable Release.gpg [836 B]
+Get:2 http://ftp.gr.debian.org unstable Release [235 kB]
+Get:3 http://ftp.gr.debian.org unstable/main Sources [6484 kB]
+Get:4 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:5 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:6 http://ftp.gr.debian.org unstable/contrib Sources [51.0 kB]
+Get:7 http://ftp.gr.debian.org unstable/non-free Sources [101 kB]
+Get:8 http://ftp.gr.debian.org unstable/main i386 Packages [6278 kB]
+Get:9 http://incoming.debian.org unstable Release [235 kB]
+Get:10 http://ftp.gr.debian.org unstable/contrib i386 Packages [44.5 kB]
+Get:11 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:12 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:15 http://incoming.debian.org unstable/main i386 Packages [6278 kB]
+Get:16 http://incoming.debian.org unstable/contrib i386 Packages [44.5 kB]
+Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:20 http://incoming.debian.org buildd-unstable/main i386 Packages [14.2 kB]
+Get:21 http://incoming.debian.org buildd-unstable/contrib i386 Packages [436 B]
+Fetched 26.5 MB in 18s (1443 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -78,12 +79,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 390 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (dsc) [1429 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-3 (diff) [8884 B]
-Fetched 390 kB in 1s (285 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (293 kB/s)
Download complete and in download only mode
Check arch
@@ -96,72 +97,74 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-4)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.2)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.7)
-e2fsprogs: already installed (1.42.4-3)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
+e2fsprogs: already installed (1.42.5-1.1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-20)
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)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
+gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.7 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
-Using default version 9.20120608
+Using default version 9.20120909
+bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
+Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0 libglib2.0-0
- libmagic1 libpcre3 libpipeline1 libtinfo-dev libunistring0 libxml2 man-db
- po-debconf
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
@@ -170,57 +173,94 @@ Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
- libglib2.0-0 libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
+Need to get 10.2 MB of archives.
+After this operation, 29.3 MB of additional disk space will be used.
+Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.2-2 [39.1 kB]
+Get:2 http://ftp.gr.debian.org/debian/ unstable/main groff-base i386 1.22.2-1 [736 kB]
+Get:3 http://ftp.gr.debian.org/debian/ unstable/main bsdmainutils i386 9.0.4 [206 kB]
+Get:4 http://ftp.gr.debian.org/debian/ unstable/main man-db i386 2.6.3-3 [890 kB]
+Get:5 http://ftp.gr.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp.gr.debian.org/debian/ unstable/main libasprintf0c2 i386 0.18.1.1-10 [27.1 kB]
+Get:7 http://ftp.gr.debian.org/debian/ unstable/main libmagic1 i386 1:5.11-2.1 [204 kB]
+Get:8 http://ftp.gr.debian.org/debian/ unstable/main libpcre3 i386 1:8.31-2 [246 kB]
+Get:9 http://ftp.gr.debian.org/debian/ unstable/main libxml2 i386 2.8.0+dfsg1-7+nmu1 [893 kB]
+Get:10 http://ftp.gr.debian.org/debian/ unstable/main libffi5 i386 3.0.10-3 [21.0 kB]
+Get:11 http://ftp.gr.debian.org/debian/ unstable/main libglib2.0-0 i386 2.33.12+really2.32.4-5 [1829 kB]
+Get:12 http://ftp.gr.debian.org/debian/ unstable/main libcroco3 i386 0.6.6-2 [133 kB]
+Get:13 http://ftp.gr.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5 [442 kB]
+Get:14 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo0 i386 0.18.1.1-10 [141 kB]
+Get:15 http://ftp.gr.debian.org/debian/ unstable/main file i386 1:5.11-2.1 [51.6 kB]
+Get:16 http://ftp.gr.debian.org/debian/ unstable/main gettext-base i386 0.18.1.1-10 [132 kB]
+Get:17 http://ftp.gr.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
+Get:18 http://ftp.gr.debian.org/debian/ unstable/main html2text i386 1.3.2a-15 [101 kB]
+Get:19 http://ftp.gr.debian.org/debian/ unstable/main libasprintf-dev i386 0.18.1.1-10 [26.6 kB]
+Get:20 http://ftp.gr.debian.org/debian/ unstable/main libgettextpo-dev i386 0.18.1.1-10 [170 kB]
+Get:21 http://ftp.gr.debian.org/debian/ unstable/main gettext i386 0.18.1.1-10 [1769 kB]
+Get:22 http://ftp.gr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp.gr.debian.org/debian/ unstable/main diffstat i386 1.55-3 [29.3 kB]
+Get:26 http://ftp.gr.debian.org/debian/ unstable/main libtinfo-dev i386 5.9-10 [93.2 kB]
+Get:27 http://ftp.gr.debian.org/debian/ unstable/main libncurses5-dev i386 5.9-10 [212 kB]
+Get:28 http://ftp.gr.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
+Get:29 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, 26 newly installed, 0 to remove and 14 not upgraded.
-Need to get 0 B/10.8 MB of archives.
-After this operation, 28.4 MB of additional disk space will be used.
+Fetched 10.2 MB in 1s (7037 kB/s)
Selecting previously unselected package libpipeline1:i386.
-(Reading database ... 10967 files and directories currently installed.)
-Unpacking libpipeline1:i386 (from .../libpipeline1_1.2.1-1_i386.deb) ...
+(Reading database ... 10888 files and directories currently installed.)
+Unpacking libpipeline1:i386 (from .../libpipeline1_1.2.2-2_i386.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.22.2-1_i386.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_i386.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_i386.deb) ...
+Selecting previously unselected package bash-completion.
+Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:i386.
-Unpacking libasprintf0c2:i386 (from .../libasprintf0c2_0.18.1.1-9_i386.deb) ...
+Unpacking libasprintf0c2:i386 (from .../libasprintf0c2_0.18.1.1-10_i386.deb) ...
Selecting previously unselected package libmagic1:i386.
-Unpacking libmagic1:i386 (from .../libmagic1_5.11-2_i386.deb) ...
+Unpacking libmagic1:i386 (from .../libmagic1_1%3a5.11-2.1_i386.deb) ...
Selecting previously unselected package libpcre3:i386.
-Unpacking libpcre3:i386 (from .../libpcre3_1%3a8.30-5_i386.deb) ...
+Unpacking libpcre3:i386 (from .../libpcre3_1%3a8.31-2_i386.deb) ...
Selecting previously unselected package libxml2:i386.
-Unpacking libxml2:i386 (from .../libxml2_2.8.0+dfsg1-5_i386.deb) ...
+Unpacking libxml2:i386 (from .../libxml2_2.8.0+dfsg1-7+nmu1_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) ...
+Unpacking libglib2.0-0:i386 (from .../libglib2.0-0_2.33.12+really2.32.4-5_i386.deb) ...
Selecting previously unselected package libcroco3:i386.
-Unpacking libcroco3:i386 (from .../libcroco3_0.6.5-1_i386.deb) ...
+Unpacking libcroco3:i386 (from .../libcroco3_0.6.6-2_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) ...
+Unpacking libgettextpo0:i386 (from .../libgettextpo0_0.18.1.1-10_i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_i386.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_i386.deb) ...
Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_i386.deb) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_i386.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.116_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_i386.deb) ...
+Selecting previously unselected package libasprintf-dev:i386.
+Unpacking libasprintf-dev:i386 (from .../libasprintf-dev_0.18.1.1-10_i386.deb) ...
+Selecting previously unselected package libgettextpo-dev:i386.
+Unpacking libgettextpo-dev:i386 (from .../libgettextpo-dev_0.18.1.1-10_i386.deb) ...
Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-9_i386.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-10_i386.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120608_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_i386.deb) ...
Selecting previously unselected package libtinfo-dev:i386.
@@ -228,48 +268,51 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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) ...
+Setting up libpipeline1:i386 (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up groff-base (1.21-9) ...
-Setting up man-db (2.6.2-1) ...
+Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
-Setting up file (5.11-2) ...
-Setting up gettext-base (0.18.1.1-9) ...
-Setting up cdbs (0.4.116) ...
+Setting up bash-completion (1:2.0-1) ...
+Setting up libasprintf0c2:i386 (0.18.1.1-10) ...
+Setting up libmagic1:i386 (1:5.11-2.1) ...
+Setting up libpcre3:i386 (1:8.31-2) ...
+Setting up libxml2:i386 (2.8.0+dfsg1-7+nmu1) ...
+Setting up libffi5:i386 (3.0.10-3) ...
+Setting up libglib2.0-0:i386 (2.33.12+really2.32.4-5) ...
+No schema files found: doing nothing.
+Setting up libcroco3:i386 (0.6.6-2) ...
+Setting up libunistring0:i386 (0.9.3-5) ...
+Setting up libgettextpo0:i386 (0.18.1.1-10) ...
+Setting up file (1:5.11-2.1) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
-Setting up gettext (0.18.1.1-9) ...
+Setting up libasprintf-dev:i386 (0.18.1.1-10) ...
+Setting up libgettextpo-dev:i386 (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120608) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:i386 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 14 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-686-bigmem i386 (i686)
-Toolchain package versions: binutils_2.22-7 dpkg-dev_1.16.7 g++-4.7_4.7.1-5 gcc-4.7_4.7.1-5 libc6-dev_2.13-34 libstdc++6_4.7.1-5 libstdc++6-4.7-dev_4.7.1-5 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 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 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_4.7.1-5 gawk_1:4.0.1+dfsg-2 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 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.2 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-3 libc-bin_2.13-34 libc-dev-bin_2.13-34 libc6_2.13-34 libc6-dev_2.13-34 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libdb5.1_5.1.29-5 libdpkg-perl_1.16.7 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-5 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-5 libitm1_4.7.1-5 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_4.7.1-5 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 libsigsegv2_2.9-4 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 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_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
+Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.7.2-1 g++-4.7_4.7.2-5 gcc_4:4.7.2-1 gcc-4.7_4.7.2-5 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libffi5_3.0.10-3 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 libitm1_4.7.2-5 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libquadmath0_4.7.2-5 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -280,13 +323,13 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 27 15:21:02 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-3.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-3.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
@@ -298,33 +341,33 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-3
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
@@ -332,7 +375,7 @@ Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -343,12 +386,13 @@ rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fa
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -360,139 +404,179 @@ patching file bam2depth.c
Now at patch fix_coverage_cap.patch
touch debian/stamp-patched
/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/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
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/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
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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':
-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_0.1.18-3-i386-D3LzxQ/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
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-i386-yTX1S8/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -514,11 +598,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtool
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -527,6 +611,7 @@ dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -545,7 +630,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -553,8 +638,10 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -568,7 +655,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -577,12 +664,12 @@ dh_link -plibbam-dev
dh_installmime -plibbam-dev
dh_installgsettings -plibbam-dev
dh_strip -psamtools
-dh_compress -psamtools
+dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-3-i386-D3LzxQ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-i386-yTX1S8/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
-dh_compress -plibbam-dev
+dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
@@ -596,69 +683,79 @@ dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is no
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-3_i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_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_0.1.18-3_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org> >../samtools_0.1.18-3_i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_i386.deb'.
+ dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../samtools_0.1.19-1_i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20120727-1540
+Build finished at 20130330-0918
-samtools_0.1.18-3_i386.changes:
+samtools_0.1.19-1_i386.changes:
Format: 1.8
-Date: Fri, 27 Jul 2012 11:11:41 -0400
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: i386
-Version: 0.1.18-3
+Version: 0.1.19-1
Distribution: sid
Urgency: low
-Maintainer: i386 Build Daemon (murphy) <buildd_i386-murphy at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 653042 671524
Changes:
- samtools (0.1.18-3) unstable; urgency=low
+ samtools (0.1.19-1) unstable; urgency=low
.
- * upload 0.1.18-2 closed the wrong bug, correction:
- * added patch to fix segfault in mpileup (Closes: #653042)
- * added patch to fix coverage cap (Closes: #671524)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- 361b092fd97df955921190b3f3dd33e09f592339 534260 samtools_0.1.18-3_i386.deb
- 142d7e62801391d8bb946b64a86ce65abb7b9cba 160760 libbam-dev_0.1.18-3_i386.deb
+ 8cb3c4917736e45c557b1b9b690bfd831d514914 564504 samtools_0.1.19-1_i386.deb
+ 88c85415b2ca939d7553b847e3bb1a7e7e7203bd 127164 libbam-dev_0.1.19-1_i386.deb
Checksums-Sha256:
- 4ce81914e581e0c10fb05a7f632f34e2096b1e90995e143632983639e03509b2 534260 samtools_0.1.18-3_i386.deb
- 39358eb7dcde66cabdf97f2c1c6bcc5d27f16abfdb587ac018c1eddbd50b9168 160760 libbam-dev_0.1.18-3_i386.deb
+ b816433ae0d856ccb4a0f4220ac5a32d1a3c254670ecc0807ef10f24f5dd3dd0 564504 samtools_0.1.19-1_i386.deb
+ 5684aadde55d2d513b96aab8791e7c8018584618ddf65e87f498024007db0147 127164 libbam-dev_0.1.19-1_i386.deb
Files:
- 422474d529562816060920858b4bb60e 534260 science optional samtools_0.1.18-3_i386.deb
- ed448671fefad2122b9144f6ddb55889 160760 libdevel optional libbam-dev_0.1.18-3_i386.deb
+ c3ae79838dad2598010a977afe2c9395 564504 science optional samtools_0.1.19-1_i386.deb
+ a3a4e27aa92be780283eae154240d4d8 127164 libdevel optional libbam-dev_0.1.19-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-3_i386.deb
+samtools_0.1.19-1_i386.deb
──────────────────────────
new debian package, version 2.0.
- size 534260 bytes: control archive= 1760 bytes.
+ size 564504 bytes: control archive= 1932 bytes.
+ 32 bytes, 1 lines conffiles
791 bytes, 16 lines control
- 2453 bytes, 37 lines md5sums
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-3
+ Version: 0.1.19-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1036
+ Installed-Size: 1351
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -671,71 +768,79 @@ samtools_0.1.18-3_i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/bin/
--rwxr-xr-x root/root 134308 2012-07-27 15:40 ./usr/bin/bcftools
--rwxr-xr-x root/root 24740 2012-07-27 15:40 ./usr/bin/razip
--rwxr-xr-x root/root 400020 2012-07-27 15:40 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/lib/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/lib/samtools/
--rwxr-xr-x root/root 7484 2012-07-27 15:40 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 6860 2012-07-27 15:40 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 16536 2012-07-27 15:40 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 10608 2012-07-27 15:40 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 6860 2012-07-27 15:40 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2012-07-27 15:40 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2012-07-27 15:40 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./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 2012-07-27 15:40 ./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 2012-07-27 15:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./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 1826 2012-07-27 15:15 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./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 2012-07-27 15:40 ./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 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 1966 2012-07-27 15:40 ./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 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 2012-07-27 15:40 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-3_i386.deb
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/samtools/
+-rwxr-xr-x root/root 9604 2013-03-30 09:18 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 9628 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 9628 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 187448 2013-03-30 09:18 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 13728 2013-03-30 09:18 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17896 2013-03-30 09:18 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 17840 2013-03-30 09:18 ./usr/lib/samtools/ace2sam
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/bin/
+-rwxr-xr-x root/root 157732 2013-03-30 09:18 ./usr/bin/bcftools
+-rwxr-xr-x root/root 26152 2013-03-30 09:18 ./usr/bin/razip
+-rwxr-xr-x root/root 439700 2013-03-30 09:18 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:18 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1966 2013-03-30 09:18 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/man1/
+-rw-r--r-- root/root 10654 2013-03-30 09:18 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2013-03-30 09:18 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:18 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+lrwxrwxrwx root/root 0 2013-03-30 09:18 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_i386.deb
────────────────────────────
new debian package, version 2.0.
- size 160760 bytes: control archive= 923 bytes.
- 673 bytes, 15 lines control
+ size 127164 bytes: control archive= 927 bytes.
+ 711 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-3
+ Version: 0.1.19-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 432
+ Installed-Size: 405
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -745,26 +850,28 @@ libbam-dev_0.1.18-3_i386.deb
Alignment/Map) format. It now supports importing from or exporting to SAM,
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/include/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./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 2012-07-27 15:40 ./usr/lib/
--rw-r--r-- root/root 299796 2012-07-27 15:40 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-07-27 15:40 ./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 1826 2012-07-27 15:15 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5502 2011-09-06 07:01 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 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
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
+-rw-r--r-- root/root 291948 2013-03-30 09:18 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/samtools/
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -778,80 +885,26 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-i386-sbuild-8ef2d0ee-2250-4951-b2c9-2f3744c63220/build/buildd-samtools_0.1.18-3-i386-D3LzxQ
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 14 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* 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, 0 newly installed, 26 to remove and 14 not upgraded.
-After this operation, 28.4 MB disk space will be freed.
-(Reading database ... 12572 files and directories currently installed.)
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing cdbs ...
-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 libasprintf0c2:i386 ...
-Removing libcroco3:i386 ...
-Purging configuration files for libcroco3:i386 ...
-Removing libglib2.0-0:i386 ...
-Purging configuration files for libglib2.0-0:i386 ...
-Removing libffi5:i386 ...
-Purging configuration files for libffi5:i386 ...
-Removing libgettextpo0:i386 ...
-Removing libmagic1:i386 ...
-Purging configuration files for libmagic1:i386 ...
-Removing libncurses5-dev ...
-Removing libpcre3:i386 ...
-Purging configuration files for libpcre3:i386 ...
-Removing libpipeline1:i386 ...
-Purging configuration files for libpipeline1:i386 ...
-Removing libtinfo-dev:i386 ...
-Removing libunistring0:i386 ...
-Purging configuration files for libunistring0:i386 ...
-Removing libxml2:i386 ...
-Purging configuration files for libxml2:i386 ...
-Removing zlib1g-dev:i386 ...
+Purging /var/lib/schroot/mount/sid-i386-sbuild-9ec63e60-6331-45ff-ad27-68acd8c0fc8c/build/buildd-samtools_0.1.19-1-i386-yTX1S8
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 11392
-Build-Time: 62
+Build-Space: 13620
+Build-Time: 59
Distribution: sid
-Install-Time: 11
-Job: samtools_0.1.18-3
+Install-Time: 52
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 90
-Source-Version: 0.1.18-3
-Space: 11392
+Package-Time: 143
+Source-Version: 0.1.19-1
+Space: 13620
Status: successful
-Version: 0.1.18-3
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20120727-1540
-Build needed 00:01:30, 11392k disc space
-Signature with key '2B54027C' requested:
+Finished at 20130330-0918
+Build needed 00:02:23, 13620k disc space
+Signature with key 'DFABA12A' requested:
diff --git a/ia64.log b/ia64.log
index 69721db..d2cc210 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,4 +1,4 @@
-From buildd at caballero.debian.org Sun Dec 23 04:58:15 2012
+From buildd at caballero.debian.org Sat Mar 30 09:19:15 2013
Return-path: <buildd at caballero.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,23 +6,23 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
- id 1Tmdde-0007aZ-Pi
- for logs at buildd.debian.org; Sun, 23 Dec 2012 04:58:15 +0000
+ id 1ULrwR-0002tw-J9
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:15 +0000
Received: from caballero.debian.org ([193.201.200.200])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=caballero.debian.org,
EMAIL=hostmaster at caballero.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
- id 1Tmddc-00083W-KO; Sun, 23 Dec 2012 04:58:12 +0000
+ id 1ULrwP-0001bN-Dq; Sat, 30 Mar 2013 09:19:13 +0000
Received: from buildd by caballero.debian.org with local (Exim 4.72)
- (envelope-from <buildd at caballero.debian.org>) id 1Tmddb-0001fs-KX
- for buildd-porters at caballero.debian.org; Sun, 23 Dec 2012 04:58:11 +0000
-Date: Sun, 23 Dec 2012 04:58:11 +0000
-Message-Id: <E1Tmddb-0001fs-KX at caballero.debian.org>
+ (envelope-from <buildd at caballero.debian.org>) id 1ULrwO-0000hZ-5g
+ for buildd-porters at caballero.debian.org; Sat, 30 Mar 2013 09:19:12 +0000
+Date: Sat, 30 Mar 2013 09:19:12 +0000
+Message-Id: <E1ULrwO-0000hZ-5g at caballero.debian.org>
From: buildd on caballero <buildd at caballero.debian.org>
To: buildd-porters at caballero.debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on ia64 (dist=sid)
+Subject: Log for successful build of samtools_0.1.19-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: buildd-porters at caballero.debian.org
@@ -31,58 +31,70 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on caballero.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (ia64) 23 Dec 2012 04:54 ║
+║ samtools 0.1.19-1 (ia64) 30 Mar 2013 09:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: ia64
-Get:1 http://ftp.uk.debian.org sid InRelease [227 kB]
+Get:1 http://ftp.uk.debian.org sid InRelease [236 kB]
Get:2 http://ftp.uk.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:3 http://incoming.debian.org sid InRelease [227 kB]
-Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
+Get:3 http://incoming.debian.org sid InRelease [236 kB]
+Get:4 http://ftp.uk.debian.org sid/contrib Sources/DiffIndex [7819 B]
+Get:5 http://ftp.uk.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
Ign http://incoming.debian.org InRelease
-Get:4 http://ftp.uk.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
Hit http://ftp.uk.debian.org sid/contrib ia64 Packages/DiffIndex
Hit http://ftp.uk.debian.org sid/contrib Translation-en/DiffIndex
-Get:5 http://ftp.uk.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:6 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:9 http://ftp.uk.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
-Get:10 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Get:11 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Get:12 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
+Get:6 http://ftp.uk.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:7 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:8 http://incoming.debian.org Release.gpg [836 B]
+Get:9 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:10 http://ftp.uk.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:11 http://ftp.uk.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
+Get:12 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:13 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:14 http://incoming.debian.org sid/contrib Sources/DiffIndex [7819 B]
+Get:15 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
-Get:13 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:16 http://incoming.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
-Get:17 http://ftp.uk.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
-Get:18 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:19 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Get:20 http://incoming.debian.org Sources [14.0 kB]
-Get:21 http://incoming.debian.org Packages [118 kB]
+Get:16 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Get:17 http://incoming.debian.org Release [1141 B]
+Get:18 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:19 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:20 http://incoming.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
+Get:21 http://ftp.uk.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:22 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:23 http://ftp.uk.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
+Get:24 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:25 http://incoming.debian.org Sources [12.5 kB]
+Get:26 http://incoming.debian.org Packages [98.1 kB]
Ign http://incoming.debian.org Translation-en
-Get:22 http://ftp.uk.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Get:23 http://ftp.uk.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
-Get:24 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3203 B]
-Get:25 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Get:26 http://incoming.debian.org sid/main ia64 2012-12-22-2010.30.pdiff [2410 B]
-Get:27 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:28 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:29 http://incoming.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
-Get:30 http://incoming.debian.org sid/main 2012-12-22-2010.30.pdiff [3423 B]
-Get:31 http://ftp.uk.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
-Get:32 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Get:33 http://ftp.uk.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Get:34 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [1193 B]
-Get:35 http://incoming.debian.org sid/main ia64 2012-12-23-0210.55.pdiff [7287 B]
-Get:36 http://incoming.debian.org sid/main 2012-12-23-0210.55.pdiff [249 B]
-Fetched 672 kB in 28s (23.3 kB/s)
+Get:27 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:28 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
+Get:29 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
+Get:30 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:31 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
+Get:32 http://incoming.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
+Get:33 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:34 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:35 http://incoming.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
+Get:36 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
+Get:37 http://ftp.uk.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:38 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
+Get:39 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:40 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:41 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
+Get:42 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
+Get:43 http://incoming.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
+Get:44 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:45 http://ftp.uk.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:46 http://incoming.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
+Get:47 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
+Get:48 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
+Get:49 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
+Get:50 http://incoming.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
+Fetched 678 kB in 37s (17.9 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -102,12 +114,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (385 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (486 kB/s)
Download complete and in download only mode
Check arch
@@ -120,81 +132,140 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 119 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-3)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
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)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-7)
+dpkg: already installed (1.16.9)
e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-16)
+perl-base: already installed (5.14.2-20)
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 (2.13-36)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6.1-dev: already installed (2.13-38)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-debhelper: already installed (9.20120909 >= 9 is satisfied)
+debhelper: missing
+Using default version 9.20120909
bash-completion: missing
cdbs: missing
quilt: missing
libncurses5-dev: missing
-zlib1g-dev: already installed (1:1.2.7.dfsg-13)
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies: bash-completion cdbs quilt libncurses5-dev
+Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- diffstat libtinfo-dev
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts ncurses-doc procmail graphviz default-mta mail-transport-agent
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
+ mail-transport-agent
+Recommended packages:
+ autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
+ xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion cdbs diffstat libncurses5-dev libtinfo-dev quilt
-0 upgraded, 6 newly installed, 0 to remove and 119 not upgraded.
-Need to get 0 B/1121 kB of archives.
-After this operation, 3871 kB of additional disk space will be used.
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 29 newly installed, 0 to remove and 12 not upgraded.
+Need to get 0 B/11.6 MB of archives.
+After this operation, 39.0 MB of additional disk space will be used.
+Selecting previously unselected package libpipeline1:ia64.
+(Reading database ... 10657 files and directories currently installed.)
+Unpacking libpipeline1:ia64 (from .../libpipeline1_1.2.2-2_ia64.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.22.2-1_ia64.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_ia64.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.3-3_ia64.deb) ...
Selecting previously unselected package bash-completion.
-(Reading database ... 28142 files and directories currently installed.)
Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
+Selecting previously unselected package libasprintf0c2:ia64.
+Unpacking libasprintf0c2:ia64 (from .../libasprintf0c2_0.18.1.1-10_ia64.deb) ...
+Selecting previously unselected package libmagic1:ia64.
+Unpacking libmagic1:ia64 (from .../libmagic1_1%3a5.11-2.1_ia64.deb) ...
+Selecting previously unselected package libpcre3:ia64.
+Unpacking libpcre3:ia64 (from .../libpcre3_1%3a8.31-2_ia64.deb) ...
+Selecting previously unselected package libxml2:ia64.
+Unpacking libxml2:ia64 (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-5_ia64.deb) ...
+Selecting previously unselected package libcroco3:ia64.
+Unpacking libcroco3:ia64 (from .../libcroco3_0.6.6-2_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_0.18.1.1-10_ia64.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../file_1%3a5.11-2.1_ia64.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_ia64.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
+Selecting previously unselected package libasprintf-dev:ia64.
+Unpacking libasprintf-dev:ia64 (from .../libasprintf-dev_0.18.1.1-10_ia64.deb) ...
+Selecting previously unselected package libgettextpo-dev:ia64.
+Unpacking libgettextpo-dev:ia64 (from .../libgettextpo-dev_0.18.1.1-10_ia64.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-10_ia64.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package diffstat.
Unpacking diffstat (from .../diffstat_1.55-3_ia64.deb) ...
Selecting previously unselected package libtinfo-dev:ia64.
@@ -202,23 +273,51 @@ 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) ...
-Processing triggers for man-db ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up man-db (2.6.3-3) ...
+Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
-Setting up cdbs (0.4.119) ...
+Setting up libasprintf0c2:ia64 (0.18.1.1-10) ...
+Setting up libmagic1:ia64 (1:5.11-2.1) ...
+Setting up libpcre3:ia64 (1:8.31-2) ...
+Setting up libxml2:ia64 (2.8.0+dfsg1-7+nmu1) ...
+Setting up libffi5:ia64 (3.0.10-3) ...
+Setting up libglib2.0-0:ia64 (2.33.12+really2.32.4-5) ...
+No schema files found: doing nothing.
+Setting up libcroco3:ia64 (0.6.6-2) ...
+Setting up libunistring0:ia64 (0.9.3-5) ...
+Setting up libgettextpo0:ia64 (0.18.1.1-10) ...
+Setting up file (1:5.11-2.1) ...
+Setting up gettext-base (0.18.1.1-10) ...
+Setting up cdbs (0.4.120) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up libasprintf-dev:ia64 (0.18.1.1-10) ...
+Setting up libgettextpo-dev:ia64 (0.18.1.1-10) ...
+Setting up gettext (0.18.1.1-10) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:ia64 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
+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 119 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6.1-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.21-3
-Package versions: apt_0.9.7.1 apt-utils_0.9.7.1 aspell_0.60.7~20110707-1 aspell-en_7.1-0-1 autoconf_2.69-1 automake_1:1.11.6-1 autopoint_0.18.1.1-9 autotools-dev_20120608.1 base-files_6.11 base-passwd_3.5.26 bash_4.2-3 bash-completion_1:2.0-1 binutils_2.22-7.1 bison_1:2.5.dfsg-2.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 ca-certificates_20121114 cdbs_0.4.119 chrpath_0.13-2 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 dconf-gsettings-backend_0.12.1-2 dconf-service_0.12.1-2 debconf_1.5.45 debfoster_2.7-1.1 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.2 dictionaries-common_1.12.10 diffstat_1.55-3 diffutils_1:3.2-6 docbook_4.5-5.1 docbook-dsssl_1.79-7 docbook-to-man_1:2.0.0-31 docbook-xml_4.5-7.1 docbook-xsl_1.76.1+dfsg-1 docutils-common_0.8.1-8 dpkg_1.16.7 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 flex_2.5.35-10.1 fontconfig_2.9.0-7 fontconfig-config_2.9.0-7 g++_4:4.6.3-7 g++-4.6_4.6.3-14 gawk_1:4.0.1+dfsg-2 gcc_4:4.6.3-8 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gir1.2-atk-1.0_2.4.0-2 gir1.2-freedesktop_1.32.1-1 gir1.2-gdkpixbuf-2.0_2.26.1-1 gir1.2-glib-2.0_1.32.1-1 gir1.2-gst-plugins-base-0.10_0.10.36-1 gir1.2-gstreamer-0.10_0.10.36-1 gir1.2-gtk-2.0_2.24.10-2 gir1.2-gtk-3.0_3.4.2-4 gir1.2-pango-1.0_1.30.0-1 gir1.2-soup-2.4_2.38.1-2 git_1:1.7.10.4-1 git-man_1:1.7.10.4-1 glib-networking_2.32.3-1 glib-networking-common_2.32.3-1 glib-networking-services_2.32.3-1 gnome-common_3.4.0.1-1 gnupg_1.4.12-4+b1 gobjc++_4:4.6.3-7 gobjc++-4.6_4.6.3-14 gobjc-4.6_4.6.3-14 gobject-introspection_1.32.1-1 gperf_3.0.3-1+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gsettings-desktop-schemas_3.4.2-3 gtk-doc-tools_1.18-2 gzip_1.5-1.1 highlight_3.9-1 highlight-common_3.9-1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-28 insserv_1.14.0-4 intltool_0.50.2-2 intltool-debian_0.35.0+20060710.1 iso-codes_3.38-1 jade_1.2.1-47.1+b1 libacl1_2.2.51-8 libapt-inst1.5_0.9.7.1 libapt-pkg-dev_0.9.7.1 libapt-pkg4.12_0.9.7.1 libaspell15_0.60.7~20110707-1 libasprintf0c2_0.18.1.1-9 libatk1.0-0_2.4.0-2 libatk1.0-data_2.4.0-2 libatk1.0-dev_2.4.0-2 libattr1_1:2.4.46-8 libavahi-client3_0.6.31-1 libavahi-common-data_0.6.31-1 libavahi-common3_0.6.31-1 libbison-dev_1:2.5.dfsg-2.1 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6.1_2.13-36 libc6.1-dev_2.13-36 libcairo-gobject2_1.12.2-2 libcairo-script-interpreter2_1.12.2-2 libcairo2_1.12.2-2 libcairo2-dev_1.12.2-2 libclass-isa-perl_0.36-3 libcolord1_0.1.21-4 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libcups2_1.5.3-2.10 libcurl3-gnutls_7.28.0-3 libdatrie1_0.2.5-3 libdb5.1_5.1.29-5 libdb5.1++_5.1.29-5 libdbus-1-3_1.6.2-2 libdbus-1-dev_1.6.2-2 libdbus-glib-1-2_0.100-1 libdbus-glib-1-dev_0.100-1 libdconf0_0.12.1-2 libdpkg-perl_1.16.9 libdrm2_2.4.33-3 libelf1_0.153-2 libenchant-dev_1.6.0-7 libenchant1c2a_1.6.0-7 libencode-locale-perl_1.03-1 liberror-perl_0.17-1 libexpat1_2.1.0-1 libexpat1-dev_2.1.0-1 libffi-dev_3.0.10-3 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libfile-listing-perl_6.04-1 libfontconfig1_2.9.0-7 libfontconfig1-dev_2.9.0-7 libfreetype6_2.4.9-1 libfreetype6-dev_2.4.9-1 libgail-3-0_3.4.2-4 libgail-3-dev_3.4.2-4 libgail-common_2.24.10-2 libgail-dev_2.24.10-2 libgail18_2.24.10-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-11 libgdk-pixbuf2.0-0_2.26.1-1 libgdk-pixbuf2.0-common_2.26.1-1 libgdk-pixbuf2.0-dev_2.26.1-1 libgeoclue-dev_0.12.0-4 libgeoclue0_0.12.0-4 libgettextpo0_0.18.1.1-9 libgirepository-1.0-1_1.32.1-1 libgirepository1.0-dev_1.32.1-1 libgl1-mesa-dev_8.0.4-2 libgl1-mesa-glx_8.0.4-2 libglapi-mesa_8.0.4-2 libglib2.0-0_2.33.12+really2.32.3-1 libglib2.0-bin_2.33.12+really2.32.3-1 libglib2.0-data_2.33.12+really2.32.3-1 libglib2.0-dev_2.33.12+really2.32.3-1 libgmp10_2:5.0.5+dfsg-2 libgnome-keyring-common_3.4.1-1 libgnome-keyring0_3.4.1-1 libgnutls26_2.12.20-2 libgomp1_4.7.2-4 libgpg-error0_1.10-3.1 libgssapi-krb5-2_1.10.1+dfsg-3 libgstreamer-plugins-base0.10-0_0.10.36-1 libgstreamer-plugins-base0.10-dev_0.10.36-1 libgstreamer0.10-0_0.10.36-1 libgstreamer0.10-dev_0.10.36-1 libgtk-3-0_3.4.2-4 libgtk-3-common_3.4.2-4 libgtk-3-dev_3.4.2-4 libgtk2.0-0_2.24.10-2 libgtk2.0-common_2.24.10-2 libgtk2.0-dev_2.24.10-2 libhtml-parser-perl_3.69-2 libhtml-tagset-perl_3.20-2 libhtml-tree-perl_5.02-1 libhttp-cookies-perl_6.00-2 libhttp-date-perl_6.02-1 libhttp-message-perl_6.03-1 libhttp-negotiate-perl_6.00-2 libhunspell-1.3-0_1.3.2-4 libice-dev_2:1.0.8-2 libice6_2:1.0.8-2 libicu-dev_4.8.1.1-9 libicu48_4.8.1.1-9 libidn11_1.25-2 libio-socket-ssl-perl_1.76-1 libjasper1_1.900.1-14 libjbig0_2.0-2 libjpeg8_8d-1 libjpeg8-dev_8d-1 libjs-jquery_1.7.2+debian-2 libjs-sphinxdoc_1.1.3+dfsg-4 libjs-underscore_1.3.3-1 libk5crypto3_1.10.1+dfsg-3 libkeyutils1_1.5.5-3 libkrb5-3_1.10.1+dfsg-3 libkrb5support0_1.10.1+dfsg-3 liblcms2-2_2.2+git20110628-2.2 libldap-2.4-2_2.4.31-1 liblua5.1-0_5.1.5-4 liblwp-mediatypes-perl_6.02-1 liblwp-protocol-https-perl_6.03-1 liblzma2_5.0.0-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libncursesw5_5.9-10 libnet-http-perl_6.03-2 libnet-ssleay-perl_1.48-1+b1 libobjc3_4.6.3-14 liborc-0.4-0_1:0.4.16-2 libp11-kit0_0.12-3 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 libpango1.0-0_1.30.0-1 libpango1.0-dev_1.30.0-1 libpcre3_1:8.30-5 libpcre3-dev_1:8.30-5 libpcrecpp0_1:8.30-5 libpipeline1_1.2.2-1 libpixman-1-0_0.26.0-3 libpixman-1-dev_0.26.0-3 libpng12-0_1.2.49-3 libpng12-dev_1.2.49-3 libpopt0_1.16-7 libproxy0_0.3.1-5.1 libpthread-stubs0_0.3-3 libpthread-stubs0-dev_0.3-3 libpython2.6_2.6.8-0.2 libpython2.7_2.7.3-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 librtmp0_2.4+20111222.git4e06e21-1 libsasl2-2_2.1.25.dfsg1-6 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libsigsegv2_2.9-4 libslang2_2.2.4-15 libsm-dev_2:1.2.1-2 libsm6_2:1.2.1-2 libsoup-gnome2.4-1_2.38.1-2 libsoup2.4-1_2.38.1-2 libsoup2.4-dev_2.38.1-2 libsp1c2_1.3.4-1.2.1-47.1+b1 libsqlite3-0_3.7.14.1-1 libsqlite3-dev_3.7.14.1-1 libss2_1.42.5-1 libssh2-1_1.4.2-1.1 libssl-dev_1.0.1c-3 libssl1.0.0_1.0.1c-3 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtasn1-3_2.13-2 libtext-iconv-perl_1.7-5 libthai-data_0.1.18-2 libthai0_0.1.18-2 libtiff4_3.9.6-10 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libtool_2.4.2-1.1 libunistring0_0.9.3-5 libunwind7_0.99-0.3 libunwind7-dev_0.99-0.3 liburi-perl_1.60-1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libwww-perl_6.04-1 libwww-robotrules-perl_6.01-1 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libx11-dev_2:1.5.0-1 libx11-xcb1_2:1.5.0-1 libxau-dev_1:1.0.7-1 libxau6_1:1.0.7-1 libxcb-glx0_1.8.1-2 libxcb-render0_1.8.1-1 libxcb-render0-dev_1.8.1-1 libxcb-shm0_1.8.1-1 libxcb-shm0-dev_1.8.1-1 libxcb1_1.8.1-1 libxcb1-dev_1.8.1-1 libxcomposite-dev_1:0.4.3-2 libxcomposite1_1:0.4.3-2 libxcursor-dev_1:1.1.13-1 libxcursor1_1:1.1.13-1 libxdamage-dev_1:1.1.3-2 libxdamage1_1:1.1.3-2 libxdmcp-dev_1:1.1.1-1 libxdmcp6_1:1.1.1-1 libxext-dev_2:1.3.1-2 libxext6_2:1.3.1-2 libxfixes-dev_1:5.0-4 libxfixes3_1:5.0-4 libxft-dev_2.3.1-1 libxft2_2.3.1-1 libxi-dev_2:1.6.1-1 libxi6_2:1.6.1-1 libxinerama-dev_2:1.1.2-1 libxinerama1_2:1.1.2-1 libxml-parser-perl_2.41-1+b1 libxml2_2.8.0+dfsg1-5 libxml2-dev_2.8.0+dfsg1-5 libxml2-utils_2.8.0+dfsg1-5 libxrandr-dev_2:1.3.2-2 libxrandr2_2:1.3.2-2 libxrender-dev_1:0.9.7-1 libxrender1_1:0.9.7-1 libxslt1-dev_1.1.26-13 libxslt1.1_1.1.26-13 libxt-dev_1:1.1.3-1 libxt6_1:1.1.3-1 libxxf86vm1_1:1.1.2-1 linux-libc-dev_3.2.21-3 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 m4_1.4.16-3 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mesa-common-dev_8.0.4-2 mime-support_3.52-1 mount_2.20.1-5.1 multiarch-support_2.13-34 ncurses-base_5.9-10 ncurses-bin_5.9-10 netbase_5.0 openssl_1.0.1c-4 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-16 perl-base_5.14.2-16 perl-modules_5.14.2-16 pkg-config_0.26-1 po-debconf_1.0.16+nmu2 python_2.7.3-1 python-all_2.7.3-1 python-all-dbg_2.7.3-1 python-all-dev_2.7.3-1 python-chardet_2.0.1-2 python-dbg_2.7.3-1 python-debian_0.1.21 python-dev_2.7.3-1 python-docutils_0.8.1-8 python-jinja2_2.6-1 python-mako_0.7.0-1 python-markupsafe_0.15-1 python-minimal_2.7.3-1 python-pygments_1.5+dfsg-1 python-roman_0.8.1-8 python-sphinx_1.1.3+dfsg-4 python-support_1.0.15 python2.6_2.6.8-0.2 python2.6-dbg_2.6.8-0.2 python2.6-dev_2.6.8-0.2 python2.6-minimal_2.6.8-0.2 python2.7_2.7.3-1 python2.7-dbg_2.7.3-1 python2.7-dev_2.7.3-1 python2.7-minimal_2.7.3-1 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sgml-base_1.26+nmu3 sgml-data_2.0.8 shared-mime-info_1.0-1 sp_1.3.4-1.2.1-47.1+b1 sphinx-common_1.1.3+dfsg-4 sudo_1.8.5p2-1 sysv-rc_2.88dsf-28 sysvinit_2.88dsf-28 sysvinit-utils_2.88dsf-28 tar_1.26-4 ttf-dejavu-core_2.33-3 tzdata_2012j-1 ucf_3.0025+nmu3 util-linux_2.20.1-5.1 x11-common_1:7.7+1 x11proto-composite-dev_1:0.4.2-2 x11proto-core-dev_7.0.23-1 x11proto-damage-dev_1:1.2.1-2 x11proto-fixes-dev_1:5.0-2 x11proto-input-dev_2.2-1 x11proto-kb-dev_1.0.6-2 x11proto-randr-dev_1.3.2-2 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.2.1-1 x11proto-xinerama-dev_1.2.1-2 xml-core_0.13+nmu1 xorg-sgml-doctools_1:1.10-1 xsltproc_1.1.26-13 xtrans-dev_1.2.7-1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6.1-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.35-2
+Package versions: apt_0.9.7.7 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.7 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6.1_2.13-38 libc6.1-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libquadmath0_4.7.2-5 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 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+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.35-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -229,16 +328,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -248,44 +346,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -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_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -k clean
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -298,11 +393,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -311,125 +406,167 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2" 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_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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 -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
+bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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 -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
+bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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 -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_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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_FORTIFY_SOURCE=2 -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 -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -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 -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -C examples all
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -451,11 +588,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtool
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -483,7 +620,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -491,8 +628,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -508,7 +645,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -520,7 +657,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-ia64-N8G1wM/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -528,88 +665,87 @@ dh_makeshlibs -plibbam-dev
dh_installdeb -psamtools
dh_perl -psamtools
dh_shlibdeps -psamtools
-dh_girepository -psamtools
dh_installdeb -plibbam-dev
dh_perl -plibbam-dev
dh_shlibdeps -plibbam-dev
-dh_girepository -plibbam-dev
dh_gencontrol -psamtools
+dpkg-gencontrol: warning: 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_0.1.18-4_ia64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_ia64.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_0.1.18-4_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../samtools_0.1.18-4_ia64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_ia64.deb'.
+ dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../samtools_0.1.19-1_ia64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0458
+Build finished at 20130330-0919
-samtools_0.1.18-4_ia64.changes:
+samtools_0.1.19-1_ia64.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: ia64
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
- .
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
- .
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- 45172beb6c41b5f181c5cc21ad82fc75daec2a40 604308 samtools_0.1.18-4_ia64.deb
- 7c71de38769e2a2646862621d617234963a49fab 195258 libbam-dev_0.1.18-4_ia64.deb
+ 08231110072e321aadf0bb616b84902899cb6f85 649304 samtools_0.1.19-1_ia64.deb
+ 260c83972875780dcadc914e1c2e4fd7e1f76055 162484 libbam-dev_0.1.19-1_ia64.deb
Checksums-Sha256:
- ae1b6fbc654cde12b271df03af334a8cb9768fa099cd469f40103988f92a6816 604308 samtools_0.1.18-4_ia64.deb
- 225a41e6558b78a9eabfd3d893df77f78b39c997f7366c17e5b4a07b49e6dc52 195258 libbam-dev_0.1.18-4_ia64.deb
+ d4aee74d03a41f6b111de6daf7a8b0a98e670aa00546784cd7f8d7485da2d7d5 649304 samtools_0.1.19-1_ia64.deb
+ 82809e9a2dbf9b3f814506bece9b63079ca9dd2bf580139efbe6463eadacbb59 162484 libbam-dev_0.1.19-1_ia64.deb
Files:
- 9c45d25cbf505dc27e239b776da69950 604308 science optional samtools_0.1.18-4_ia64.deb
- e3027eaac8d82994998ea490b9a7ae1b 195258 libdevel optional libbam-dev_0.1.18-4_ia64.deb
+ be183fa863a5afe3f488d229c29ceb7d 649304 science optional samtools_0.1.19-1_ia64.deb
+ 9d9068029d621e4507e82e9ee0d06b38 162484 libdevel optional libbam-dev_0.1.19-1_ia64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_ia64.deb
+samtools_0.1.19-1_ia64.deb
──────────────────────────
new debian package, version 2.0.
- size 604308 bytes: control archive= 1815 bytes.
+ size 649304 bytes: control archive= 1935 bytes.
32 bytes, 1 lines conffiles
793 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1697
+ Installed-Size: 2268
Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -622,74 +758,79 @@ samtools_0.1.18-4_ia64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126583 2012-12-23 04:57 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-12-23 04:57 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 04:57 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 04:57 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 04:57 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/bin/
--rwxr-xr-x root/root 303936 2012-12-23 04:57 ./usr/bin/bcftools
--rwxr-xr-x root/root 50640 2012-12-23 04:57 ./usr/bin/razip
--rwxr-xr-x root/root 826736 2012-12-23 04:57 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/lib/samtools/
--rwxr-xr-x root/root 30976 2012-12-23 04:57 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 13136 2012-12-23 04:57 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13136 2012-12-23 04:57 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 21952 2012-12-23 04:57 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 14944 2012-12-23 04:57 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2012-12-23 04:57 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_ia64.deb
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:18 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2013-03-30 09:18 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 09:18 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 09:18 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:18 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/bin/
+-rwxr-xr-x root/root 355552 2013-03-30 09:18 ./usr/bin/bcftools
+-rwxr-xr-x root/root 50912 2013-03-30 09:18 ./usr/bin/razip
+-rwxr-xr-x root/root 911304 2013-03-30 09:18 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/samtools/
+-rwxr-xr-x root/root 31264 2013-03-30 09:18 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 37152 2013-03-30 09:18 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 378512 2013-03-30 09:18 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 13200 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13200 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 22400 2013-03-30 09:18 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 15072 2013-03-30 09:18 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:18 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_ia64.deb
────────────────────────────
new debian package, version 2.0.
- size 195258 bytes: control archive= 941 bytes.
+ size 162484 bytes: control archive= 923 bytes.
711 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: ia64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 707
+ Installed-Size: 680
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -702,25 +843,25 @@ libbam-dev_0.1.18-4_ia64.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/lib/
--rw-r--r-- root/root 581690 2012-12-23 04:57 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/include/samtools/
--rw-r--r-- root/root 24732 2012-12-23 04:55 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
+-rw-r--r-- root/root 573810 2013-03-30 09:18 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/samtools/
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -734,46 +875,84 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-1e30fda6-a8b8-4d82-8ebc-fef7a1b61ffb/build/buildd-samtools_0.1.18-4-ia64-N8G1wM
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-d68654b1-c4f1-4be0-bbbc-6fab61321d58/build/buildd-samtools_0.1.19-1-ia64-lETMhD
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- bash-completion* cdbs* diffstat* libncurses5-dev* libtinfo-dev* quilt*
-0 upgraded, 0 newly installed, 6 to remove and 119 not upgraded.
-After this operation, 3871 kB disk space will be freed.
-(Reading database ... 28873 files and directories currently installed.)
+ bash-completion* bsdmainutils* cdbs* debhelper* diffstat* file* gettext*
+ gettext-base* groff-base* html2text* intltool-debian* libasprintf-dev*
+ libasprintf0c2* libcroco3* libffi5* libgettextpo-dev* libgettextpo0*
+ libglib2.0-0* libmagic1* libncurses5-dev* libpcre3* libpipeline1*
+ libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 29 to remove and 12 not upgraded.
+After this operation, 39.0 MB disk space will be freed.
+(Reading database ... 12825 files and directories currently installed.)
Removing bash-completion ...
Purging configuration files for bash-completion ...
-Removing cdbs ...
Removing quilt ...
Purging configuration files for quilt ...
+Removing debhelper ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing cdbs ...
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 libasprintf-dev:ia64 ...
+Removing libasprintf0c2:ia64 ...
+Removing libcroco3:ia64 ...
+Purging configuration files for libcroco3:ia64 ...
+Removing libglib2.0-0:ia64 ...
+Purging configuration files for libglib2.0-0:ia64 ...
+Removing libffi5:ia64 ...
+Purging configuration files for libffi5:ia64 ...
+Removing libgettextpo-dev:ia64 ...
+Removing libgettextpo0:ia64 ...
+Removing libmagic1:ia64 ...
+Purging configuration files for libmagic1:ia64 ...
Removing libncurses5-dev ...
+Removing libpcre3:ia64 ...
+Purging configuration files for libpcre3:ia64 ...
+Removing libpipeline1:ia64 ...
+Purging configuration files for libpipeline1:ia64 ...
Removing libtinfo-dev:ia64 ...
-Processing triggers for man-db ...
+Removing libunistring0:ia64 ...
+Purging configuration files for libunistring0:ia64 ...
+Removing libxml2:ia64 ...
+Purging configuration files for libxml2:ia64 ...
+Removing zlib1g-dev:ia64 ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 15720
-Build-Time: 149
+Build-Space: 18476
+Build-Time: 162
Distribution: sid
-Install-Time: 18
-Job: samtools_0.1.18-4
+Install-Time: 30
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 209
-Source-Version: 0.1.18-4
-Space: 15720
+Package-Time: 243
+Source-Version: 0.1.19-1
+Space: 18476
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0458
-Build needed 00:03:29, 15720k disc space
+Finished at 20130330-0919
+Build needed 00:04:03, 18476k disc space
diff --git a/info b/info
index 714cce6..0b93a66 100644
--- a/info
+++ b/info
@@ -1,13 +1,13 @@
-amd64~1356238515~sid~successful
-s390x~1356238574~sid~failed
-powerpc~1356238584~sid~successful
-s390~1356238691~sid~successful
-ia64~1356238695~sid~successful
-kfreebsd-i386~1356238784~sid~successful
-sparc~1356238821~sid~failed
-kfreebsd-amd64~1356238866~sid~successful
-armel~1356238970~sid~failed
-armhf~1356238971~sid~successful
-mipsel~1356239092~sid~successful
-mips~1356239928~sid~successful
-hurd-i386~1356240303~sid~successful
+powerpc~1364634980~sid~successful
+s390~1364635066~sid~successful
+s390x~1364635068~sid~successful
+i386~1364635134~sid~successful
+ia64~1364635156~sid~successful
+kfreebsd-i386~1364635168~sid~successful
+sparc~1364635192~sid~failed
+kfreebsd-amd64~1364635194~sid~successful
+hurd-i386~1364635200~sid~successful
+armhf~1364635392~sid~successful
+mipsel~1364635510~sid~successful
+armel~1364636399~sid~failed
+mips~1364653370~sid~successful
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 95fa07f..a9baa66 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,62 +1,65 @@
-From buildd at fano.debian.org Sun Dec 23 05:01:05 2012
+From buildd at fano.debian.org Sat Mar 30 09:19:54 2013
Return-path: <buildd at fano.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from muffat.debian.org ([206.12.19.146])
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)
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
(Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1TmdgP-0008AA-N2
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:01:05 +0000
+ id 1ULrx3-0002vl-LS
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:54 +0000
Received: from fano.debian.org ([206.12.19.110])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1TmdgO-0008GF-5F; Sun, 23 Dec 2012 05:01:04 +0000
+ by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at fano.debian.org>)
+ id 1ULrwz-0007Sg-Lo; Sat, 30 Mar 2013 09:19:49 +0000
Received: from buildd by fano.debian.org with local (Exim 4.72)
(envelope-from <buildd at fano.debian.org>)
- id 1TmdgL-000OD4-OH; Sun, 23 Dec 2012 05:01:01 +0000
-Message-Id: <E1TmdgL-000OD4-OH at fano.debian.org>
+ id 1ULrwx-000LeB-NA; Sat, 30 Mar 2013 09:19:47 +0000
+Message-Id: <E1ULrwx-000LeB-NA 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: Sun, 23 Dec 2012 05:01:01 +0000
+Date: Sat, 30 Mar 2013 09:19:47 +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_0.1.18-4 on kfreebsd-amd64
+Subject: Log for successful build of samtools_0.1.19-1 on kfreebsd-amd64
(dist=sid)
-Key-Id: 4584BE29
+Key-Id: 1B08409D
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (kfreebsd-amd64) 23 Dec 2012 04:57 ║
+║ samtools 0.1.19-1 (kfreebsd-amd64) 30 Mar 2013 09:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: kfreebsd-amd64
-Get:1 http://incoming.debian.org unstable InRelease [227 kB]
-Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:3 http://mirror-ubc.debian.org unstable InRelease [227 kB]
-Get:4 http://mirror-ubc.debian.org unstable/main Sources [6458 kB]
-Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [53.0 kB]
-Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5770 kB]
-Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [36.4 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://incoming.debian.org unstable/main kfreebsd-amd64 Packages [5770 kB]
-Get:12 http://incoming.debian.org unstable/contrib kfreebsd-amd64 Packages [36.4 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 25.4 MB in 13s (1900 kB/s)
+Get:1 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:2 http://mirror-ubc.debian.org unstable Release.gpg [836 B]
+Get:3 http://mirror-ubc.debian.org unstable Release [235 kB]
+Get:4 http://mirror-ubc.debian.org unstable/main Sources [6484 kB]
+Get:5 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:6 http://incoming.debian.org unstable Release [235 kB]
+Get:7 http://mirror-ubc.debian.org unstable/contrib Sources [51.0 kB]
+Get:8 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:9 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [5785 kB]
+Get:10 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:11 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:12 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [35.4 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:15 http://incoming.debian.org unstable/main kfreebsd-amd64 Packages [5785 kB]
+Get:16 http://incoming.debian.org unstable/contrib kfreebsd-amd64 Packages [35.4 kB]
+Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:20 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [13.4 kB]
+Get:21 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [14 B]
+Fetched 25.5 MB in 13s (1915 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,14 +77,13 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 0s (391 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (444 kB/s)
Download complete and in download only mode
Check arch
@@ -94,56 +96,55 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.12)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-7)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
+e2fsprogs: already installed (1.42.5-1.1)
findutils: already installed (4.4.2-5)
-freebsd-utils: already installed (9.0+ds1-8)
+freebsd-utils: already installed (9.0+ds1-11)
grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-15)
+perl-base: already installed (5.14.2-20)
sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-34)
-sysvinit: already installed (2.88dsf-34)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.2)
-util-linux: already installed (2.20.1-5.2)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
libc6-dev: already installed (~*=PROVIDED=*=)
gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120909
bash-completion: missing
@@ -155,61 +156,65 @@ Checking for dependency conflicts...
Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
-Reading state information...
The following extra packages will be installed:
- diffstat file gettext gettext-base groff-base html2text intltool-debian
- libasprintf-dev libasprintf0c2 libcroco3 libffi5 libgettextpo-dev
- libgettextpo0 libglib2.0-0 libmagic1 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl procmail graphviz default-mta mail-transport-agent
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
+ mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev
- libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
-0 upgraded, 27 newly installed, 0 to remove and 17 not upgraded.
-Need to get 10.3 MB of archives.
-After this operation, 27.3 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.2.2-1 [39.8 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.21-9 [1113 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.6.3-3 [893 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.18.1.1-10 [27.2 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 5.11-2 [202 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.8.0+dfsg1-7 [914 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-amd64 3.0.10-3 [23.9 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.33.12+really2.32.4-3 [1831 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.6-2 [133 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5 [434 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-amd64 0.18.1.1-10 [145 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 5.11-2 [51.8 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.18.1.1-10 [153 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-amd64 1.3.2a-15 [104 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev kfreebsd-amd64 0.18.1.1-10 [27.0 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev kfreebsd-amd64 0.18.1.1-10 [184 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.18.1.1-10 [1805 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-amd64 1.55-3 [29.9 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9-10 [105 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9-10 [220 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.7.dfsg-13 [215 kB]
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded.
+Need to get 10.4 MB of archives.
+After this operation, 28.2 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.2.2-2 [39.9 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.2-1 [743 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.4 [210 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.6.3-3 [893 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.18.1.1-10 [27.2 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.11-2.1 [202 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-amd64 1:8.31-2 [247 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.8.0+dfsg1-7+nmu1 [914 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-amd64 3.0.10-3 [23.9 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.33.12+really2.32.4-5 [1831 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.6-2 [133 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5 [434 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-amd64 0.18.1.1-10 [145 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.11-2.1 [51.9 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.18.1.1-10 [153 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-amd64 1.3.2a-15 [104 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev kfreebsd-amd64 0.18.1.1-10 [27.0 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev kfreebsd-amd64 0.18.1.1-10 [184 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.18.1.1-10 [1805 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-amd64 1.55-3 [29.9 kB]
+Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9-10 [105 kB]
+Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9-10 [220 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
+Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.7.dfsg-13 [215 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.3 MB in 2s (3923 kB/s)
+Fetched 10.4 MB in 3s (3406 kB/s)
Selecting previously unselected package libpipeline1:kfreebsd-amd64.
-(Reading database ... 11630 files and directories currently installed.)
-Unpacking libpipeline1:kfreebsd-amd64 (from .../libpipeline1_1.2.2-1_kfreebsd-amd64.deb) ...
+(Reading database ... 11512 files and directories currently installed.)
+Unpacking libpipeline1:kfreebsd-amd64 (from .../libpipeline1_1.2.2-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-amd64.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_kfreebsd-amd64.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package bash-completion.
@@ -217,13 +222,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:kfreebsd-amd64.
Unpacking libasprintf0c2:kfreebsd-amd64 (from .../libasprintf0c2_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package libmagic1:kfreebsd-amd64.
-Unpacking libmagic1:kfreebsd-amd64 (from .../libmagic1_5.11-2_kfreebsd-amd64.deb) ...
+Unpacking libmagic1:kfreebsd-amd64 (from .../libmagic1_1%3a5.11-2.1_kfreebsd-amd64.deb) ...
+Selecting previously unselected package libpcre3:kfreebsd-amd64.
+Unpacking libpcre3:kfreebsd-amd64 (from .../libpcre3_1%3a8.31-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libxml2:kfreebsd-amd64.
-Unpacking libxml2:kfreebsd-amd64 (from .../libxml2_2.8.0+dfsg1-7_kfreebsd-amd64.deb) ...
+Unpacking libxml2:kfreebsd-amd64 (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_kfreebsd-amd64.deb) ...
+Unpacking libglib2.0-0:kfreebsd-amd64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package libcroco3:kfreebsd-amd64.
Unpacking libcroco3:kfreebsd-amd64 (from .../libcroco3_0.6.6-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libunistring0:kfreebsd-amd64.
@@ -231,11 +238,11 @@ Unpacking libunistring0:kfreebsd-amd64 (from .../libunistring0_0.9.3-5_kfreebsd-
Selecting previously unselected package libgettextpo0:kfreebsd-amd64.
Unpacking libgettextpo0:kfreebsd-amd64 (from .../libgettextpo0_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.11-2_kfreebsd-amd64.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_kfreebsd-amd64.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_kfreebsd-amd64.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-amd64.deb) ...
Selecting previously unselected package libasprintf-dev:kfreebsd-amd64.
@@ -257,26 +264,30 @@ Unpacking libtinfo-dev:kfreebsd-amd64 (from .../libtinfo-dev_5.9-10_kfreebsd-amd
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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
+Setting up libpipeline1:kfreebsd-amd64 (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:kfreebsd-amd64 (0.18.1.1-10) ...
-Setting up libmagic1:kfreebsd-amd64 (5.11-2) ...
-Setting up libxml2:kfreebsd-amd64 (2.8.0+dfsg1-7) ...
+Setting up libmagic1:kfreebsd-amd64 (1:5.11-2.1) ...
+Setting up libpcre3:kfreebsd-amd64 (1:8.31-2) ...
+Setting up libxml2:kfreebsd-amd64 (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:kfreebsd-amd64 (3.0.10-3) ...
-Setting up libglib2.0-0:kfreebsd-amd64 (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:kfreebsd-amd64 (0.6.6-2) ...
Setting up libunistring0:kfreebsd-amd64 (0.9.3-5) ...
Setting up libgettextpo0:kfreebsd-amd64 (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:kfreebsd-amd64 (0.18.1.1-10) ...
Setting up libgettextpo-dev:kfreebsd-amd64 (0.18.1.1-10) ...
@@ -287,17 +298,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:kfreebsd-amd64 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 freebsd-utils_9.0+ds1-8 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-34 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-8 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libblkid1_2.20.1-5.2 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc0.1_2.13-37 libc0.1-dev_2.13-37 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 kfreebsd-kernel-headers_0.83 libc0.1-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 freebsd-utils_9.0+ds1-11 g++_4:4.7.2-1 g++-4.7_4.7.2-5 gcc_4:4.7.2-1 gcc-4.7_4.7.2-5 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-11 kfreebsd-kernel-headers_0.83 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc0.1_2.13-38 libc0.1-dev_2.13-38 libcam6_9.0+ds1-4 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libexpat1_2.1.0-1 libffi5_3.0.10-3 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-4 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 libgssglue1_0.4-2 libjail1_9.0+ds1-4 libkiconv4_9.0+ds1-4 libkvm0_9.0+ds1-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libquadmath0_4.7.2-5 libreadline6_6.2+dfsg-0.1 libsbuf6_9.0+ds1-4 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5 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_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-2 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -308,16 +319,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -327,44 +337,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -377,11 +384,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -390,131 +397,173 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -536,11 +585,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3A
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -568,7 +617,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -576,8 +625,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -593,7 +642,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -605,7 +654,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -617,82 +666,83 @@ 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_0.1.18-4_kfreebsd-amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_kfreebsd-amd64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.18-4_kfreebsd-amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_0.1.19-1_kfreebsd-amd64.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0500
+Build finished at 20130330-0919
-samtools_0.1.18-4_kfreebsd-amd64.changes:
+samtools_0.1.19-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-amd64
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
- .
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- 51fac14f1315cc152443896ec0f2192f1323eeb4 532760 samtools_0.1.18-4_kfreebsd-amd64.deb
- b4a056c0a13dff3710cd4a20c6d4753a7d1c1123 156700 libbam-dev_0.1.18-4_kfreebsd-amd64.deb
+ e6b77d210ee76ccaceb71d1a49773e310f3689dc 561946 samtools_0.1.19-1_kfreebsd-amd64.deb
+ bc07e63bff213ff9cbcbfba001b5cda8ecdbc80f 123294 libbam-dev_0.1.19-1_kfreebsd-amd64.deb
Checksums-Sha256:
- 765b5352bd24b050d7b39a5aea5e51d6bc2eef6ec33b3e9ec6ec681effa69928 532760 samtools_0.1.18-4_kfreebsd-amd64.deb
- 247833939f60e02970b8c915fc8c59f59235b67d84a0457478653539b5f9afa8 156700 libbam-dev_0.1.18-4_kfreebsd-amd64.deb
+ 5db3eb47c85a70f9b85565411e8f9479a777bc02cfe3150015303c35e6b3488a 561946 samtools_0.1.19-1_kfreebsd-amd64.deb
+ ea157bd5664ee38511f9c3839df6a152d7a55346648c2d781c7cf4eabac7f660 123294 libbam-dev_0.1.19-1_kfreebsd-amd64.deb
Files:
- 48ddfb74dd07c26e6b8eb385489a79fc 532760 science optional samtools_0.1.18-4_kfreebsd-amd64.deb
- 1dc14418bd4cb404378cf8a0bd73db9f 156700 libdevel optional libbam-dev_0.1.18-4_kfreebsd-amd64.deb
+ 9c22dfdef81ef7a079844de427d336c5 561946 science optional samtools_0.1.19-1_kfreebsd-amd64.deb
+ e387a1b9b0891720e37e44a27f2854cc 123294 libdevel optional libbam-dev_0.1.19-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_kfreebsd-amd64.deb
+samtools_0.1.19-1_kfreebsd-amd64.deb
────────────────────────────────────
new debian package, version 2.0.
- size 532760 bytes: control archive= 1820 bytes.
+ size 561946 bytes: control archive= 1937 bytes.
32 bytes, 1 lines conffiles
- 802 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 803 bytes, 16 lines control
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 969
+ Installed-Size: 1267
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -705,74 +755,79 @@ samtools_0.1.18-4_kfreebsd-amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126583 2012-12-23 05:00 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-12-23 05:00 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 05:00 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 05:00 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 05:00 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/bin/
--rwxr-xr-x root/root 130696 2012-12-23 05:00 ./usr/bin/bcftools
--rwxr-xr-x root/root 24912 2012-12-23 05:00 ./usr/bin/razip
--rwxr-xr-x root/root 372448 2012-12-23 05:00 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/lib/samtools/
--rwxr-xr-x root/root 18208 2012-12-23 05:00 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8440 2012-12-23 05:00 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 8360 2012-12-23 05:00 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12104 2012-12-23 05:00 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 8896 2012-12-23 05:00 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_kfreebsd-amd64.deb
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:19 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2013-03-30 09:19 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 09:19 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 09:19 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:19 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/bin/
+-rwxr-xr-x root/root 154664 2013-03-30 09:19 ./usr/bin/bcftools
+-rwxr-xr-x root/root 27032 2013-03-30 09:19 ./usr/bin/razip
+-rwxr-xr-x root/root 416672 2013-03-30 09:19 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18680 2013-03-30 09:19 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 22696 2013-03-30 09:19 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 172720 2013-03-30 09:19 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 10368 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10368 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 14472 2013-03-30 09:19 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 10320 2013-03-30 09:19 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_kfreebsd-amd64.deb
──────────────────────────────────────
new debian package, version 2.0.
- size 156700 bytes: control archive= 947 bytes.
+ size 123294 bytes: control archive= 934 bytes.
721 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 432
+ Installed-Size: 407
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -785,25 +840,25 @@ libbam-dev_0.1.18-4_kfreebsd-amd64.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/lib/
--rw-r--r-- root/root 332346 2012-12-23 05:00 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 05:00 ./usr/include/samtools/
--rw-r--r-- root/root 24732 2012-12-23 05:00 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
+-rw-r--r-- root/root 326938 2013-03-30 09:19 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/samtools/
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -817,7 +872,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1356238677-90509/build/buildd-samtools_0.1.18-4-kfreebsd-amd64-FK3AKe
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1364634988-80311/build/buildd-samtools_0.1.19-1-kfreebsd-amd64-A2ON5o
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -825,18 +880,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 13492
-Build-Time: 62
+Build-Space: 16316
+Build-Time: 67
Distribution: sid
-Install-Time: 32
-Job: samtools_0.1.18-4
+Install-Time: 33
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 180
-Source-Version: 0.1.18-4
-Space: 13492
+Package-Time: 197
+Source-Version: 0.1.19-1
+Space: 16316
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0500
-Build needed 00:03:00, 13492k disc space
-Signature with key '4584BE29' requested:
+Finished at 20130330-0919
+Build needed 00:03:17, 16316k disc space
+Signature with key '1B08409D' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 6465bde..c66f0dc 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,4 +1,4 @@
-From buildd at finzi.debian.org Sun Dec 23 04:59:44 2012
+From buildd at finzi.debian.org Sat Mar 30 09:19:27 2013
Return-path: <buildd at finzi.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,57 +6,61 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1Tmdf5-0007t2-RS
- for logs at buildd.debian.org; Sun, 23 Dec 2012 04:59:44 +0000
+ id 1ULrwd-0002uH-7n
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:27 +0000
Received: from finzi.debian.org ([206.12.19.111])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1Tmdf3-00083t-M1; Sun, 23 Dec 2012 04:59:42 +0000
+ id 1ULrwb-0001bT-UT; Sat, 30 Mar 2013 09:19:26 +0000
Received: from buildd by finzi.debian.org with local (Exim 4.72)
(envelope-from <buildd at finzi.debian.org>)
- id 1Tmdf1-0004Lm-Ag; Sun, 23 Dec 2012 04:59:39 +0000
-Message-Id: <E1Tmdf1-0004Lm-Ag at finzi.debian.org>
+ id 1ULrwZ-0008MU-BL; Sat, 30 Mar 2013 09:19:23 +0000
+Message-Id: <E1ULrwZ-0008MU-BL at finzi.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sun, 23 Dec 2012 04:59:39 +0000
+Date: Sat, 30 Mar 2013 09:19:23 +0000
From: buildd on finzi <buildd at finzi.debian.org>
To: logs at buildd.debian.org,christoph at debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on kfreebsd-i386
+Subject: Log for successful build of samtools_0.1.19-1 on kfreebsd-i386
(dist=sid)
-Key-Id: B3DA9773
+Key-Id: B31C365A
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (kfreebsd-i386) 23 Dec 2012 04:56 ║
+║ samtools 0.1.19-1 (kfreebsd-i386) 30 Mar 2013 09:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: kfreebsd-i386
-Get:1 http://incoming.debian.org unstable InRelease [227 kB]
-Get:2 http://mirror-ubc.debian.org unstable InRelease [227 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [6458 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [53.0 kB]
-Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [5765 kB]
-Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [36.4 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5765 kB]
-Get:12 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [36.4 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 25.4 MB in 15s (1667 kB/s)
+Get:1 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:2 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:3 http://incoming.debian.org unstable Release [235 kB]
+Get:4 http://mirror-ubc.debian.org unstable Release.gpg [836 B]
+Get:5 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:6 http://mirror-ubc.debian.org unstable Release [235 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main Sources [6484 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib Sources [51.0 kB]
+Get:10 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [5786 kB]
+Get:12 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [35.4 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:15 http://incoming.debian.org unstable/main kfreebsd-i386 Packages [5786 kB]
+Get:16 http://incoming.debian.org unstable/contrib kfreebsd-i386 Packages [35.4 kB]
+Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:20 http://incoming.debian.org buildd-unstable/main kfreebsd-i386 Packages [13.7 kB]
+Get:21 http://incoming.debian.org buildd-unstable/contrib kfreebsd-i386 Packages [14 B]
+Fetched 25.5 MB in 16s (1552 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -74,14 +78,13 @@ Download source files with APT
Reading package lists...
Building dependency tree...
-Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (360 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (432 kB/s)
Download complete and in download only mode
Check arch
@@ -94,56 +97,55 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.12)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-7)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
+e2fsprogs: already installed (1.42.5-1.1)
findutils: already installed (4.4.2-5)
-freebsd-utils: already installed (9.0+ds1-8)
+freebsd-utils: already installed (9.0+ds1-10)
grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-15)
+perl-base: already installed (5.14.2-20)
sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-34)
-sysvinit: already installed (2.88dsf-34)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.2)
-util-linux: already installed (2.20.1-5.2)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
libc6-dev: already installed (~*=PROVIDED=*=)
gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120909
bash-completion: missing
@@ -155,7 +157,6 @@ Checking for dependency conflicts...
Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
Reading package lists...
Building dependency tree...
-Reading state information...
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
@@ -174,26 +175,26 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 17 not upgraded.
-Need to get 10.5 MB of archives.
+0 upgraded, 29 newly installed, 0 to remove and 3 not upgraded.
+Need to get 10.2 MB of archives.
After this operation, 27.3 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.2-1 [38.8 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.21-9 [1095 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.3 [204 kB]
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.2.2-2 [38.9 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.22.2-1 [733 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.4 [205 kB]
Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.6.3-3 [889 kB]
Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.18.1.1-10 [27.0 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 5.11-2 [204 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.31-1 [247 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-7 [904 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 1:5.11-2.1 [204 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 kfreebsd-i386 1:8.31-2 [247 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.8.0+dfsg1-7+nmu1 [905 kB]
Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 kfreebsd-i386 3.0.10-3 [20.3 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.33.12+really2.32.4-3 [1819 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.33.12+really2.32.4-5 [1819 kB]
Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.6-2 [133 kB]
Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5 [440 kB]
Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 kfreebsd-i386 0.18.1.1-10 [141 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 5.11-2 [51.5 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 1:5.11-2.1 [51.6 kB]
Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.18.1.1-10 [131 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text kfreebsd-i386 1.3.2a-15 [101 kB]
Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev kfreebsd-i386 0.18.1.1-10 [26.6 kB]
Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev kfreebsd-i386 0.18.1.1-10 [170 kB]
@@ -204,17 +205,17 @@ Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.201209
Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat kfreebsd-i386 1.55-3 [29.0 kB]
Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9-10 [93.1 kB]
Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9-10 [210 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.5 MB in 2s (4996 kB/s)
+Fetched 10.2 MB in 9s (1081 kB/s)
Selecting previously unselected package libpipeline1:kfreebsd-i386.
-(Reading database ... 11298 files and directories currently installed.)
-Unpacking libpipeline1:kfreebsd-i386 (from .../libpipeline1_1.2.2-1_kfreebsd-i386.deb) ...
+(Reading database ... 11302 files and directories currently installed.)
+Unpacking libpipeline1:kfreebsd-i386 (from .../libpipeline1_1.2.2-2_kfreebsd-i386.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_kfreebsd-i386.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_kfreebsd-i386.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_kfreebsd-i386.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_kfreebsd-i386.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_kfreebsd-i386.deb) ...
Selecting previously unselected package bash-completion.
@@ -222,15 +223,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:kfreebsd-i386.
Unpacking libasprintf0c2:kfreebsd-i386 (from .../libasprintf0c2_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package libmagic1:kfreebsd-i386.
-Unpacking libmagic1:kfreebsd-i386 (from .../libmagic1_5.11-2_kfreebsd-i386.deb) ...
+Unpacking libmagic1:kfreebsd-i386 (from .../libmagic1_1%3a5.11-2.1_kfreebsd-i386.deb) ...
Selecting previously unselected package libpcre3:kfreebsd-i386.
-Unpacking libpcre3:kfreebsd-i386 (from .../libpcre3_1%3a8.31-1_kfreebsd-i386.deb) ...
+Unpacking libpcre3:kfreebsd-i386 (from .../libpcre3_1%3a8.31-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libxml2:kfreebsd-i386.
-Unpacking libxml2:kfreebsd-i386 (from .../libxml2_2.8.0+dfsg1-7_kfreebsd-i386.deb) ...
+Unpacking libxml2:kfreebsd-i386 (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_kfreebsd-i386.deb) ...
+Unpacking libglib2.0-0:kfreebsd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-5_kfreebsd-i386.deb) ...
Selecting previously unselected package libcroco3:kfreebsd-i386.
Unpacking libcroco3:kfreebsd-i386 (from .../libcroco3_0.6.6-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libunistring0:kfreebsd-i386.
@@ -238,11 +239,11 @@ Unpacking libunistring0:kfreebsd-i386 (from .../libunistring0_0.9.3-5_kfreebsd-i
Selecting previously unselected package libgettextpo0:kfreebsd-i386.
Unpacking libgettextpo0:kfreebsd-i386 (from .../libgettextpo0_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.11-2_kfreebsd-i386.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_kfreebsd-i386.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_kfreebsd-i386.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_kfreebsd-i386.deb) ...
Selecting previously unselected package libasprintf-dev:kfreebsd-i386.
@@ -264,30 +265,30 @@ Unpacking libtinfo-dev:kfreebsd-i386 (from .../libtinfo-dev_5.9-10_kfreebsd-i386
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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:kfreebsd-i386 (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:kfreebsd-i386 (0.18.1.1-10) ...
-Setting up libmagic1:kfreebsd-i386 (5.11-2) ...
-Setting up libpcre3:kfreebsd-i386 (1:8.31-1) ...
-Setting up libxml2:kfreebsd-i386 (2.8.0+dfsg1-7) ...
+Setting up libmagic1:kfreebsd-i386 (1:5.11-2.1) ...
+Setting up libpcre3:kfreebsd-i386 (1:8.31-2) ...
+Setting up libxml2:kfreebsd-i386 (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:kfreebsd-i386 (3.0.10-3) ...
-Setting up libglib2.0-0:kfreebsd-i386 (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:kfreebsd-i386 (0.6.6-2) ...
Setting up libunistring0:kfreebsd-i386 (0.9.3-5) ...
Setting up libgettextpo0:kfreebsd-i386 (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:kfreebsd-i386 (0.18.1.1-10) ...
Setting up libgettextpo-dev:kfreebsd-i386 (0.18.1.1-10) ...
@@ -298,17 +299,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:kfreebsd-i386 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 17 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.7_4.7.2-4 gcc-4.7_4.7.2-4 kfreebsd-kernel-headers_0.82 libc0.1-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-4 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 freebsd-utils_9.0+ds1-8 g++_4:4.7.2-1 g++-4.7_4.7.2-4 gcc_4:4.7.2-1 gcc-4.7_4.7.2-4 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-34 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-8 kfreebsd-kernel-headers_0.82 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libblkid1_2.20.1-5.2 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc0.1_2.13-37 libc0.1-dev_2.13-37 libcam6_9.0+ds1-3 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libexpat1_2.1.0-1 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-3 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 libgssglue1_0.4-2 libjail1_9.0+ds1-3 libkiconv4_9.0+ds1-3 libkvm0_9.0+ds1-3 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libquadmath0_4.7.2-4 libreadline6_6.2-9 libsbuf6_9.0+ds1-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.7-dev_4.7.2-4 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 kfreebsd-kernel-headers_0.83 libc0.1-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 freebsd-utils_9.0+ds1-10 g++_4:4.7.2-1 g++-4.7_4.7.2-5 gcc_4:4.7.2-1 gcc-4.7_4.7.2-5 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 kbdcontrol_9.0+ds1-10 kfreebsd-kernel-headers_0.83 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbsd0_0.4.2-1 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc0.1_2.13-38 libc0.1-dev_2.13-38 libcam6_9.0+ds1-4 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libexpat1_2.1.0-1 libffi5_3.0.10-3 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgeom1_9.0+ds1-4 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 libgssglue1_0.4-2 libjail1_9.0+ds1-4 libkiconv4_9.0+ds1-4 libkvm0_9.0+ds1-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libquadmath0_4.7.2-5 libreadline6_6.2+dfsg-0.1 libsbuf6_9.0+ds1-4 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5 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_2:0.1.12-23+nmu1 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -319,16 +320,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -338,44 +338,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -388,11 +385,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -401,145 +398,182 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
md5.c: In function 'MD5Final':
md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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':
-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_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -561,11 +595,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PV
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -593,7 +627,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -601,8 +635,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -618,7 +652,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -630,7 +664,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -642,82 +676,83 @@ 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_0.1.18-4_kfreebsd-i386.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_kfreebsd-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_0.1.18-4_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.18-4_kfreebsd-i386.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../samtools_0.1.19-1_kfreebsd-i386.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0459
+Build finished at 20130330-0919
-samtools_0.1.18-4_kfreebsd-i386.changes:
+samtools_0.1.19-1_kfreebsd-i386.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: kfreebsd-i386
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
- .
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- 8f5b3ae4cbe37d42d0acb3fa121e89d72c50b081 534414 samtools_0.1.18-4_kfreebsd-i386.deb
- daeb3b47e6efa643c4ebe62a90623b39a5d9d308 160998 libbam-dev_0.1.18-4_kfreebsd-i386.deb
+ 27b9febcc040764f37a46813eba6a7ad4cf0e829 563422 samtools_0.1.19-1_kfreebsd-i386.deb
+ e6a74f1cd847e4b67206ba343a2f880ceaf269fd 126860 libbam-dev_0.1.19-1_kfreebsd-i386.deb
Checksums-Sha256:
- ba217ba846aa5abd85dcb03fa1509b6ccdbe7ca709dbb199045ee021fa4b5c4c 534414 samtools_0.1.18-4_kfreebsd-i386.deb
- e5e6e16b17ac42608e37b95146ff1ee355cc36f712338a40f27548206735bd01 160998 libbam-dev_0.1.18-4_kfreebsd-i386.deb
+ 0728e1915c932f365f494d7561232329b2b908d090e06dc8fcd2e54fa41a7236 563422 samtools_0.1.19-1_kfreebsd-i386.deb
+ 126393589b66b1279cec18a24dd5b8e58ba5ffe25d7e76baf409934ef41b2c1c 126860 libbam-dev_0.1.19-1_kfreebsd-i386.deb
Files:
- 15e3c265d578110987dfea084ed8dfd6 534414 science optional samtools_0.1.18-4_kfreebsd-i386.deb
- 45e5729f94233e78cd653d45271a6c5f 160998 libdevel optional libbam-dev_0.1.18-4_kfreebsd-i386.deb
+ 57b519fdea3b23c74169e55f1638881c 563422 science optional samtools_0.1.19-1_kfreebsd-i386.deb
+ c94271270f5dd96bcf856e8b2f4ce86b 126860 libdevel optional libbam-dev_0.1.19-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_kfreebsd-i386.deb
+samtools_0.1.19-1_kfreebsd-i386.deb
───────────────────────────────────
new debian package, version 2.0.
- size 534414 bytes: control archive= 1813 bytes.
+ size 563422 bytes: control archive= 1941 bytes.
32 bytes, 1 lines conffiles
- 801 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 802 bytes, 16 lines control
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 992
+ Installed-Size: 1298
Depends: libc0.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -730,74 +765,79 @@ samtools_0.1.18-4_kfreebsd-i386.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126583 2012-12-23 04:59 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-12-23 04:59 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 04:59 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 04:59 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 04:59 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/bin/
--rwxr-xr-x root/root 134212 2012-12-23 04:59 ./usr/bin/bcftools
--rwxr-xr-x root/root 24676 2012-12-23 04:59 ./usr/bin/razip
--rwxr-xr-x root/root 399988 2012-12-23 04:59 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/lib/samtools/
--rwxr-xr-x root/root 16472 2012-12-23 04:59 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 6844 2012-12-23 04:59 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 6844 2012-12-23 04:59 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10576 2012-12-23 04:59 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7452 2012-12-23 04:59 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_kfreebsd-i386.deb
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:18 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2013-03-30 09:19 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 09:19 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 09:19 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:19 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/bin/
+-rwxr-xr-x root/root 157732 2013-03-30 09:19 ./usr/bin/bcftools
+-rwxr-xr-x root/root 26152 2013-03-30 09:19 ./usr/bin/razip
+-rwxr-xr-x root/root 439700 2013-03-30 09:19 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/samtools/
+-rwxr-xr-x root/root 17896 2013-03-30 09:19 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 17840 2013-03-30 09:19 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 187448 2013-03-30 09:19 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 9628 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 9628 2013-03-30 09:19 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 13728 2013-03-30 09:19 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 9604 2013-03-30 09:19 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_kfreebsd-i386.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 160998 bytes: control archive= 946 bytes.
+ size 126860 bytes: control archive= 931 bytes.
720 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 401
+ Installed-Size: 373
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -810,25 +850,25 @@ libbam-dev_0.1.18-4_kfreebsd-i386.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/lib/
--rw-r--r-- root/root 299848 2012-12-23 04:59 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 04:59 ./usr/include/samtools/
--rw-r--r-- root/root 24732 2012-12-23 04:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/lib/
+-rw-r--r-- root/root 291856 2013-03-30 09:19 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:19 ./usr/include/samtools/
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -842,7 +882,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1356238605-13802/build/buildd-samtools_0.1.18-4-kfreebsd-i386-wC4PVN
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1364634959-29231/build/buildd-samtools_0.1.19-1-kfreebsd-i386-xI3hSM
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -850,18 +890,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 11086
-Build-Time: 72
+Build-Space: 13164
+Build-Time: 75
Distribution: sid
-Install-Time: 35
-Job: samtools_0.1.18-4
+Install-Time: 34
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 169
-Source-Version: 0.1.18-4
-Space: 11086
+Package-Time: 199
+Source-Version: 0.1.19-1
+Space: 13164
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0459
-Build needed 00:02:49, 11086k disc space
-Signature with key 'B3DA9773' requested:
+Finished at 20130330-0919
+Build needed 00:03:19, 13164k disc space
+Signature with key 'B31C365A' requested:
diff --git a/mips.log b/mips.log
index 36e3ad0..dc278ca 100644
--- a/mips.log
+++ b/mips.log
@@ -1,29 +1,28 @@
-From buildd2 at lucatelli.debian.org Sun Dec 23 05:18:47 2012
-Return-path: <buildd2 at lucatelli.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at lucatelli.debian.org Sat Mar 30 14:22:50 2013
+Return-path: <buildd at lucatelli.debian.org>
+Received: from mailly.debian.org ([82.195.75.114])
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 <buildd2 at lucatelli.debian.org>)
- id 1TmdxX-0003Ro-IT
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:18:47 +0000
-Received: from lucatelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4141])
+ CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
+ (Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
+ id 1ULwgE-0006uV-58
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 14:22:50 +0000
+Received: from lucatelli.debian.org ([206.12.19.15])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=lucatelli.debian.org,
EMAIL=hostmaster at lucatelli.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd2 at lucatelli.debian.org>)
- id 1TmdxW-00014y-5G
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:18:46 +0000
-Received: from buildd2 by lucatelli.debian.org with local (Exim 4.72)
- (envelope-from <buildd2 at lucatelli.debian.org>) id 1TmdxT-0007jO-8m
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:18:43 +0000
-Date: Sun, 23 Dec 2012 05:18:43 +0000
-Message-Id: <E1TmdxT-0007jO-8m at lucatelli.debian.org>
-From: buildd on lucatelli <buildd2 at lucatelli.debian.org>
+ by mailly.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at lucatelli.debian.org>)
+ id 1ULwgC-00049P-JK
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 14:22:49 +0000
+Received: from buildd by lucatelli.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lucatelli.debian.org>) id 1ULwYe-0006xs-4T
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 14:15:00 +0000
+Date: Sat, 30 Mar 2013 14:15:00 +0000
+Message-Id: <E1ULwYe-0006xs-4T at lucatelli.debian.org>
+From: buildd on lucatelli <buildd at lucatelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on mips (dist=sid)
+Subject: Log for successful build of samtools_0.1.19-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -31,31 +30,35 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (mips) 23 Dec 2012 04:53 ║
+║ samtools 0.1.19-1 (mips) 30 Mar 2013 13:47 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable InRelease [227 kB]
-Get:2 http://incoming.debian.org unstable InRelease [227 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [6458 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [53.0 kB]
-Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [6059 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://incoming.debian.org unstable/main mips Packages [6059 kB]
-Get:12 http://mirror-ubc.debian.org unstable/contrib mips Packages [37.1 kB]
-Get:13 http://incoming.debian.org unstable/contrib mips Packages [37.1 kB]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 26.0 MB in 1min 38s (264 kB/s)
+Get:1 http://mirror-ubc.debian.org unstable Release.gpg [836 B]
+Get:2 http://mirror-ubc.debian.org unstable Release [235 kB]
+Get:3 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:4 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:5 http://mirror-ubc.debian.org unstable/main Sources [6484 kB]
+Get:6 http://incoming.debian.org unstable Release [235 kB]
+Get:7 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:9 http://mirror-ubc.debian.org unstable/contrib Sources [51.0 kB]
+Get:10 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://mirror-ubc.debian.org unstable/main mips Packages [6073 kB]
+Get:12 http://mirror-ubc.debian.org unstable/contrib mips Packages [36.1 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:15 http://incoming.debian.org unstable/main mips Packages [6073 kB]
+Get:16 http://incoming.debian.org unstable/contrib mips Packages [36.1 kB]
+Get:17 http://incoming.debian.org buildd-unstable/main Sources [18.3 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:20 http://incoming.debian.org buildd-unstable/main mips Packages [13.4 kB]
+Get:21 http://incoming.debian.org buildd-unstable/contrib mips Packages [14 B]
+Fetched 26.1 MB in 1min 43s (252 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -75,12 +78,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (347 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (404 kB/s)
Download complete and in download only mode
Check arch
@@ -93,56 +96,57 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 56 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 56 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.20-3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.3)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.8)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-20)
sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-32)
-sysvinit: already installed (2.88dsf-32)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-mount: already installed (2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-35)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120909
bash-completion: missing
@@ -173,26 +177,26 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 56 not upgraded.
-Need to get 10.4 MB of archives.
-After this operation, 30.3 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.2-1 [37.1 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.21-9 [1156 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.3 [208 kB]
+0 upgraded, 29 newly installed, 0 to remove and 6 not upgraded.
+Need to get 9994 kB of archives.
+After this operation, 30.2 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.2-2 [37.2 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.22.2-1 [708 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.4 [209 kB]
Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.3-3 [867 kB]
Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 mips 0.18.1.1-10 [27.1 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 5.11-2 [201 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 1:8.31-1 [250 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-7 [870 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 1:5.11-2.1 [201 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 1:8.31-2 [250 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-7+nmu1 [870 kB]
Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.33.12+really2.32.4-3 [1685 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.33.12+really2.32.4-5 [1686 kB]
Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.6-2 [118 kB]
Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 mips 0.18.1.1-10 [140 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file mips 5.11-2 [51.5 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file mips 1:5.11-2.1 [51.6 kB]
Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-10 [141 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev mips 0.18.1.1-10 [26.9 kB]
Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev mips 0.18.1.1-10 [189 kB]
@@ -203,17 +207,17 @@ Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.201209
Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev mips 5.9-10 [104 kB]
Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-10 [223 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.7.dfsg-13 [213 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 10s (1000 kB/s)
+Fetched 9994 kB in 10s (995 kB/s)
Selecting previously unselected package libpipeline1:mips.
-(Reading database ... 10735 files and directories currently installed.)
-Unpacking libpipeline1:mips (from .../libpipeline1_1.2.2-1_mips.deb) ...
+(Reading database ... 10799 files and directories currently installed.)
+Unpacking libpipeline1:mips (from .../libpipeline1_1.2.2-2_mips.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_mips.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_mips.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_mips.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_mips.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_mips.deb) ...
Selecting previously unselected package bash-completion.
@@ -221,15 +225,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:mips.
Unpacking libasprintf0c2:mips (from .../libasprintf0c2_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package libmagic1:mips.
-Unpacking libmagic1:mips (from .../libmagic1_5.11-2_mips.deb) ...
+Unpacking libmagic1:mips (from .../libmagic1_1%3a5.11-2.1_mips.deb) ...
Selecting previously unselected package libpcre3:mips.
-Unpacking libpcre3:mips (from .../libpcre3_1%3a8.31-1_mips.deb) ...
+Unpacking libpcre3:mips (from .../libpcre3_1%3a8.31-2_mips.deb) ...
Selecting previously unselected package libxml2:mips.
-Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-7_mips.deb) ...
+Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_mips.deb) ...
+Unpacking libglib2.0-0:mips (from .../libglib2.0-0_2.33.12+really2.32.4-5_mips.deb) ...
Selecting previously unselected package libcroco3:mips.
Unpacking libcroco3:mips (from .../libcroco3_0.6.6-2_mips.deb) ...
Selecting previously unselected package libunistring0:mips.
@@ -237,11 +241,11 @@ Unpacking libunistring0:mips (from .../libunistring0_0.9.3-5_mips.deb) ...
Selecting previously unselected package libgettextpo0:mips.
Unpacking libgettextpo0:mips (from .../libgettextpo0_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_mips.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_mips.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mips.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
Selecting previously unselected package libasprintf-dev:mips.
@@ -263,30 +267,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:mips (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:mips (0.18.1.1-10) ...
-Setting up libmagic1:mips (5.11-2) ...
-Setting up libpcre3:mips (1:8.31-1) ...
-Setting up libxml2:mips (2.8.0+dfsg1-7) ...
+Setting up libmagic1:mips (1:5.11-2.1) ...
+Setting up libpcre3:mips (1:8.31-2) ...
+Setting up libxml2:mips (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:mips (3.0.10-3) ...
-Setting up libglib2.0-0:mips (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:mips (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:mips (0.6.6-2) ...
Setting up libunistring0:mips (0.9.3-5) ...
Setting up libgettextpo0:mips (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:mips (0.18.1.1-10) ...
Setting up libgettextpo-dev:mips (0.18.1.1-10) ...
@@ -297,17 +301,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:mips (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
Setting up zlib1g-dev:mips (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 56 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 3.2.0-0.bpo.3-octeon mips (mips64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
-Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Kernel: Linux 3.2.0-0.bpo.4-octeon mips (mips64)
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -317,17 +321,16 @@ Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash
Unpack source
─────────────
-gpgv: keyblock resource `/home/buildd2/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -337,44 +340,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -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_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/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_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -387,11 +387,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -400,139 +400,176 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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 -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
+bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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':
-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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mips-5n0bWE/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -554,11 +591,11 @@ make[1]: Entering directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtoo
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -586,7 +623,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -594,8 +631,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -611,7 +648,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -623,7 +660,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd2-samtools_0.1.18-4-mips-UhvVCE/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -638,79 +675,78 @@ 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_0.1.18-4_mips.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_mips.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org> >../samtools_0.1.18-4_mips.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_mips.deb'.
+ dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.19-1_mips.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0518
+Build finished at 20130330-1414
-samtools_0.1.18-4_mips.changes:
+samtools_0.1.19-1_mips.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli2 at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
- .
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- 293e544fe85a2978220887552b654ee1fe51c1a4 525938 samtools_0.1.18-4_mips.deb
- 9a3aef658319c24ab965ea8a4e291d33833f87ef 163590 libbam-dev_0.1.18-4_mips.deb
+ 25756739b5ab40f2bdf4a9e66464948459c07689 552640 samtools_0.1.19-1_mips.deb
+ f3b538a87375e06336c19afa8374732f072312fb 129524 libbam-dev_0.1.19-1_mips.deb
Checksums-Sha256:
- 01bc7f18c1d1ec407511bf5fed18b7189f4d1af2febb3a921501d682ad217f4d 525938 samtools_0.1.18-4_mips.deb
- c93149d09a6b57e5a629957e98d7cdc63ad5becf57665aecc5ebc83dec384d22 163590 libbam-dev_0.1.18-4_mips.deb
+ d174a100849d8d5b42662b084beb54e3f990fc9e822f604c20ff2acf3a32bb06 552640 samtools_0.1.19-1_mips.deb
+ 0a4ec06874f80151a9fa41ef9962e94eb399028786b7386e05105a73cd568fb7 129524 libbam-dev_0.1.19-1_mips.deb
Files:
- 3d619f6a934917cb1eac0369633839e4 525938 science optional samtools_0.1.18-4_mips.deb
- 2f8476f717beb2f942766d073de51831 163590 libdevel optional libbam-dev_0.1.18-4_mips.deb
+ d26e2e39fbd0fa15e5d42808aa721dd1 552640 science optional samtools_0.1.19-1_mips.deb
+ 4a5151e4f29a9ad33fde3b1b59a2457a 129524 libdevel optional libbam-dev_0.1.19-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_mips.deb
+samtools_0.1.19-1_mips.deb
──────────────────────────
new debian package, version 2.0.
- size 525938 bytes: control archive= 1810 bytes.
+ size 552640 bytes: control archive= 1935 bytes.
32 bytes, 1 lines conffiles
791 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1115
+ Installed-Size: 1439
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -723,74 +759,79 @@ samtools_0.1.18-4_mips.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/lib/samtools/
--rwxr-xr-x root/root 7472 2012-12-23 05:17 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9252 2012-12-23 05:17 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 12432 2012-12-23 05:17 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7472 2012-12-23 05:17 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 17692 2012-12-23 05:17 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/bin/
--rwxr-xr-x root/root 155204 2012-12-23 05:17 ./usr/bin/bcftools
--rwxr-xr-x root/root 440320 2012-12-23 05:17 ./usr/bin/samtools
--rwxr-xr-x root/root 29296 2012-12-23 05:17 ./usr/bin/razip
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 05:17 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126583 2012-12-23 05:04 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2012-12-23 05:17 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 05:17 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 05:17 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2012-12-23 05:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_mips.deb
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18192 2013-03-30 14:13 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 10032 2013-03-30 14:13 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10068 2013-03-30 14:13 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 14224 2013-03-30 14:13 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 10032 2013-03-30 14:13 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 207416 2013-03-30 14:13 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 18508 2013-03-30 14:13 ./usr/lib/samtools/wgsim
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/bin/
+-rwxr-xr-x root/root 176252 2013-03-30 14:13 ./usr/bin/bcftools
+-rwxr-xr-x root/root 483460 2013-03-30 14:13 ./usr/bin/samtools
+-rwxr-xr-x root/root 31780 2013-03-30 14:13 ./usr/bin/razip
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 14:13 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126580 2013-03-30 14:00 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1966 2013-03-30 14:13 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 14:13 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 14:13 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 14:13 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_mips.deb
────────────────────────────
new debian package, version 2.0.
- size 163590 bytes: control archive= 946 bytes.
+ size 129524 bytes: control archive= 928 bytes.
711 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 467
+ Installed-Size: 441
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -803,25 +844,25 @@ libbam-dev_0.1.18-4_mips.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/lib/
--rw-r--r-- root/root 335618 2012-12-23 05:17 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/include/samtools/
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 24732 2012-12-23 04:58 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:17 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/lib/
+-rw-r--r-- root/root 328998 2013-03-30 14:13 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/include/samtools/
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -835,57 +876,54 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mips-sbuild-cb17ab87-f16e-4459-bb11-3f44ac7e51c0/build/buildd2-samtools_0.1.18-4-mips-UhvVCE
+Purging /var/lib/schroot/mount/sid-mips-sbuild-d7aeb6e0-a385-42f3-8e4b-724cf54e9acc/build/buildd-samtools_0.1.19-1-mips-5n0bWE
Not cleaning session: cloned chroot in use
-Can't open average time db /var/lib/sbuild/avg-build-times
-Can't open average space db /var/lib/sbuild/avg-build-space
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 11012
-Build-Time: 1286
+Build-Space: 12848
+Build-Time: 1396
Distribution: sid
-Install-Time: 87
-Job: samtools_0.1.18-4
+Install-Time: 108
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 1519
-Source-Version: 0.1.18-4
-Space: 11012
+Package-Time: 1660
+Source-Version: 0.1.19-1
+Space: 12848
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0518
-Build needed 00:25:19, 11012k disc space
-Signature with key '86ADA8B4' requested:
+Finished at 20130330-1414
+Build needed 00:27:40, 12848k disc space
+Signature with key 'A2DB4074' requested:
-From buildd at mayer.debian.org Sun Dec 23 05:04:52 2012
+From buildd at mayer.debian.org Sat Mar 30 09:25:04 2013
Return-path: <buildd at mayer.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from muffat.debian.org ([206.12.19.146])
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)
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1Tmdk4-0000P2-3B
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:52 +0000
+ id 1ULs22-0003vN-UH
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:25:03 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1Tmdk2-0008JB-FH
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:51 +0000
+ by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at mayer.debian.org>)
+ id 1ULs1z-0007jf-Uy
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:25:00 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mayer.debian.org>) id 1Tmdjz-00014d-0i
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:47 +0000
-Date: Sun, 23 Dec 2012 05:04:47 +0000
-Message-Id: <E1Tmdjz-00014d-0i at mayer.debian.org>
+ (envelope-from <buildd at mayer.debian.org>) id 1ULs1x-0005a0-Te
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:24:58 +0000
+Date: Sat, 30 Mar 2013 09:24:57 +0000
+Message-Id: <E1ULs1x-0005a0-Te at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.19-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -893,29 +931,30 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (mipsel) 23 Dec 2012 04:56 ║
+║ samtools 0.1.19-1 (mipsel) 30 Mar 2013 09:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: mipsel
-Get:1 http://incoming.debian.org sid InRelease [227 kB]
-Get:2 http://debian.oregonstate.edu sid InRelease [227 kB]
-Get:3 http://debian.oregonstate.edu sid/main Sources [6458 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org sid/main Sources [6458 kB]
-Get:6 http://debian.oregonstate.edu sid/contrib Sources [53.0 kB]
-Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [6064 kB]
-Get:8 http://incoming.debian.org sid/contrib Sources [53.0 kB]
-Get:9 http://incoming.debian.org sid/main mipsel Packages [6064 kB]
-Get:10 http://debian.oregonstate.edu sid/contrib mipsel Packages [37.1 kB]
-Get:11 http://incoming.debian.org sid/contrib mipsel Packages [37.1 kB]
-Get:12 http://incoming.debian.org Release [1141 B]
-Get:13 http://incoming.debian.org Sources [14.0 kB]
-Get:14 http://incoming.debian.org Packages [118 kB]
-Fetched 25.8 MB in 1min 25s (301 kB/s)
+Hit http://debian.oregonstate.edu sid Release.gpg
+Hit http://debian.oregonstate.edu sid Release
+Get:1 http://incoming.debian.org sid Release.gpg [836 B]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+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
+Get:3 http://incoming.debian.org sid Release [235 kB]
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Get:4 http://incoming.debian.org Release [1141 B]
+Get:5 http://incoming.debian.org sid/main Sources [6484 kB]
+Get:6 http://incoming.debian.org sid/contrib Sources [51.0 kB]
+Get:7 http://incoming.debian.org sid/main mipsel Packages [6075 kB]
+Get:8 http://incoming.debian.org sid/contrib mipsel Packages [36.1 kB]
+Get:9 http://incoming.debian.org Sources [12.5 kB]
+Get:10 http://incoming.debian.org Packages [98.1 kB]
+Fetched 13.0 MB in 38s (334 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -935,12 +974,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (378 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (449 kB/s)
Download complete and in download only mode
Check arch
@@ -953,56 +992,57 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.20-3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.3)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.8)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
+e2fsprogs: already installed (1.42.5-1.1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-16)
+perl-base: already installed (5.14.2-20)
sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-32)
-sysvinit: already installed (2.88dsf-32)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-mount: already installed (2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-37)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120909
bash-completion: missing
@@ -1016,31 +1056,36 @@ 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
- libasprintf-dev libasprintf0c2 libcroco3 libffi5 libgettextpo-dev
- libgettextpo0 libglib2.0-0 libmagic1 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl procmail graphviz default-mta mail-transport-agent
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
+ mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev
- libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
+Need to get 193 kB/9997 kB of archives.
+After this operation, 30.2 MB of additional disk space will be used.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main bash-completion all 1:2.0-1 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 27 newly installed, 0 to remove and 30 not upgraded.
-Need to get 0 B/9966 kB of archives.
-After this operation, 29.2 MB of additional disk space will be used.
+Fetched 193 kB in 0s (2393 kB/s)
Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10942 files and directories currently installed.)
-Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-1_mipsel.deb) ...
+(Reading database ... 10900 files and directories currently installed.)
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-2_mipsel.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_mipsel.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_mipsel.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_mipsel.deb) ...
Selecting previously unselected package bash-completion.
@@ -1048,13 +1093,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:mipsel.
Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package libmagic1:mipsel.
-Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
+Unpacking libmagic1:mipsel (from .../libmagic1_1%3a5.11-2.1_mipsel.deb) ...
+Selecting previously unselected package libpcre3:mipsel.
+Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.31-2_mipsel.deb) ...
Selecting previously unselected package libxml2:mipsel.
-Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7_mipsel.deb) ...
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_mipsel.deb) ...
+Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-5_mipsel.deb) ...
Selecting previously unselected package libcroco3:mipsel.
Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-2_mipsel.deb) ...
Selecting previously unselected package libunistring0:mipsel.
@@ -1062,11 +1109,11 @@ Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
Selecting previously unselected package libgettextpo0:mipsel.
Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.11-2_mipsel.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_mipsel.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously unselected package libasprintf-dev:mipsel.
@@ -1088,26 +1135,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
+Setting up libpipeline1:mipsel (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:mipsel (0.18.1.1-10) ...
-Setting up libmagic1:mipsel (5.11-2) ...
-Setting up libxml2:mipsel (2.8.0+dfsg1-7) ...
+Setting up libmagic1:mipsel (1:5.11-2.1) ...
+Setting up libpcre3:mipsel (1:8.31-2) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:mipsel (3.0.10-3) ...
-Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:mipsel (0.6.6-2) ...
Setting up libunistring0:mipsel (0.9.3-5) ...
Setting up libgettextpo0:mipsel (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:mipsel (0.18.1.1-10) ...
Setting up libgettextpo-dev:mipsel (0.18.1.1-10) ...
@@ -1118,17 +1169,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:mipsel (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.23-1
-Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-14 gcc_4:4.6.3-8 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-16 perl-base_5.14.2-16 perl-modules_5.14.2-16 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libffi5_3.0.10-3 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1139,16 +1190,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -1158,44 +1208,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -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_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -1208,11 +1255,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -1221,139 +1268,176 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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 -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
+bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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':
-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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1375,11 +1459,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samto
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -1407,7 +1491,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -1415,8 +1499,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -1432,7 +1516,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -1444,7 +1528,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -1460,80 +1544,79 @@ dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is no
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-4_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.19-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0504
+Build finished at 20130330-0924
-samtools_0.1.18-4_mipsel.changes:
+samtools_0.1.19-1_mipsel.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
- .
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
- .
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- e38f3d105ff9aec1e46a1cf7df50d9d690daa854 528822 samtools_0.1.18-4_mipsel.deb
- e3bac066a176abf71ac601f7cc5b7f6a8115b949 165950 libbam-dev_0.1.18-4_mipsel.deb
+ 403caf7143bf1b0b949196cf55cbd1d1768f15d5 555674 samtools_0.1.19-1_mipsel.deb
+ 271275f5ed7142222ac09a9549835fb3c72c542b 131464 libbam-dev_0.1.19-1_mipsel.deb
Checksums-Sha256:
- deeeaee3478547fe36bf464cd72db5a97f311564984c636f1d526d583edbf645 528822 samtools_0.1.18-4_mipsel.deb
- 755ab8c730bd35963f3d8c2ff6d6e4a53e0819099742a8a1d994d1f983628ece 165950 libbam-dev_0.1.18-4_mipsel.deb
+ 07ca0979fd1bb36fa4702e2f481309bf72b72e6634a306e5d3a8e9570509f099 555674 samtools_0.1.19-1_mipsel.deb
+ 68096b1306f84e6e4014eaa37e6cb444cf51fc927245a65f88d793407cb82301 131464 libbam-dev_0.1.19-1_mipsel.deb
Files:
- 9654a2be2233c1816ecc00d751ce655c 528822 science optional samtools_0.1.18-4_mipsel.deb
- 0f8f4860ecf69157bff1f30b8435bf0a 165950 libdevel optional libbam-dev_0.1.18-4_mipsel.deb
+ 44d1f7279db85e98bfe8666397f898ef 555674 science optional samtools_0.1.19-1_mipsel.deb
+ 6d14454cb9202d9a7fcf084e040f43a8 131464 libdevel optional libbam-dev_0.1.19-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_mipsel.deb
+samtools_0.1.19-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 528822 bytes: control archive= 1809 bytes.
+ size 555674 bytes: control archive= 1937 bytes.
32 bytes, 1 lines conffiles
793 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1115
+ Installed-Size: 1439
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -1546,74 +1629,79 @@ samtools_0.1.18-4_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126583 2012-12-23 05:03 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-12-23 05:03 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 05:03 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 05:03 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 05:03 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/bin/
--rwxr-xr-x root/root 155204 2012-12-23 05:03 ./usr/bin/bcftools
--rwxr-xr-x root/root 29168 2012-12-23 05:03 ./usr/bin/razip
--rwxr-xr-x root/root 440320 2012-12-23 05:03 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/samtools/
--rwxr-xr-x root/root 17692 2012-12-23 05:03 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12432 2012-12-23 05:03 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9252 2012-12-23 05:03 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2012-12-23 05:03 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_mipsel.deb
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:23 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2013-03-30 09:23 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 09:23 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 09:23 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:24 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/bin/
+-rwxr-xr-x root/root 176252 2013-03-30 09:24 ./usr/bin/bcftools
+-rwxr-xr-x root/root 31780 2013-03-30 09:24 ./usr/bin/razip
+-rwxr-xr-x root/root 483460 2013-03-30 09:24 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18508 2013-03-30 09:24 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 18192 2013-03-30 09:24 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 207416 2013-03-30 09:24 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 14224 2013-03-30 09:24 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 10068 2013-03-30 09:24 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:23 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165950 bytes: control archive= 942 bytes.
+ size 131464 bytes: control archive= 924 bytes.
713 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 467
+ Installed-Size: 441
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -1626,25 +1714,25 @@ libbam-dev_0.1.18-4_mipsel.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
--rw-r--r-- root/root 335698 2012-12-23 05:03 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/samtools/
--rw-r--r-- root/root 24732 2012-12-23 04:59 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/
+-rw-r--r-- root/root 328990 2013-03-30 09:24 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/samtools/
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1658,37 +1746,39 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-3334b19a-a1bc-4c57-a8db-8e6c3252fce1/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ca64eee5-03d6-4a10-836c-decf0e5e9b54/build/buildd-samtools_0.1.19-1-mipsel-muFrrg
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- bash-completion* cdbs* debhelper* diffstat* file* gettext* gettext-base*
- groff-base* html2text* intltool-debian* libasprintf-dev* libasprintf0c2*
- libcroco3* libffi5* libgettextpo-dev* libgettextpo0* libglib2.0-0*
- libmagic1* libncurses5-dev* libpipeline1* libtinfo-dev* libunistring0*
- libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 27 to remove and 30 not upgraded.
-After this operation, 29.2 MB disk space will be freed.
-(Reading database ... 12988 files and directories currently installed.)
+ bash-completion* bsdmainutils* cdbs* debhelper* diffstat* file* gettext*
+ gettext-base* groff-base* html2text* intltool-debian* libasprintf-dev*
+ libasprintf0c2* libcroco3* libffi5* libgettextpo-dev* libgettextpo0*
+ libglib2.0-0* libmagic1* libncurses5-dev* libpcre3* libpipeline1*
+ libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 29 to remove and 2 not upgraded.
+After this operation, 30.2 MB disk space will be freed.
+(Reading database ... 13074 files and directories currently installed.)
Removing bash-completion ...
Purging configuration files for bash-completion ...
-Removing cdbs ...
-Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
+Removing debhelper ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing cdbs ...
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 ...
@@ -1706,6 +1796,8 @@ Removing libgettextpo0:mipsel ...
Removing libmagic1:mipsel ...
Purging configuration files for libmagic1:mipsel ...
Removing libncurses5-dev ...
+Removing libpcre3:mipsel ...
+Purging configuration files for libpcre3:mipsel ...
Removing libpipeline1:mipsel ...
Purging configuration files for libpipeline1:mipsel ...
Removing libtinfo-dev:mipsel ...
@@ -1720,19 +1812,19 @@ Removing zlib1g-dev:mipsel ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 11016
-Build-Time: 320
+Build-Space: 12852
+Build-Time: 342
Distribution: sid
-Install-Time: 54
-Job: samtools_0.1.18-4
+Install-Time: 58
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 496
-Source-Version: 0.1.18-4
-Space: 11016
+Package-Time: 479
+Source-Version: 0.1.19-1
+Space: 12852
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0504
-Build needed 00:08:16, 11016k disc space
-Signature with key '8C9FAB20' requested:
+Finished at 20130330-0924
+Build needed 00:07:59, 12852k disc space
+Signature with key '4A2D13C7' requested:
diff --git a/mipsel.log b/mipsel.log
index eb807a8..0adf0e4 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,28 +1,27 @@
-From buildd at mayer.debian.org Sun Dec 23 05:04:52 2012
+From buildd at mayer.debian.org Sat Mar 30 09:25:04 2013
Return-path: <buildd at mayer.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from muffat.debian.org ([206.12.19.146])
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)
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
(Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1Tmdk4-0000P2-3B
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:52 +0000
+ id 1ULs22-0003vN-UH
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:25:03 +0000
Received: from mayer.debian.org ([140.211.166.78])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1Tmdk2-0008JB-FH
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:51 +0000
+ by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at mayer.debian.org>)
+ id 1ULs1z-0007jf-Uy
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:25:00 +0000
Received: from buildd by mayer.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mayer.debian.org>) id 1Tmdjz-00014d-0i
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:04:47 +0000
-Date: Sun, 23 Dec 2012 05:04:47 +0000
-Message-Id: <E1Tmdjz-00014d-0i at mayer.debian.org>
+ (envelope-from <buildd at mayer.debian.org>) id 1ULs1x-0005a0-Te
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:24:58 +0000
+Date: Sat, 30 Mar 2013 09:24:57 +0000
+Message-Id: <E1ULs1x-0005a0-Te at mayer.debian.org>
From: buildd on mayer <buildd at mayer.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on mipsel (dist=sid)
+Subject: Log for successful build of samtools_0.1.19-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,29 +29,30 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (mipsel) 23 Dec 2012 04:56 ║
+║ samtools 0.1.19-1 (mipsel) 30 Mar 2013 09:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: mipsel
-Get:1 http://incoming.debian.org sid InRelease [227 kB]
-Get:2 http://debian.oregonstate.edu sid InRelease [227 kB]
-Get:3 http://debian.oregonstate.edu sid/main Sources [6458 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org sid/main Sources [6458 kB]
-Get:6 http://debian.oregonstate.edu sid/contrib Sources [53.0 kB]
-Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [6064 kB]
-Get:8 http://incoming.debian.org sid/contrib Sources [53.0 kB]
-Get:9 http://incoming.debian.org sid/main mipsel Packages [6064 kB]
-Get:10 http://debian.oregonstate.edu sid/contrib mipsel Packages [37.1 kB]
-Get:11 http://incoming.debian.org sid/contrib mipsel Packages [37.1 kB]
-Get:12 http://incoming.debian.org Release [1141 B]
-Get:13 http://incoming.debian.org Sources [14.0 kB]
-Get:14 http://incoming.debian.org Packages [118 kB]
-Fetched 25.8 MB in 1min 25s (301 kB/s)
+Hit http://debian.oregonstate.edu sid Release.gpg
+Hit http://debian.oregonstate.edu sid Release
+Get:1 http://incoming.debian.org sid Release.gpg [836 B]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+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
+Get:3 http://incoming.debian.org sid Release [235 kB]
+Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
+Get:4 http://incoming.debian.org Release [1141 B]
+Get:5 http://incoming.debian.org sid/main Sources [6484 kB]
+Get:6 http://incoming.debian.org sid/contrib Sources [51.0 kB]
+Get:7 http://incoming.debian.org sid/main mipsel Packages [6075 kB]
+Get:8 http://incoming.debian.org sid/contrib mipsel Packages [36.1 kB]
+Get:9 http://incoming.debian.org Sources [12.5 kB]
+Get:10 http://incoming.debian.org Packages [98.1 kB]
+Fetched 13.0 MB in 38s (334 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -72,12 +72,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (378 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (449 kB/s)
Download complete and in download only mode
Check arch
@@ -90,56 +90,57 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.20-3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.3)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.8)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
+e2fsprogs: already installed (1.42.5-1.1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-16)
+perl-base: already installed (5.14.2-20)
sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-32)
-sysvinit: already installed (2.88dsf-32)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-mount: already installed (2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-37)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120909
bash-completion: missing
@@ -153,31 +154,36 @@ 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
- libasprintf-dev libasprintf0c2 libcroco3 libffi5 libgettextpo-dev
- libgettextpo0 libglib2.0-0 libmagic1 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf
+ bsdmainutils diffstat file gettext gettext-base groff-base html2text
+ intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
+ libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf
Suggested packages:
- devscripts dh-make gettext-doc groff ncurses-doc less www-browser
- libmail-box-perl procmail graphviz default-mta mail-transport-agent
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
+ mail-transport-agent
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion cdbs debhelper diffstat file gettext gettext-base groff-base
- html2text intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev
- libpipeline1 libtinfo-dev libunistring0 libxml2 man-db po-debconf quilt
- zlib1g-dev
+ bash-completion bsdmainutils cdbs debhelper diffstat file gettext
+ gettext-base groff-base html2text intltool-debian libasprintf-dev
+ libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
+ libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
+ libxml2 man-db po-debconf quilt zlib1g-dev
+0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
+Need to get 193 kB/9997 kB of archives.
+After this operation, 30.2 MB of additional disk space will be used.
+Get:1 http://debian.oregonstate.edu/debian/ sid/main bash-completion all 1:2.0-1 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 27 newly installed, 0 to remove and 30 not upgraded.
-Need to get 0 B/9966 kB of archives.
-After this operation, 29.2 MB of additional disk space will be used.
+Fetched 193 kB in 0s (2393 kB/s)
Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10942 files and directories currently installed.)
-Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-1_mipsel.deb) ...
+(Reading database ... 10900 files and directories currently installed.)
+Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-2_mipsel.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_mipsel.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_mipsel.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_mipsel.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_mipsel.deb) ...
Selecting previously unselected package bash-completion.
@@ -185,13 +191,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:mipsel.
Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package libmagic1:mipsel.
-Unpacking libmagic1:mipsel (from .../libmagic1_5.11-2_mipsel.deb) ...
+Unpacking libmagic1:mipsel (from .../libmagic1_1%3a5.11-2.1_mipsel.deb) ...
+Selecting previously unselected package libpcre3:mipsel.
+Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.31-2_mipsel.deb) ...
Selecting previously unselected package libxml2:mipsel.
-Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7_mipsel.deb) ...
+Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_mipsel.deb) ...
+Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-5_mipsel.deb) ...
Selecting previously unselected package libcroco3:mipsel.
Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-2_mipsel.deb) ...
Selecting previously unselected package libunistring0:mipsel.
@@ -199,11 +207,11 @@ Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
Selecting previously unselected package libgettextpo0:mipsel.
Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.11-2_mipsel.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_mipsel.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mipsel.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
Selecting previously unselected package libasprintf-dev:mipsel.
@@ -225,26 +233,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
+Setting up libpipeline1:mipsel (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:mipsel (0.18.1.1-10) ...
-Setting up libmagic1:mipsel (5.11-2) ...
-Setting up libxml2:mipsel (2.8.0+dfsg1-7) ...
+Setting up libmagic1:mipsel (1:5.11-2.1) ...
+Setting up libpcre3:mipsel (1:8.31-2) ...
+Setting up libxml2:mipsel (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:mipsel (3.0.10-3) ...
-Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:mipsel (0.6.6-2) ...
Setting up libunistring0:mipsel (0.9.3-5) ...
Setting up libgettextpo0:mipsel (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:mipsel (0.18.1.1-10) ...
Setting up libgettextpo-dev:mipsel (0.18.1.1-10) ...
@@ -255,17 +267,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:mipsel (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.23-1
-Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-14 gcc_4:4.6.3-8 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-16 perl-base_5.14.2-16 perl-modules_5.14.2-16 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libffi5_3.0.10-3 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1.1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -276,16 +288,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -295,44 +306,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -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_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -345,11 +353,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -358,139 +366,176 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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 -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
+bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -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_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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':
-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 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
+gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -512,11 +557,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samto
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -544,7 +589,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -552,8 +597,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -569,7 +614,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -581,7 +626,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -597,80 +642,79 @@ dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is no
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.18-4_mipsel.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_mipsel.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.18-4_mipsel.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.19-1_mipsel.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0504
+Build finished at 20130330-0924
-samtools_0.1.18-4_mipsel.changes:
+samtools_0.1.19-1_mipsel.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mipsel
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
- .
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- e38f3d105ff9aec1e46a1cf7df50d9d690daa854 528822 samtools_0.1.18-4_mipsel.deb
- e3bac066a176abf71ac601f7cc5b7f6a8115b949 165950 libbam-dev_0.1.18-4_mipsel.deb
+ 403caf7143bf1b0b949196cf55cbd1d1768f15d5 555674 samtools_0.1.19-1_mipsel.deb
+ 271275f5ed7142222ac09a9549835fb3c72c542b 131464 libbam-dev_0.1.19-1_mipsel.deb
Checksums-Sha256:
- deeeaee3478547fe36bf464cd72db5a97f311564984c636f1d526d583edbf645 528822 samtools_0.1.18-4_mipsel.deb
- 755ab8c730bd35963f3d8c2ff6d6e4a53e0819099742a8a1d994d1f983628ece 165950 libbam-dev_0.1.18-4_mipsel.deb
+ 07ca0979fd1bb36fa4702e2f481309bf72b72e6634a306e5d3a8e9570509f099 555674 samtools_0.1.19-1_mipsel.deb
+ 68096b1306f84e6e4014eaa37e6cb444cf51fc927245a65f88d793407cb82301 131464 libbam-dev_0.1.19-1_mipsel.deb
Files:
- 9654a2be2233c1816ecc00d751ce655c 528822 science optional samtools_0.1.18-4_mipsel.deb
- 0f8f4860ecf69157bff1f30b8435bf0a 165950 libdevel optional libbam-dev_0.1.18-4_mipsel.deb
+ 44d1f7279db85e98bfe8666397f898ef 555674 science optional samtools_0.1.19-1_mipsel.deb
+ 6d14454cb9202d9a7fcf084e040f43a8 131464 libdevel optional libbam-dev_0.1.19-1_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_mipsel.deb
+samtools_0.1.19-1_mipsel.deb
────────────────────────────
new debian package, version 2.0.
- size 528822 bytes: control archive= 1809 bytes.
+ size 555674 bytes: control archive= 1937 bytes.
32 bytes, 1 lines conffiles
793 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1115
+ Installed-Size: 1439
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -683,74 +727,79 @@ samtools_0.1.18-4_mipsel.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126583 2012-12-23 05:03 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2012-12-23 05:03 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 05:03 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 05:03 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 05:03 ./usr/share/samtools/varfilter.py
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/bin/
--rwxr-xr-x root/root 155204 2012-12-23 05:03 ./usr/bin/bcftools
--rwxr-xr-x root/root 29168 2012-12-23 05:03 ./usr/bin/razip
--rwxr-xr-x root/root 440320 2012-12-23 05:03 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/samtools/
--rwxr-xr-x root/root 17692 2012-12-23 05:03 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 7472 2012-12-23 05:03 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 12432 2012-12-23 05:03 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9252 2012-12-23 05:03 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2012-12-23 05:03 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_mipsel.deb
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:23 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2013-03-30 09:23 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 09:23 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 09:23 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/samtools/
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:24 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/bin/
+-rwxr-xr-x root/root 176252 2013-03-30 09:24 ./usr/bin/bcftools
+-rwxr-xr-x root/root 31780 2013-03-30 09:24 ./usr/bin/razip
+-rwxr-xr-x root/root 483460 2013-03-30 09:24 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/samtools/
+-rwxr-xr-x root/root 18508 2013-03-30 09:24 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 18192 2013-03-30 09:24 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 207416 2013-03-30 09:24 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 14224 2013-03-30 09:24 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 10068 2013-03-30 09:24 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:23 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_mipsel.deb
──────────────────────────────
new debian package, version 2.0.
- size 165950 bytes: control archive= 942 bytes.
+ size 131464 bytes: control archive= 924 bytes.
713 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 467
+ Installed-Size: 441
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -763,25 +812,25 @@ libbam-dev_0.1.18-4_mipsel.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/lib/
--rw-r--r-- root/root 335698 2012-12-23 05:03 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 05:03 ./usr/include/samtools/
--rw-r--r-- root/root 24732 2012-12-23 04:59 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/
+-rw-r--r-- root/root 328990 2013-03-30 09:24 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/samtools/
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -795,37 +844,39 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-3334b19a-a1bc-4c57-a8db-8e6c3252fce1/build/buildd-samtools_0.1.18-4-mipsel-qoNf_Z
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ca64eee5-03d6-4a10-836c-decf0e5e9b54/build/buildd-samtools_0.1.19-1-mipsel-muFrrg
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 30 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- bash-completion* cdbs* debhelper* diffstat* file* gettext* gettext-base*
- groff-base* html2text* intltool-debian* libasprintf-dev* libasprintf0c2*
- libcroco3* libffi5* libgettextpo-dev* libgettextpo0* libglib2.0-0*
- libmagic1* libncurses5-dev* libpipeline1* libtinfo-dev* libunistring0*
- libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 27 to remove and 30 not upgraded.
-After this operation, 29.2 MB disk space will be freed.
-(Reading database ... 12988 files and directories currently installed.)
+ bash-completion* bsdmainutils* cdbs* debhelper* diffstat* file* gettext*
+ gettext-base* groff-base* html2text* intltool-debian* libasprintf-dev*
+ libasprintf0c2* libcroco3* libffi5* libgettextpo-dev* libgettextpo0*
+ libglib2.0-0* libmagic1* libncurses5-dev* libpcre3* libpipeline1*
+ libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
+0 upgraded, 0 newly installed, 29 to remove and 2 not upgraded.
+After this operation, 30.2 MB disk space will be freed.
+(Reading database ... 13074 files and directories currently installed.)
Removing bash-completion ...
Purging configuration files for bash-completion ...
-Removing cdbs ...
-Removing debhelper ...
Removing quilt ...
Purging configuration files for quilt ...
+Removing debhelper ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing bsdmainutils ...
+Purging configuration files for bsdmainutils ...
+Removing cdbs ...
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 ...
@@ -843,6 +894,8 @@ Removing libgettextpo0:mipsel ...
Removing libmagic1:mipsel ...
Purging configuration files for libmagic1:mipsel ...
Removing libncurses5-dev ...
+Removing libpcre3:mipsel ...
+Purging configuration files for libpcre3:mipsel ...
Removing libpipeline1:mipsel ...
Purging configuration files for libpipeline1:mipsel ...
Removing libtinfo-dev:mipsel ...
@@ -857,19 +910,19 @@ Removing zlib1g-dev:mipsel ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 11016
-Build-Time: 320
+Build-Space: 12852
+Build-Time: 342
Distribution: sid
-Install-Time: 54
-Job: samtools_0.1.18-4
+Install-Time: 58
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 496
-Source-Version: 0.1.18-4
-Space: 11016
+Package-Time: 479
+Source-Version: 0.1.19-1
+Space: 12852
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0504
-Build needed 00:08:16, 11016k disc space
-Signature with key '8C9FAB20' requested:
+Finished at 20130330-0924
+Build needed 00:07:59, 12852k disc space
+Signature with key '4A2D13C7' requested:
diff --git a/powerpc.log b/powerpc.log
index 5324f13..97c86bd 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,62 +1,62 @@
-From buildd at porpora.debian.org Sun Dec 23 04:56:24 2012
-Return-path: <buildd at porpora.debian.org>
+From buildd at praetorius.debian.org Sat Mar 30 09:16:10 2013
+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=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 porpora.debian.org>)
- id 1Tmdbs-0007LE-7V
- for logs at buildd.debian.org; Sun, 23 Dec 2012 04:56:24 +0000
-Received: from porpora.ynic.york.ac.uk ([144.32.168.78]
- helo=porpora.debian.org)
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1ULrtR-0002L4-GV
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:16:09 +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=porpora.debian.org, EMAIL=hostmaster at porpora.debian.org (verified)
+ 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 porpora.debian.org>)
- id 1Tmdbr-00082h-58; Sun, 23 Dec 2012 04:56:23 +0000
-Received: from buildd by porpora.debian.org with local (Exim 4.72)
- (envelope-from <buildd at porpora.debian.org>)
- id 1Tmdbq-0003nE-9Q; Sun, 23 Dec 2012 04:56:22 +0000
-Message-Id: <E1Tmdbq-0003nE-9Q at porpora.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sun, 23 Dec 2012 04:56:22 +0000
-From: buildd on porpora <buildd at porpora.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.18-4 on powerpc (dist=sid)
-Key-Id: EABF3A35
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1ULrtQ-0001WL-61; Sat, 30 Mar 2013 09:16:08 +0000
+Received: from buildd by praetorius.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at praetorius.debian.org>)
+ id 1ULrtP-0002Ne-3Z; Sat, 30 Mar 2013 09:16:07 +0000
+Date: Sat, 30 Mar 2013 09:16:07 +0000
+Message-Id: <E1ULrtP-0002Ne-3Z 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_0.1.19-1 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 porpora.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (powerpc) 23 Dec 2012 04:53 ║
+║ samtools 0.1.19-1 (powerpc) 30 Mar 2013 09:12 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [227 kB]
-Get:2 http://incoming.debian.org unstable InRelease [227 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6458 kB]
-Get:4 http://ftp.uk.debian.org unstable/contrib Sources [53.0 kB]
-Get:5 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
-Get:6 http://ftp.uk.debian.org unstable/main powerpc Packages [6131 kB]
-Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:8 http://ftp.uk.debian.org unstable/contrib powerpc Packages [36.8 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://incoming.debian.org unstable/main powerpc Packages [6131 kB]
-Get:12 http://incoming.debian.org unstable/contrib powerpc Packages [36.8 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 26.1 MB in 28s (933 kB/s)
+Get:1 http://ftp.se.debian.org unstable InRelease [236 kB]
+Get:2 http://ftp.se.debian.org unstable/main Sources [6484 kB]
+Get:3 http://incoming.debian.org unstable InRelease [236 kB]
+Get:4 http://ftp.se.debian.org unstable/contrib Sources [51.0 kB]
+Get:5 http://ftp.se.debian.org unstable/non-free Sources [101 kB]
+Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [6144 kB]
+Get:7 http://incoming.debian.org buildd-unstable InRelease [110 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:9 http://ftp.se.debian.org unstable/contrib powerpc Packages [35.8 kB]
+Get:10 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:12 http://incoming.debian.org unstable/main powerpc Packages [6144 kB]
+Get:13 http://incoming.debian.org unstable/contrib powerpc Packages [35.8 kB]
+Get:14 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:15 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:16 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:17 http://incoming.debian.org buildd-unstable/main powerpc Packages [14.0 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib powerpc Packages [14 B]
+Fetched 26.2 MB in 21s (1199 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,12 +76,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (196 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 2s (283 kB/s)
Download complete and in download only mode
Check arch
@@ -101,12 +101,12 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 35 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 35 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -115,9 +115,9 @@ 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 (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.12)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
+bash: already installed (4.2-5.1)
coreutils: already installed (8.13-3.2)
dash: already installed (0.5.7-3)
debianutils: already installed (4.3.4)
@@ -127,19 +127,19 @@ e2fsprogs: already installed (1.42.5-1)
findutils: already installed (4.4.2-5)
grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-15)
+perl-base: already installed (5.14.2-16)
sed: already installed (4.2.1-10)
login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-32)
-sysvinit: already installed (2.88dsf-32)
+sysvinit-utils: already installed (2.88dsf-35)
+sysvinit: already installed (2.88dsf-35)
tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.2)
-mount: already installed (2.20.1-5.2)
-util-linux: already installed (2.20.1-5.2)
-libc6-dev: already installed (2.13-36)
+bsdutils: already installed (1:2.20.1-5.3)
+mount: already installed (2.20.1-5.3)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-37)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
@@ -174,47 +174,47 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 35 not upgraded.
-Need to get 10.5 MB of archives.
+0 upgraded, 29 newly installed, 0 to remove and 49 not upgraded.
+Need to get 10.0 MB of archives.
After this operation, 29.8 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.2-1 [39.0 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-9 [1179 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.3 [208 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.3-3 [872 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-10 [27.4 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.11-2 [201 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 1:8.31-1 [246 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-7 [852 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.33.12+really2.32.4-3 [1713 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.6-2 [121 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-10 [138 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.11-2 [51.7 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-10 [130 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev powerpc 0.18.1.1-10 [26.9 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev powerpc 0.18.1.1-10 [184 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-10 [1766 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev powerpc 5.9-10 [105 kB]
-Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-10 [211 kB]
-Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.7.dfsg-13 [213 kB]
+Get:1 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.2-2 [39.0 kB]
+Get:2 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.22.2-1 [727 kB]
+Get:3 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 9.0.4 [210 kB]
+Get:4 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.3-3 [872 kB]
+Get:5 http://ftp.se.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp.se.debian.org/debian/ unstable/main libasprintf0c2 powerpc 0.18.1.1-10 [27.4 kB]
+Get:7 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 1:5.11-2.1 [201 kB]
+Get:8 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 1:8.31-2 [246 kB]
+Get:9 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-7+nmu1 [852 kB]
+Get:10 http://ftp.se.debian.org/debian/ unstable/main libffi5 powerpc 3.0.10-3 [25.5 kB]
+Get:11 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.33.12+really2.32.4-5 [1712 kB]
+Get:12 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.6-2 [121 kB]
+Get:13 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:14 http://ftp.se.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-10 [138 kB]
+Get:15 http://ftp.se.debian.org/debian/ unstable/main file powerpc 1:5.11-2.1 [51.7 kB]
+Get:16 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-10 [130 kB]
+Get:17 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
+Get:18 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:19 http://ftp.se.debian.org/debian/ unstable/main libasprintf-dev powerpc 0.18.1.1-10 [26.9 kB]
+Get:20 http://ftp.se.debian.org/debian/ unstable/main libgettextpo-dev powerpc 0.18.1.1-10 [184 kB]
+Get:21 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-10 [1766 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 9.20120909 [705 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 0.60-8 [381 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 10.5 MB in 1s (5887 kB/s)
+Fetched 10.0 MB in 1s (5075 kB/s)
Selecting previously unselected package libpipeline1:powerpc.
-(Reading database ... 10804 files and directories currently installed.)
-Unpacking libpipeline1:powerpc (from .../libpipeline1_1.2.2-1_powerpc.deb) ...
+(Reading database ... 10827 files and directories currently installed.)
+Unpacking libpipeline1:powerpc (from .../libpipeline1_1.2.2-2_powerpc.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_powerpc.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_powerpc.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_powerpc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_powerpc.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_powerpc.deb) ...
Selecting previously unselected package bash-completion.
@@ -222,15 +222,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:powerpc.
Unpacking libasprintf0c2:powerpc (from .../libasprintf0c2_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package libmagic1:powerpc.
-Unpacking libmagic1:powerpc (from .../libmagic1_5.11-2_powerpc.deb) ...
+Unpacking libmagic1:powerpc (from .../libmagic1_1%3a5.11-2.1_powerpc.deb) ...
Selecting previously unselected package libpcre3:powerpc.
-Unpacking libpcre3:powerpc (from .../libpcre3_1%3a8.31-1_powerpc.deb) ...
+Unpacking libpcre3:powerpc (from .../libpcre3_1%3a8.31-2_powerpc.deb) ...
Selecting previously unselected package libxml2:powerpc.
-Unpacking libxml2:powerpc (from .../libxml2_2.8.0+dfsg1-7_powerpc.deb) ...
+Unpacking libxml2:powerpc (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_powerpc.deb) ...
+Unpacking libglib2.0-0:powerpc (from .../libglib2.0-0_2.33.12+really2.32.4-5_powerpc.deb) ...
Selecting previously unselected package libcroco3:powerpc.
Unpacking libcroco3:powerpc (from .../libcroco3_0.6.6-2_powerpc.deb) ...
Selecting previously unselected package libunistring0:powerpc.
@@ -238,11 +238,11 @@ Unpacking libunistring0:powerpc (from .../libunistring0_0.9.3-5_powerpc.deb) ...
Selecting previously unselected package libgettextpo0:powerpc.
Unpacking libgettextpo0:powerpc (from .../libgettextpo0_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../file_5.11-2_powerpc.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_powerpc.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_powerpc.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
Selecting previously unselected package libasprintf-dev:powerpc.
@@ -264,30 +264,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:powerpc (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:powerpc (0.18.1.1-10) ...
-Setting up libmagic1:powerpc (5.11-2) ...
-Setting up libpcre3:powerpc (1:8.31-1) ...
-Setting up libxml2:powerpc (2.8.0+dfsg1-7) ...
+Setting up libmagic1:powerpc (1:5.11-2.1) ...
+Setting up libpcre3:powerpc (1:8.31-2) ...
+Setting up libxml2:powerpc (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:powerpc (3.0.10-3) ...
-Setting up libglib2.0-0:powerpc (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:powerpc (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:powerpc (0.6.6-2) ...
Setting up libunistring0:powerpc (0.9.3-5) ...
Setting up libgettextpo0:powerpc (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:powerpc (0.18.1.1-10) ...
Setting up libgettextpo-dev:powerpc (0.18.1.1-10) ...
@@ -298,17 +298,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:powerpc (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 35 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.35-2
+Package versions: apt_0.9.7.7 base-files_7.1 base-passwd_3.5.26 bash_4.2-5.1 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.48 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-14 gcc_4:4.6.3-8 gcc-4.4-base_4.4.7-3 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-35 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.7 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.35-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-16 perl-base_5.14.2-16 perl-modules_5.14.2-16 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-35 sysvinit_2.88dsf-35 sysvinit-utils_2.88dsf-35 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -319,16 +319,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -338,44 +337,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -388,11 +384,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -401,139 +397,176 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -555,11 +588,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samt
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -587,7 +620,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -595,8 +628,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -612,7 +645,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -624,7 +657,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -639,79 +672,78 @@ 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_0.1.18-4_powerpc.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_powerpc.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../samtools_0.1.18-4_powerpc.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_powerpc.deb'.
+ dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../samtools_0.1.19-1_powerpc.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0456
+Build finished at 20130330-0916
-samtools_0.1.18-4_powerpc.changes:
+samtools_0.1.19-1_powerpc.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: powerpc
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
-Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
- .
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- 7bb08ccce05f69ee084da8679dccab57311a93ee 514514 samtools_0.1.18-4_powerpc.deb
- e2f269d69d62772bcc2c66f70580ffef7a4384f2 150306 libbam-dev_0.1.18-4_powerpc.deb
+ bc79b2d19863315cae32a48cdf70c20ba475e82c 536000 samtools_0.1.19-1_powerpc.deb
+ 0faf6c3cec234f37a77e07ced7bbfe098d26f957 116042 libbam-dev_0.1.19-1_powerpc.deb
Checksums-Sha256:
- 6193e557996e6254ab95be4b513423f5c798324bdaa583039941d7fb8d8c6408 514514 samtools_0.1.18-4_powerpc.deb
- 86c8d69e99f4aea11551af696ee8bae614459446722c4e4e7f9f9d71983fca62 150306 libbam-dev_0.1.18-4_powerpc.deb
+ aae2820e92c0f383e1a5f47e380d8961cc415d93326d0d628d8e0740f2115ace 536000 samtools_0.1.19-1_powerpc.deb
+ 247e56f8c2ce2d645706ce2b775d50c83fe61e4986943f1c5748310d1baa924a 116042 libbam-dev_0.1.19-1_powerpc.deb
Files:
- 53d98ebf397242f3efd11db5b21a124f 514514 science optional samtools_0.1.18-4_powerpc.deb
- 40ba965ac8b1fdc393ea53c9a1c2d3ac 150306 libdevel optional libbam-dev_0.1.18-4_powerpc.deb
+ 11edcf731d65e17ea5527d9acd7f5334 536000 science optional samtools_0.1.19-1_powerpc.deb
+ 26e39ba519db79a253337b6d9fe4c237 116042 libdevel optional libbam-dev_0.1.19-1_powerpc.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_powerpc.deb
+samtools_0.1.19-1_powerpc.deb
─────────────────────────────
new debian package, version 2.0.
- size 514514 bytes: control archive= 1806 bytes.
+ size 536000 bytes: control archive= 1931 bytes.
32 bytes, 1 lines conffiles
794 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1022
+ Installed-Size: 1319
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -724,74 +756,79 @@ samtools_0.1.18-4_powerpc.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/bin/
--rwxr-xr-x root/root 130976 2012-12-23 04:56 ./usr/bin/bcftools
--rwxr-xr-x root/root 375144 2012-12-23 04:56 ./usr/bin/samtools
--rwxr-xr-x root/root 25484 2012-12-23 04:56 ./usr/bin/razip
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/samtools/
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 04:56 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/man/man1/
--rw-r--r-- root/root 9890 2012-12-23 04:56 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2012-12-23 04:56 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/samtools/
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 126583 2012-12-23 04:55 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2012-12-23 04:56 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/lib/samtools/
--rwxr-xr-x root/root 18528 2012-12-23 04:56 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8036 2012-12-23 04:56 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7348 2012-12-23 04:56 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 7348 2012-12-23 04:56 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 11080 2012-12-23 04:56 ./usr/lib/samtools/md5fa
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2012-12-23 04:56 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_powerpc.deb
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/bin/
+-rwxr-xr-x root/root 153760 2013-03-30 09:15 ./usr/bin/bcftools
+-rwxr-xr-x root/root 26228 2013-03-30 09:15 ./usr/bin/razip
+-rwxr-xr-x root/root 419208 2013-03-30 09:15 ./usr/bin/samtools
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/lib/samtools/
+-rwxr-xr-x root/root 175244 2013-03-30 09:15 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 17908 2013-03-30 09:15 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 9700 2013-03-30 09:15 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13796 2013-03-30 09:15 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 22064 2013-03-30 09:15 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9700 2013-03-30 09:15 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9672 2013-03-30 09:15 ./usr/lib/samtools/md5sum-lite
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/man/man1/
+-rw-r--r-- root/root 10654 2013-03-30 09:15 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2013-03-30 09:15 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:15 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 1966 2013-03-30 09:15 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/samtools/
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:15 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:15 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_powerpc.deb
───────────────────────────────
new debian package, version 2.0.
- size 150306 bytes: control archive= 941 bytes.
+ size 116042 bytes: control archive= 926 bytes.
714 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: powerpc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 409
+ Installed-Size: 385
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -804,25 +841,25 @@ libbam-dev_0.1.18-4_powerpc.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/include/samtools/
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 24732 2012-12-23 04:54 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2012-12-23 04:56 ./usr/lib/
--rw-r--r-- root/root 276306 2012-12-23 04:56 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/lib/
+-rw-r--r-- root/root 271770 2013-03-30 09:15 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/include/samtools/
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -836,7 +873,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-28506304-0b95-400a-b3e5-77aab2cbf363/build/buildd-samtools_0.1.18-4-powerpc-W3B6pZ
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-4da4802a-fbb1-47e3-b713-2d08e5d84ffc/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -844,18 +881,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 10560
-Build-Time: 91
+Build-Space: 12352
+Build-Time: 88
Distribution: sid
Install-Time: 57
-Job: samtools_0.1.18-4
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 192
-Source-Version: 0.1.18-4
-Space: 10560
+Package-Time: 184
+Source-Version: 0.1.19-1
+Space: 12352
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0456
-Build needed 00:03:12, 10560k disc space
-Signature with key 'EABF3A35' requested:
+Finished at 20130330-0916
+Build needed 00:03:04, 12352k disc space
+Signature with key '0E6E7223' requested:
+
diff --git a/s390.log b/s390.log
index 29de407..a3ec27a 100644
--- a/s390.log
+++ b/s390.log
@@ -1,62 +1,65 @@
-From buildd at zemlinsky.debian.org Sun Dec 23 04:58:10 2012
-Return-path: <buildd at zemlinsky.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+From buildd at zandonai.debian.org Sat Mar 30 09:17:45 2013
+Return-path: <buildd at zandonai.debian.org>
+Received: from muffat.debian.org ([206.12.19.146])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1Tmdda-0007ZI-3r
- for logs at buildd.debian.org; Sun, 23 Dec 2012 04:58:10 +0000
-Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
+ (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
+ id 1ULruy-0002aJ-S8
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:17:45 +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=zemlinsky.debian.org,
- EMAIL=hostmaster at zemlinsky.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1TmddZ-00083S-1Z; Sun, 23 Dec 2012 04:58:09 +0000
-Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
- (envelope-from <buildd at zemlinsky.debian.org>)
- id 1TmddY-0007r5-Dr; Sun, 23 Dec 2012 04:58:08 +0000
-Message-Id: <E1TmddY-0007r5-Dr at zemlinsky.debian.org>
+ CN=zandonai.debian.org,
+ EMAIL=hostmaster at zandonai.debian.org (verified)
+ by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at zandonai.debian.org>)
+ id 1ULruv-0007Rf-J7; Sat, 30 Mar 2013 09:17:42 +0000
+Received: from buildd by zandonai.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at zandonai.debian.org>)
+ id 1ULrut-0004a6-2O; Sat, 30 Mar 2013 09:17:39 +0000
+Message-Id: <E1ULrut-0004a6-2O 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: Sun, 23 Dec 2012 04:58:08 +0000
-From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
+Date: Sat, 30 Mar 2013 09:17:39 +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_0.1.18-4 on s390 (dist=sid)
-Key-Id: E0AC2C92
+Subject: Log for successful build of samtools_0.1.19-1 on s390 (dist=sid)
+Key-Id: B6E651D0
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (s390) 23 Dec 2012 04:56 ║
+║ samtools 0.1.19-1 (s390) 30 Mar 2013 09:16 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: s390
-Get:1 http://ftp-stud.hs-esslingen.de unstable InRelease [227 kB]
-Get:2 http://ftp-stud.hs-esslingen.de unstable/main Sources [6458 kB]
-Get:3 http://incoming.debian.org unstable InRelease [227 kB]
-Get:4 http://ftp-stud.hs-esslingen.de unstable/contrib Sources [53.0 kB]
-Get:5 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
-Get:6 http://ftp-stud.hs-esslingen.de unstable/main s390 Packages [6028 kB]
-Ign http://incoming.debian.org InRelease
-Get:7 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:8 http://ftp-stud.hs-esslingen.de unstable/contrib s390 Packages [36.3 kB]
-Get:9 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:10 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://incoming.debian.org unstable/main s390 Packages [6028 kB]
-Get:12 http://incoming.debian.org unstable/contrib s390 Packages [36.3 kB]
-Get:13 http://incoming.debian.org Release.gpg [836 B]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 25.9 MB in 22s (1166 kB/s)
+Get:1 http://ftp.de.debian.org unstable Release.gpg [836 B]
+Get:2 http://ftp.de.debian.org unstable Release [235 kB]
+Get:3 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:4 http://ftp.de.debian.org unstable/main Sources [6484 kB]
+Get:5 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:6 http://incoming.debian.org unstable Release [235 kB]
+Get:7 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:9 http://ftp.de.debian.org unstable/contrib Sources [51.0 kB]
+Get:10 http://ftp.de.debian.org unstable/non-free Sources [101 kB]
+Get:11 http://ftp.de.debian.org unstable/main s390 Packages [6043 kB]
+Get:12 http://ftp.de.debian.org unstable/contrib s390 Packages [35.3 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:15 http://incoming.debian.org unstable/main s390 Packages [6043 kB]
+Get:16 http://incoming.debian.org unstable/contrib s390 Packages [35.3 kB]
+Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:20 http://incoming.debian.org buildd-unstable/main s390 Packages [13.1 kB]
+Get:21 http://incoming.debian.org buildd-unstable/contrib s390 Packages [14 B]
+Fetched 26.0 MB in 24s (1072 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,12 +79,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (313 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (370 kB/s)
Download complete and in download only mode
Check arch
@@ -94,56 +97,57 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 58 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 58 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.11)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
-coreutils: already installed (8.13-3.2)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.20-3)
dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.3)
-diffutils: already installed (1:3.2-6)
-dpkg: already installed (1.16.8)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-4)
-grep: already installed (2.12-2)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-12)
+perl-base: already installed (5.14.2-20)
sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-32)
-sysvinit: already installed (2.88dsf-32)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.1)
-mount: already installed (2.20.1-5.1)
-util-linux: already installed (2.20.1-5.1)
-libc6-dev: already installed (2.13-35)
-gcc: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-7 >= 4:4.4.3 is satisfied)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
+gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.8 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120909
bash-completion: missing
@@ -174,47 +178,47 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 58 not upgraded.
-Need to get 10.7 MB of archives.
-After this operation, 30.1 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390 1.2.2-1 [40.6 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390 1.21-9 [1148 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390 9.0.3 [213 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390 2.6.3-3 [884 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-10 [27.2 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390 5.11-2 [205 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390 1:8.31-1 [253 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-7 [892 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390 2.33.12+really2.32.4-3 [1785 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390 0.6.6-2 [128 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390 0.18.1.1-10 [147 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390 5.11-2 [52.0 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390 0.18.1.1-10 [152 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390 0.18.1.1-10 [27.1 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390 0.18.1.1-10 [182 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390 0.18.1.1-10 [1800 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
-Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
-Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 kB]
-Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
-Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390 1:1.2.7.dfsg-13 [215 kB]
+0 upgraded, 29 newly installed, 0 to remove and 6 not upgraded.
+Need to get 10.2 MB of archives.
+After this operation, 30.0 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.2-2 [40.6 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.22.2-1 [713 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 9.0.4 [214 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.3-3 [884 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-10 [27.2 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 1:5.11-2.1 [205 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 1:8.31-2 [253 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-7+nmu1 [892 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.33.12+really2.32.4-5 [1788 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.6-2 [128 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390 0.18.1.1-10 [147 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main file s390 1:5.11-2.1 [52.1 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-10 [152 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main libasprintf-dev s390 0.18.1.1-10 [27.1 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main libgettextpo-dev s390 0.18.1.1-10 [182 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-10 [1800 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
+Get:26 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
+Get:27 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 kB]
+Get:28 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
+Get:29 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 10.7 MB in 1s (5921 kB/s)
+Fetched 10.2 MB in 3s (3278 kB/s)
Selecting previously unselected package libpipeline1:s390.
-(Reading database ... 10815 files and directories currently installed.)
-Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.2-1_s390.deb) ...
+(Reading database ... 10740 files and directories currently installed.)
+Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.2-2_s390.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_s390.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_s390.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_s390.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_s390.deb) ...
Selecting previously unselected package bash-completion.
@@ -222,15 +226,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:s390.
Unpacking libasprintf0c2:s390 (from .../libasprintf0c2_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package libmagic1:s390.
-Unpacking libmagic1:s390 (from .../libmagic1_5.11-2_s390.deb) ...
+Unpacking libmagic1:s390 (from .../libmagic1_1%3a5.11-2.1_s390.deb) ...
Selecting previously unselected package libpcre3:s390.
-Unpacking libpcre3:s390 (from .../libpcre3_1%3a8.31-1_s390.deb) ...
+Unpacking libpcre3:s390 (from .../libpcre3_1%3a8.31-2_s390.deb) ...
Selecting previously unselected package libxml2:s390.
-Unpacking libxml2:s390 (from .../libxml2_2.8.0+dfsg1-7_s390.deb) ...
+Unpacking libxml2:s390 (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_s390.deb) ...
+Unpacking libglib2.0-0:s390 (from .../libglib2.0-0_2.33.12+really2.32.4-5_s390.deb) ...
Selecting previously unselected package libcroco3:s390.
Unpacking libcroco3:s390 (from .../libcroco3_0.6.6-2_s390.deb) ...
Selecting previously unselected package libunistring0:s390.
@@ -238,11 +242,11 @@ Unpacking libunistring0:s390 (from .../libunistring0_0.9.3-5_s390.deb) ...
Selecting previously unselected package libgettextpo0:s390.
Unpacking libgettextpo0:s390 (from .../libgettextpo0_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_s390.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_s390.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
Selecting previously unselected package libasprintf-dev:s390.
@@ -264,30 +268,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:s390 (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:s390 (0.18.1.1-10) ...
-Setting up libmagic1:s390 (5.11-2) ...
-Setting up libpcre3:s390 (1:8.31-1) ...
-Setting up libxml2:s390 (2.8.0+dfsg1-7) ...
+Setting up libmagic1:s390 (1:5.11-2.1) ...
+Setting up libpcre3:s390 (1:8.31-2) ...
+Setting up libxml2:s390 (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:s390 (3.0.10-3) ...
-Setting up libglib2.0-0:s390 (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:s390 (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:s390 (0.6.6-2) ...
Setting up libunistring0:s390 (0.9.3-5) ...
Setting up libgettextpo0:s390 (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:s390 (0.18.1.1-10) ...
Setting up libgettextpo-dev:s390 (0.18.1.1-10) ...
@@ -298,17 +302,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:s390 (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 58 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.8 g++-4.6_4.6.3-9 gcc-4.6_4.6.3-9 libc6-dev_2.13-35 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 linux-libc-dev_3.2.23-1
-Package versions: apt_0.9.7.4 base-files_6.11 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.1 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.2 cpp_4:4.6.3-7 cpp-4.6_4.6.3-9 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.3 diffstat_1.55-3 diffutils_1:3.2-6 dpkg_1.16.8 dpkg-dev_1.16.8 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-4 g++_4:4.6.3-7 g++-4.6_4.6.3-9 gcc_4:4.6.3-7 gcc-4.4-base_4.4.7-2 gcc-4.6_4.6.3-9 gcc-4.6-base_4.6.3-9 gcc-4.7-base_4.7.1-7 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-4+b1 gpgv_1.4.12-4+b1 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-32 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.4 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.1 libbz2-1.0_1.0.6-4 libc-bin_2.13-35 libc-dev-bin_2.13-35 libc6_2.13-35 libc6-dev_2.13-35 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.8 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.1-7 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.1-7 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.1 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.1-7 libstdc++6-4.6-dev_4.6.3-9 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.1 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.23-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.1 multiarch-support_2.13-35 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-32 sysvinit_2.88dsf-32 sysvinit-utils_2.88dsf-32 tar_1.26-4 tzdata_2012e-1 util-linux_2.20.1-5.1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -319,16 +323,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -338,44 +341,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -388,11 +388,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -401,125 +401,167 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
-seqtk.c: In function 'stk_comp':
-seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390-TTe7pN/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -541,11 +583,11 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtool
../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
+gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary-arch
test -x debian/rules
@@ -573,7 +615,7 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools ./ChangeLog
+dh_installchangelogs -psamtools NEWS
dh_installudev -psamtools
dh_lintian -psamtools
dh_bugfiles -psamtools
@@ -581,8 +623,8 @@ dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_bash-completion
dh_bash-completion: file-list parsing failed, installing as proper snippet
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
@@ -598,7 +640,7 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev ./ChangeLog
+dh_installchangelogs -plibbam-dev NEWS
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
dh_bugfiles -plibbam-dev
@@ -610,7 +652,7 @@ dh_strip -psamtools
dh_compress -psamtools -X .bam
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.18-4-s390-fy7gJA/samtools-0.1.18/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev -X .bam
dh_fixperms -plibbam-dev
@@ -625,79 +667,78 @@ 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_0.1.18-4_s390.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_s390.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-4_s390.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../samtools_0.1.18-4_s390.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_s390.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.19-1_s390.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.18
+ dpkg-source --after-build samtools-0.1.19
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0458
+Build finished at 20130330-0917
-samtools_0.1.18-4_s390.changes:
+samtools_0.1.19-1_s390.changes:
Format: 1.8
-Date: Fri, 21 Dec 2012 12:09:18 -0500
+Date: Sat, 30 Mar 2013 17:31:47 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: s390
-Version: 0.1.18-4
+Version: 0.1.19-1
Distribution: sid
Urgency: low
-Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
-Changed-By: Dominique Belhachemi <domibel at debian.org>
+Maintainer: s390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.18-4) unstable; urgency=low
- .
- [Charles Plessy]
- debian/copyright: Normalised with config-model
- added bash completion
- Build-depend on Debhelper 9
- Pass build flaggs set by dpkg-buildflags via Debhelper
- Moved DOI and PubMed to the Reference namespace
- Do not compress the example binary alignment file
- Mention ‘SAMtools’ in libbam-dev's description
- .
- [Andreas Tille]
- debian/upstream: replaced BibTeX entry
+ samtools (0.1.19-1) unstable; urgency=low
.
- [Dominique Belhachemi]
- added patch to fix float tag bug (upstream bug 71)
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
Checksums-Sha1:
- b2d769caeb5b8884842ba76182403fdc4dc9c821 528596 samtools_0.1.18-4_s390.deb
- 2c66f9597dd415f351e13a1a5c745041ee1cbe63 156368 libbam-dev_0.1.18-4_s390.deb
+ b3bd6cd9c24ec4850474f6634a58edc446ef7442 558568 samtools_0.1.19-1_s390.deb
+ ad9c7a43cb6be3006c9786bcf3e0a5b172a484c0 124686 libbam-dev_0.1.19-1_s390.deb
Checksums-Sha256:
- 4f7784b66c2ac85aeb4c3d8835c063dd85621dcee62e179ccd340f96496b9d63 528596 samtools_0.1.18-4_s390.deb
- 61d0f830db9ff217e0c41071690eed9513f75a2708ef83cde61ae66e0e57e756 156368 libbam-dev_0.1.18-4_s390.deb
+ 193cd1de13932b41c6b5cb54c63457c7fdcb67683ed01cc25a3d9b38f7ae8096 558568 samtools_0.1.19-1_s390.deb
+ f575369d52f329061d6f354b1a2bf20603572c68ecb65105ef1c2f3ffb6f738d 124686 libbam-dev_0.1.19-1_s390.deb
Files:
- a72c1363daaa7998ff9cf38f647d2cbb 528596 science optional samtools_0.1.18-4_s390.deb
- 31be5fb71631d5c3fb84dfa647c93291 156368 libdevel optional libbam-dev_0.1.18-4_s390.deb
+ e6a78223f763b1c03642bf878a27185e 558568 science optional samtools_0.1.19-1_s390.deb
+ 153c42643e10f72b7617f80ce957c285 124686 libdevel optional libbam-dev_0.1.19-1_s390.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.18-4_s390.deb
+samtools_0.1.19-1_s390.deb
──────────────────────────
new debian package, version 2.0.
- size 528596 bytes: control archive= 1811 bytes.
+ size 558568 bytes: control archive= 1932 bytes.
32 bytes, 1 lines conffiles
791 bytes, 16 lines control
- 2450 bytes, 37 lines md5sums
+ 2766 bytes, 42 lines md5sums
Package: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1075
+ Installed-Size: 1398
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Suggests: python
Section: science
@@ -710,74 +751,79 @@ samtools_0.1.18-4_s390.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2012-12-23 04:58 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2012-12-23 03:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2012-12-23 03:33 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 786 2011-04-22 03:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126583 2012-12-23 04:57 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/samtools/
--rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 15707 2011-07-07 02:59 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2012-12-23 04:58 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 4996 2010-11-17 04:16 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 18572 2011-03-22 03:09 ./usr/share/samtools/export2sam.pl
-drwxr-xr-x root/root 0 2012-12-23 04:57 ./usr/share/man/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2012-12-23 04:57 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 9890 2012-12-23 04:57 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/bin/
--rwxr-xr-x root/root 416744 2012-12-23 04:58 ./usr/bin/samtools
--rwxr-xr-x root/root 141452 2012-12-23 04:58 ./usr/bin/bcftools
--rwxr-xr-x root/root 27584 2012-12-23 04:58 ./usr/bin/razip
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/lib/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/lib/samtools/
--rwxr-xr-x root/root 17340 2012-12-23 04:58 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 7596 2012-12-23 04:58 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8424 2012-12-23 04:58 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 11488 2012-12-23 04:58 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7596 2012-12-23 04:58 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./etc/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-12-23 03:33 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2012-12-23 04:58 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.18-4_s390.deb
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/bin/
+-rwxr-xr-x root/root 165852 2013-03-30 09:17 ./usr/bin/bcftools
+-rwxr-xr-x root/root 464120 2013-03-30 09:17 ./usr/bin/samtools
+-rwxr-xr-x root/root 30216 2013-03-30 09:17 ./usr/bin/razip
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/samtools/
+-rwxr-xr-x root/root 13680 2013-03-30 09:17 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17796 2013-03-30 09:17 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 9592 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 9592 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 9556 2013-03-30 09:17 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 17868 2013-03-30 09:17 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 199656 2013-03-30 09:17 ./usr/lib/samtools/bamcheck
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/man1/
+-rw-r--r-- root/root 10654 2013-03-30 09:17 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2013-03-30 09:17 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/samtools/
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:17 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1966 2013-03-30 09:17 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 126580 2013-03-30 09:17 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_s390.deb
────────────────────────────
new debian package, version 2.0.
- size 156368 bytes: control archive= 943 bytes.
+ size 124686 bytes: control archive= 922 bytes.
711 bytes, 17 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.18-4
+ Version: 0.1.19-1
Architecture: s390
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 421
+ Installed-Size: 399
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -790,25 +836,25 @@ libbam-dev_0.1.18-4_s390.deb
.
This library is part of SAMtools.
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/doc/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 2067 2012-12-23 03:33 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5522 2012-12-23 03:33 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 33578 2011-03-01 19:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10122 2011-09-02 16:58 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/include/
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/include/samtools/
--rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2625 2010-11-17 04:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 4617 2011-04-10 22:33 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 24732 2012-12-23 04:57 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2011-03-01 19:50 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2012-12-23 04:58 ./usr/lib/
--rw-r--r-- root/root 289042 2012-12-23 04:58 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/samtools/
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
+-rw-r--r-- root/root 286026 2013-03-30 09:17 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -822,7 +868,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-s390-sbuild-5192ef59-16ac-48fe-9a5f-9585e6c01c45/build/buildd-samtools_0.1.18-4-s390-fy7gJA
+Purging /var/lib/schroot/mount/sid-s390-sbuild-296b5c29-f621-4e79-8986-bd8896aed292/build/buildd-samtools_0.1.19-1-s390-TTe7pN
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -830,80 +876,83 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 11148
-Build-Time: 60
+Build-Space: 13264
+Build-Time: 34
Distribution: sid
-Install-Time: 16
-Job: samtools_0.1.18-4
+Install-Time: 11
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 104
-Source-Version: 0.1.18-4
-Space: 11148
+Package-Time: 80
+Source-Version: 0.1.19-1
+Space: 13264
Status: successful
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0458
-Build needed 00:01:44, 11148k disc space
-Signature with key 'E0AC2C92' requested:
-From buildd at zemlinsky.debian.org Sun Dec 23 04:56:12 2012
+Finished at 20130330-0917
+Build needed 00:01:20, 13264k disc space
+Signature with key 'B6E651D0' requested:
+From buildd at zemlinsky.debian.org Sat Mar 30 09:17:41 2013
Return-path: <buildd at zemlinsky.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from muffat.debian.org ([206.12.19.146])
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)
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
(Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1Tmdbg-0007GK-Cf
- for logs at buildd.debian.org; Sun, 23 Dec 2012 04:56:12 +0000
-Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
+ id 1ULruv-0002ZT-20
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:17:41 +0000
+Received: from zemlinsky.debian.org ([129.143.160.6])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zemlinsky.debian.org,
EMAIL=hostmaster at zemlinsky.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1Tmdbf-0007z3-9r; Sun, 23 Dec 2012 04:56:11 +0000
+ by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1ULruq-0007Ra-Sh; Sat, 30 Mar 2013 09:17:37 +0000
Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
(envelope-from <buildd at zemlinsky.debian.org>)
- id 1Tmdbe-00075S-0j; Sun, 23 Dec 2012 04:56:10 +0000
-Message-Id: <E1Tmdbe-00075S-0j at zemlinsky.debian.org>
+ id 1ULruo-0004v0-E5; Sat, 30 Mar 2013 09:17:34 +0000
+Message-Id: <E1ULruo-0004v0-E5 at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sun, 23 Dec 2012 04:56:09 +0000
+Date: Sat, 30 Mar 2013 09:17:34 +0000
From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-4 on s390x (dist=sid)
-Key-Id: 6A3F7E2B
+Subject: Log for successful build of samtools_0.1.19-1 on s390x (dist=sid)
+Key-Id: 52DC96B8
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (s390x) 23 Dec 2012 04:54 ║
+║ samtools 0.1.19-1 (s390x) 30 Mar 2013 09:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: s390x
-Hit http://ftp-stud.hs-esslingen.de unstable InRelease
+Hit http://ftp-stud.hs-esslingen.de unstable Release.gpg
+Hit http://ftp-stud.hs-esslingen.de unstable Release
Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
-Hit http://incoming.debian.org unstable InRelease
-Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org unstable/main Sources
-Hit http://incoming.debian.org unstable/contrib Sources
-Get:2 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Hit http://incoming.debian.org unstable/main s390x Packages
-Hit http://incoming.debian.org unstable/contrib s390x Packages
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://incoming.debian.org Release [1141 B]
-Get:5 http://incoming.debian.org Sources [14.0 kB]
-Get:6 http://incoming.debian.org Packages [118 kB]
-Fetched 337 kB in 1s (176 kB/s)
+Get:2 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:3 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:4 http://incoming.debian.org unstable Release [235 kB]
+Get:5 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:7 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:8 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:9 http://incoming.debian.org unstable/main s390x Packages [6017 kB]
+Get:10 http://incoming.debian.org unstable/contrib s390x Packages [35.3 kB]
+Get:11 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:12 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:13 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:14 http://incoming.debian.org buildd-unstable/main s390x Packages [13.1 kB]
+Get:15 http://incoming.debian.org buildd-unstable/contrib s390x Packages [14 B]
+Fetched 13.2 MB in 9s (1356 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -923,12 +972,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (339 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (342 kB/s)
Download complete and in download only mode
Check arch
@@ -941,28 +990,59 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5+b1)
+build-essential: already installed (11.6)
fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-36)
+base-files: already installed (7.1)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.20-3)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-20)
+sed: already installed (4.2.1-10)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
@@ -979,6 +1059,9 @@ Installing positive dependencies: debhelper bash-completion cdbs quilt libncurse
Reading package lists...
Building dependency tree...
Reading state information...
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
@@ -997,26 +1080,26 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 36 not upgraded.
-Need to get 10.9 MB of archives.
+0 upgraded, 29 newly installed, 0 to remove and 11 not upgraded.
+Need to get 10.4 MB of archives.
After this operation, 31.6 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-1 [41.0 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-2 [41.1 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.22.2-1+b1 [738 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.4 [215 kB]
Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-3 [888 kB]
Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-10 [27.2 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-1 [259 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7 [901 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 1:5.11-2.1 [201 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-2 [259 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7+nmu1 [902 kB]
Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-3 [1798 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-5 [1798 kB]
Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-2 [129 kB]
Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-10 [158 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 1:5.11-2.1 [52.0 kB]
Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-10 [156 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390x 0.18.1.1-10 [26.8 kB]
Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390x 0.18.1.1-10 [195 kB]
@@ -1027,17 +1110,17 @@ Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.201
Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
-Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-8 [381 kB]
Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.9 MB in 1s (10.9 MB/s)
+Fetched 10.4 MB in 1s (9424 kB/s)
Selecting previously unselected package libpipeline1:s390x.
-(Reading database ... 10867 files and directories currently installed.)
-Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-1_s390x.deb) ...
+(Reading database ... 10875 files and directories currently installed.)
+Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-2_s390x.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1+b1_s390x.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_s390x.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_s390x.deb) ...
Selecting previously unselected package bash-completion.
@@ -1045,15 +1128,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:s390x.
Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package libmagic1:s390x.
-Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
+Unpacking libmagic1:s390x (from .../libmagic1_1%3a5.11-2.1_s390x.deb) ...
Selecting previously unselected package libpcre3:s390x.
-Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-1_s390x.deb) ...
+Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-2_s390x.deb) ...
Selecting previously unselected package libxml2:s390x.
-Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-7_s390x.deb) ...
+Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-7+nmu1_s390x.deb) ...
Selecting previously unselected package libffi5:s390x.
Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
Selecting previously unselected package libglib2.0-0:s390x.
-Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390x.deb) ...
+Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-5_s390x.deb) ...
Selecting previously unselected package libcroco3:s390x.
Unpacking libcroco3:s390x (from .../libcroco3_0.6.6-2_s390x.deb) ...
Selecting previously unselected package libunistring0:s390x.
@@ -1061,11 +1144,11 @@ Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
Selecting previously unselected package libgettextpo0:s390x.
Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_s390x.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package libasprintf-dev:s390x.
@@ -1087,30 +1170,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
Selecting previously unselected package zlib1g-dev:s390x.
Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
-Setting up libpipeline1:s390x (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:s390x (1.2.2-2) ...
+Setting up groff-base (1.22.2-1+b1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:s390x (0.18.1.1-10) ...
-Setting up libmagic1:s390x (5.11-2) ...
-Setting up libpcre3:s390x (1:8.31-1) ...
-Setting up libxml2:s390x (2.8.0+dfsg1-7) ...
+Setting up libmagic1:s390x (1:5.11-2.1) ...
+Setting up libpcre3:s390x (1:8.31-2) ...
+Setting up libxml2:s390x (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:s390x (3.0.10-3+b1) ...
-Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:s390x (0.6.6-2) ...
Setting up libunistring0:s390x (0.9.3-5+b1) ...
Setting up libgettextpo0:s390x (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15+b1) ...
Setting up libasprintf-dev:s390x (0.18.1.1-10) ...
Setting up libgettextpo-dev:s390x (0.18.1.1-10) ...
@@ -1121,17 +1204,20 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:s390x (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.20-1 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-34 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1+b1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15+b1 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4+b1 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -1142,16 +1228,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -1161,44 +1246,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
dpkg-buildpackage: host architecture s390x
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -1211,11 +1293,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -1224,125 +1306,167 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
-seqtk.c: In function 'stk_comp':
-seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -1353,15 +1477,303 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtoo
[samopen] SAM header is present: 2 sequences.
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-make[1]: *** [ex1f.bam] Killed
-make: *** [debian/stamp-makefile-check] Error 2
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
-dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+../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 -lpthread
+
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
+DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
+Adding cdbs dependencies to debian/samtools.substvars
+dh_installdirs -psamtools
+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 NEWS
+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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
+dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
+dh_installexamples -plibbam-dev
+dh_installman -plibbam-dev
+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 NEWS
+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 -X .bam
+dh_fixperms -psamtools
+dh_makeshlibs -psamtools
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
+dh_strip -plibbam-dev
+dh_compress -plibbam-dev -X .bam
+dh_fixperms -plibbam-dev
+dh_makeshlibs -plibbam-dev
+dh_installdeb -psamtools
+dh_perl -psamtools
+dh_shlibdeps -psamtools
+dh_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_0.1.19-1_s390x.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_0.1.19-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../samtools_0.1.19-1_s390x.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-0.1.19
+dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0456
-FAILED [dpkg-buildpackage died]
+Build finished at 20130330-0917
+
+samtools_0.1.19-1_s390x.changes:
+Format: 1.8
+Date: Sat, 30 Mar 2013 17:31:47 +0900
+Source: samtools
+Binary: samtools libbam-dev
+Architecture: s390x
+Version: 0.1.19-1
+Distribution: sid
+Urgency: low
+Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description:
+ libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
+ samtools - processing sequence alignments in SAM and BAM formats
+Changes:
+ samtools (0.1.19-1) unstable; urgency=low
+ .
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
+Checksums-Sha1:
+ 44b0ad7015c66de7ea61172247a7884218c5b8aa 560790 samtools_0.1.19-1_s390x.deb
+ 884eb297e57fc14d47b73d4655e291f6fc9ff0c3 122144 libbam-dev_0.1.19-1_s390x.deb
+Checksums-Sha256:
+ 8764098ec4269510b9054964c3ca0ebff7c1324ece301d60f210457d23150f54 560790 samtools_0.1.19-1_s390x.deb
+ 3afb93b0941f94245f8f25c53d68d10cd5d425e46769655e1a396442e4afc034 122144 libbam-dev_0.1.19-1_s390x.deb
+Files:
+ 13d6e54829d787f92d2d384d1febce1e 560790 science optional samtools_0.1.19-1_s390x.deb
+ af7829858681083a1704e14e55263cd6 122144 libdevel optional libbam-dev_0.1.19-1_s390x.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_0.1.19-1_s390x.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 560790 bytes: control archive= 1937 bytes.
+ 32 bytes, 1 lines conffiles
+ 793 bytes, 16 lines control
+ 2766 bytes, 42 lines md5sums
+ Package: samtools
+ Version: 0.1.19-1
+ Architecture: s390x
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1452
+ Depends: libc6 (>= 2.13), 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 2013-03-30 09:17 ./
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2013-03-30 09:17 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126580 2013-03-30 09:17 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/samtools/
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:17 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 09:17 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 09:17 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/bin/
+-rwxr-xr-x root/root 494752 2013-03-30 09:17 ./usr/bin/samtools
+-rwxr-xr-x root/root 175256 2013-03-30 09:17 ./usr/bin/bcftools
+-rwxr-xr-x root/root 31136 2013-03-30 09:17 ./usr/bin/razip
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/samtools/
+-rwxr-xr-x root/root 22768 2013-03-30 09:17 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10272 2013-03-30 09:17 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 22656 2013-03-30 09:17 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 14424 2013-03-30 09:17 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 201392 2013-03-30 09:17 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_s390x.deb
+─────────────────────────────
+
+ new debian package, version 2.0.
+ size 122144 bytes: control archive= 924 bytes.
+ 712 bytes, 17 lines control
+ 715 bytes, 11 lines md5sums
+ Package: libbam-dev
+ Source: samtools
+ Version: 0.1.19-1
+ Architecture: s390x
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 461
+ 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.
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/samtools/
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
+-rw-r--r-- root/root 349450 2013-03-30 09:17 ./usr/lib/libbam.a
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Finished │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-87753949-4301-408f-ad75-3e402223fe91/build/buildd-samtools_0.1.18-4-s390x-3fMAMA
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-683aa926-ac15-426d-91c5-f4f101ce8fb3/build/buildd-samtools_0.1.19-1-s390x-JVvJbf
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1369,18 +1781,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 9652
-Build-Time: 70
+Build-Space: 15508
+Build-Time: 65
Distribution: sid
-Fail-Stage: build
Install-Time: 15
-Job: samtools_0.1.18-4
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 94
-Source-Version: 0.1.18-4
-Space: 9652
-Status: attempted
-Version: 0.1.18-4
+Package-Time: 97
+Source-Version: 0.1.19-1
+Space: 15508
+Status: successful
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0456
-Build needed 00:01:34, 9652k disc space
+Finished at 20130330-0917
+Build needed 00:01:37, 15508k disc space
+Signature with key '52DC96B8' requested:
diff --git a/s390x.log b/s390x.log
index 8ed5856..90f21ac 100644
--- a/s390x.log
+++ b/s390x.log
@@ -1,62 +1,65 @@
-From buildd at zemlinsky.debian.org Sun Dec 23 04:56:12 2012
+From buildd at zemlinsky.debian.org Sat Mar 30 09:17:41 2013
Return-path: <buildd at zemlinsky.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
+Received: from muffat.debian.org ([206.12.19.146])
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)
+ CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
+ by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
(Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1Tmdbg-0007GK-Cf
- for logs at buildd.debian.org; Sun, 23 Dec 2012 04:56:12 +0000
-Received: from zemlinsky.debian.org ([2001:7c0:400:1337::818f:a006])
+ id 1ULruv-0002ZT-20
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:17:41 +0000
+Received: from zemlinsky.debian.org ([129.143.160.6])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zemlinsky.debian.org,
EMAIL=hostmaster at zemlinsky.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1Tmdbf-0007z3-9r; Sun, 23 Dec 2012 04:56:11 +0000
+ by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
+ (Exim 4.80) (envelope-from <buildd at zemlinsky.debian.org>)
+ id 1ULruq-0007Ra-Sh; Sat, 30 Mar 2013 09:17:37 +0000
Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
(envelope-from <buildd at zemlinsky.debian.org>)
- id 1Tmdbe-00075S-0j; Sun, 23 Dec 2012 04:56:10 +0000
-Message-Id: <E1Tmdbe-00075S-0j at zemlinsky.debian.org>
+ id 1ULruo-0004v0-E5; Sat, 30 Mar 2013 09:17:34 +0000
+Message-Id: <E1ULruo-0004v0-E5 at zemlinsky.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sun, 23 Dec 2012 04:56:09 +0000
+Date: Sat, 30 Mar 2013 09:17:34 +0000
From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_0.1.18-4 on s390x (dist=sid)
-Key-Id: 6A3F7E2B
+Subject: Log for successful build of samtools_0.1.19-1 on s390x (dist=sid)
+Key-Id: 52DC96B8
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (s390x) 23 Dec 2012 04:54 ║
+║ samtools 0.1.19-1 (s390x) 30 Mar 2013 09:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: s390x
-Hit http://ftp-stud.hs-esslingen.de unstable InRelease
+Hit http://ftp-stud.hs-esslingen.de unstable Release.gpg
+Hit http://ftp-stud.hs-esslingen.de unstable Release
Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
-Hit http://incoming.debian.org unstable InRelease
-Ign http://incoming.debian.org InRelease
-Hit http://incoming.debian.org unstable/main Sources
-Hit http://incoming.debian.org unstable/contrib Sources
-Get:2 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Hit http://incoming.debian.org unstable/main s390x Packages
-Hit http://incoming.debian.org unstable/contrib s390x Packages
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://incoming.debian.org Release [1141 B]
-Get:5 http://incoming.debian.org Sources [14.0 kB]
-Get:6 http://incoming.debian.org Packages [118 kB]
-Fetched 337 kB in 1s (176 kB/s)
+Get:2 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:3 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:4 http://incoming.debian.org unstable Release [235 kB]
+Get:5 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:6 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:7 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:8 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:9 http://incoming.debian.org unstable/main s390x Packages [6017 kB]
+Get:10 http://incoming.debian.org unstable/contrib s390x Packages [35.3 kB]
+Get:11 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:12 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:13 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:14 http://incoming.debian.org buildd-unstable/main s390x Packages [13.1 kB]
+Get:15 http://incoming.debian.org buildd-unstable/contrib s390x Packages [14 B]
+Fetched 13.2 MB in 9s (1356 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,12 +79,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (339 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (342 kB/s)
Download complete and in download only mode
Check arch
@@ -94,28 +97,59 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5+b1)
+build-essential: already installed (11.6)
fakeroot: already installed (1.18.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-libc6-dev: already installed (2.13-36)
+base-files: already installed (7.1)
+base-passwd: already installed (3.5.26)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
+coreutils: already installed (8.20-3)
+dash: already installed (0.5.7-3)
+debianutils: already installed (4.3.4)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.9)
+e2fsprogs: already installed (1.42.5-1)
+findutils: already installed (4.4.2-5)
+grep: already installed (2.14-1)
+gzip: already installed (1.5-1.1)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
+ncurses-base: already installed (5.9-10)
+ncurses-bin: already installed (5.9-10)
+perl-base: already installed (5.14.2-20)
+sed: already installed (4.2.1-10)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
@@ -132,6 +166,9 @@ Installing positive dependencies: debhelper bash-completion cdbs quilt libncurse
Reading package lists...
Building dependency tree...
Reading state information...
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
The following extra packages will be installed:
bsdmainutils diffstat file gettext gettext-base groff-base html2text
intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
@@ -150,26 +187,26 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 36 not upgraded.
-Need to get 10.9 MB of archives.
+0 upgraded, 29 newly installed, 0 to remove and 11 not upgraded.
+Need to get 10.4 MB of archives.
After this operation, 31.6 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-1 [41.0 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.21-9 [1187 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.3 [215 kB]
+Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-2 [41.1 kB]
+Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.22.2-1+b1 [738 kB]
+Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.4 [215 kB]
Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-3 [888 kB]
Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-10 [27.2 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 5.11-2 [200 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-1 [259 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7 [901 kB]
+Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 1:5.11-2.1 [201 kB]
+Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-2 [259 kB]
+Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7+nmu1 [902 kB]
Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-3 [1798 kB]
+Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-5 [1798 kB]
Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-2 [129 kB]
Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-10 [158 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 5.11-2 [51.9 kB]
+Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 1:5.11-2.1 [52.0 kB]
Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-10 [156 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390x 0.18.1.1-10 [26.8 kB]
Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390x 0.18.1.1-10 [195 kB]
@@ -180,17 +217,17 @@ Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.201
Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
-Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-8 [381 kB]
Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.9 MB in 1s (10.9 MB/s)
+Fetched 10.4 MB in 1s (9424 kB/s)
Selecting previously unselected package libpipeline1:s390x.
-(Reading database ... 10867 files and directories currently installed.)
-Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-1_s390x.deb) ...
+(Reading database ... 10875 files and directories currently installed.)
+Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-2_s390x.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_s390x.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1+b1_s390x.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_s390x.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_s390x.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_s390x.deb) ...
Selecting previously unselected package bash-completion.
@@ -198,15 +235,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:s390x.
Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package libmagic1:s390x.
-Unpacking libmagic1:s390x (from .../libmagic1_5.11-2_s390x.deb) ...
+Unpacking libmagic1:s390x (from .../libmagic1_1%3a5.11-2.1_s390x.deb) ...
Selecting previously unselected package libpcre3:s390x.
-Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-1_s390x.deb) ...
+Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-2_s390x.deb) ...
Selecting previously unselected package libxml2:s390x.
-Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-7_s390x.deb) ...
+Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-7+nmu1_s390x.deb) ...
Selecting previously unselected package libffi5:s390x.
Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
Selecting previously unselected package libglib2.0-0:s390x.
-Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-3_s390x.deb) ...
+Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-5_s390x.deb) ...
Selecting previously unselected package libcroco3:s390x.
Unpacking libcroco3:s390x (from .../libcroco3_0.6.6-2_s390x.deb) ...
Selecting previously unselected package libunistring0:s390x.
@@ -214,11 +251,11 @@ Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
Selecting previously unselected package libgettextpo0:s390x.
Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_s390x.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_s390x.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390x.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
Selecting previously unselected package libasprintf-dev:s390x.
@@ -240,30 +277,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
Selecting previously unselected package zlib1g-dev:s390x.
Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
-Setting up libpipeline1:s390x (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:s390x (1.2.2-2) ...
+Setting up groff-base (1.22.2-1+b1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:s390x (0.18.1.1-10) ...
-Setting up libmagic1:s390x (5.11-2) ...
-Setting up libpcre3:s390x (1:8.31-1) ...
-Setting up libxml2:s390x (2.8.0+dfsg1-7) ...
+Setting up libmagic1:s390x (1:5.11-2.1) ...
+Setting up libpcre3:s390x (1:8.31-2) ...
+Setting up libxml2:s390x (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:s390x (3.0.10-3+b1) ...
-Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:s390x (0.6.6-2) ...
Setting up libunistring0:s390x (0.9.3-5+b1) ...
Setting up libgettextpo0:s390x (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15+b1) ...
Setting up libasprintf-dev:s390x (0.18.1.1-10) ...
Setting up libgettextpo-dev:s390x (0.18.1.1-10) ...
@@ -274,17 +311,20 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:s390x (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 36 not upgraded.
+The following package was automatically installed and is no longer required:
+ libapt-pkg4.12
+Use 'apt-get autoremove' to remove it.
+0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-12 gcc-4.6_4.6.3-12 libc6-dev_2.13-36 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5+b1 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.20-1 cpp_4:4.6.3-8 cpp-4.6_4.6.3-12 dash_0.5.7-3 debconf_1.5.46 debconf-i18n_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-12 gcc_4:4.6.3-8 gcc-4.6_4.6.3-12 gcc-4.6-base_4.6.3-12 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15+b1 initscripts_2.88dsf-34 insserv_1.14.0-4 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-36 libc-dev-bin_2.13-36 libc6_2.13-36 libc6-dev_2.13-36 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4+b1 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-36 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012i-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1+b1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15+b1 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3+b1 libfile-fcntllock-perl_0.14-2 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblocale-gettext-perl_1.05-7+b2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4+b1 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5+b1 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -295,16 +335,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -314,44 +353,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
dpkg-buildpackage: host architecture s390x
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -364,11 +400,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -377,125 +413,167 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
-seqtk.c: In function 'stk_comp':
-seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o seqtk seqtk.o -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -506,15 +584,303 @@ make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtoo
[samopen] SAM header is present: 2 sequences.
(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-make[1]: *** [ex1f.bam] Killed
-make: *** [debian/stamp-makefile-check] Error 2
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-s390x-3fMAMA/samtools-0.1.18/examples'
-dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+../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 -lpthread
+
+# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
+
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/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
+/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
+DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
+Adding cdbs dependencies to debian/samtools.substvars
+dh_installdirs -psamtools
+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 NEWS
+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_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
+dh_bash-completion
+dh_bash-completion: file-list parsing failed, installing as proper snippet
+dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
+dh_installexamples -plibbam-dev
+dh_installman -plibbam-dev
+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 NEWS
+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 -X .bam
+dh_fixperms -psamtools
+dh_makeshlibs -psamtools
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
+dh_strip -plibbam-dev
+dh_compress -plibbam-dev -X .bam
+dh_fixperms -plibbam-dev
+dh_makeshlibs -plibbam-dev
+dh_installdeb -psamtools
+dh_perl -psamtools
+dh_shlibdeps -psamtools
+dh_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_0.1.19-1_s390x.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_0.1.19-1_s390x.deb'.
+ dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../samtools_0.1.19-1_s390x.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-0.1.19
+dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0456
-FAILED [dpkg-buildpackage died]
+Build finished at 20130330-0917
+
+samtools_0.1.19-1_s390x.changes:
+Format: 1.8
+Date: Sat, 30 Mar 2013 17:31:47 +0900
+Source: samtools
+Binary: samtools libbam-dev
+Architecture: s390x
+Version: 0.1.19-1
+Distribution: sid
+Urgency: low
+Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description:
+ libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
+ samtools - processing sequence alignments in SAM and BAM formats
+Changes:
+ samtools (0.1.19-1) unstable; urgency=low
+ .
+ cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
+ 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
+ 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
+ e194f9e Removed fix_float_tag.patch, corrected upstream.
+ 9c0e543 Refreshed patches.
+ 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
+ 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
+ fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
+ 6f75b48 debian/control: normalised with cme.
+ e13bb5e debian/control: normalised VCS URLs.
+ a1b1b00 debian/control: deleted DM-Upload-Allowed field.
+ ddcd54e Use NEWS as upstream changelog.
+ 81ad760 Conforms to Policy version 3.9.4.
+Checksums-Sha1:
+ 44b0ad7015c66de7ea61172247a7884218c5b8aa 560790 samtools_0.1.19-1_s390x.deb
+ 884eb297e57fc14d47b73d4655e291f6fc9ff0c3 122144 libbam-dev_0.1.19-1_s390x.deb
+Checksums-Sha256:
+ 8764098ec4269510b9054964c3ca0ebff7c1324ece301d60f210457d23150f54 560790 samtools_0.1.19-1_s390x.deb
+ 3afb93b0941f94245f8f25c53d68d10cd5d425e46769655e1a396442e4afc034 122144 libbam-dev_0.1.19-1_s390x.deb
+Files:
+ 13d6e54829d787f92d2d384d1febce1e 560790 science optional samtools_0.1.19-1_s390x.deb
+ af7829858681083a1704e14e55263cd6 122144 libdevel optional libbam-dev_0.1.19-1_s390x.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_0.1.19-1_s390x.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 560790 bytes: control archive= 1937 bytes.
+ 32 bytes, 1 lines conffiles
+ 793 bytes, 16 lines control
+ 2766 bytes, 42 lines md5sums
+ Package: samtools
+ Version: 0.1.19-1
+ Architecture: s390x
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1452
+ Depends: libc6 (>= 2.13), 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 2013-03-30 09:17 ./
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1966 2013-03-30 09:17 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
+-rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
+-rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
+-rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
+-rw-r--r-- root/root 126580 2013-03-30 09:17 ./usr/share/doc/samtools/examples/ex1.bam
+-rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/samtools/
+-rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
+-rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
+-rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
+-rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
+-rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
+-rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
+-rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
+-rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
+-rwxr-xr-x root/root 5778 2013-03-30 09:17 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
+-rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
+-rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
+-rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
+-rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
+-rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2013-03-30 09:17 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 10654 2013-03-30 09:17 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/bin/
+-rwxr-xr-x root/root 494752 2013-03-30 09:17 ./usr/bin/samtools
+-rwxr-xr-x root/root 175256 2013-03-30 09:17 ./usr/bin/bcftools
+-rwxr-xr-x root/root 31136 2013-03-30 09:17 ./usr/bin/razip
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/samtools/
+-rwxr-xr-x root/root 22768 2013-03-30 09:17 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 10272 2013-03-30 09:17 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 22656 2013-03-30 09:17 ./usr/lib/samtools/ace2sam
+-rwxr-xr-x root/root 14424 2013-03-30 09:17 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 201392 2013-03-30 09:17 ./usr/lib/samtools/bamcheck
+-rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/bash_completion.d/
+-rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
+lrwxrwxrwx root/root 0 2013-03-30 09:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.19-1_s390x.deb
+─────────────────────────────
+
+ new debian package, version 2.0.
+ size 122144 bytes: control archive= 924 bytes.
+ 712 bytes, 17 lines control
+ 715 bytes, 11 lines md5sums
+ Package: libbam-dev
+ Source: samtools
+ Version: 0.1.19-1
+ Architecture: s390x
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 461
+ 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.
+ .
+ This library is part of SAMtools.
+
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
+-rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/samtools/
+-rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
+-rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
+-rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
+-rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
+-rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
+drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
+-rw-r--r-- root/root 349450 2013-03-30 09:17 ./usr/lib/libbam.a
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Finished │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-87753949-4301-408f-ad75-3e402223fe91/build/buildd-samtools_0.1.18-4-s390x-3fMAMA
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /var/lib/schroot/mount/sid-s390x-sbuild-683aa926-ac15-426d-91c5-f4f101ce8fb3/build/buildd-samtools_0.1.19-1-s390x-JVvJbf
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -522,18 +888,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390x
-Build-Space: 9652
-Build-Time: 70
+Build-Space: 15508
+Build-Time: 65
Distribution: sid
-Fail-Stage: build
Install-Time: 15
-Job: samtools_0.1.18-4
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 94
-Source-Version: 0.1.18-4
-Space: 9652
-Status: attempted
-Version: 0.1.18-4
+Package-Time: 97
+Source-Version: 0.1.19-1
+Space: 15508
+Status: successful
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0456
-Build needed 00:01:34, 9652k disc space
+Finished at 20130330-0917
+Build needed 00:01:37, 15508k disc space
+Signature with key '52DC96B8' requested:
diff --git a/sparc.log b/sparc.log
index a06fa21..4140d4f 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,4 +1,4 @@
-From buildd at lebrun.debian.org Sun Dec 23 05:00:21 2012
+From buildd at lebrun.debian.org Sat Mar 30 09:19:52 2013
Return-path: <buildd at lebrun.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,57 +6,61 @@ Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1Tmdfg-000816-Qb
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:00:20 +0000
+ id 1ULrx1-0002vg-Ph
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:51 +0000
Received: from [2001:b68:ff:5:203:baff:fe59:abad] (helo=lebrun.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1Tmdff-00084R-SU
- for logs at buildd.debian.org; Sun, 23 Dec 2012 05:00:19 +0000
+ id 1ULrx0-0001bZ-R6
+ for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:50 +0000
Received: from buildd by lebrun.debian.org with local (Exim 4.72)
(envelope-from <buildd at lebrun.debian.org>)
- id 1Tmdfe-0001kg-3i; Sun, 23 Dec 2012 05:00:18 +0000
-Message-Id: <E1Tmdfe-0001kg-3i at lebrun.debian.org>
+ id 1ULrwy-0005Aj-VO; Sat, 30 Mar 2013 09:19:49 +0000
+Message-Id: <E1ULrwy-0005Aj-VO at lebrun.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sun, 23 Dec 2012 05:00:17 +0000
+Date: Sat, 30 Mar 2013 09:19:48 +0000
From: buildd on lebrun <buildd at lebrun.debian.org>
To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
-Subject: Log for attempted build of samtools_0.1.18-4 on sparc (dist=sid)
-Key-Id: E1D842D6
+Subject: Log for attempted build of samtools_0.1.19-1 on sparc (dist=sid)
+Key-Id: B16CDE7F
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.18-4 (sparc) 23 Dec 2012 04:55 ║
+║ samtools 0.1.19-1 (sparc) 30 Mar 2013 09:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.18-4
-Source Version: 0.1.18-4
+Version: 0.1.19-1
+Source Version: 0.1.19-1
Architecture: sparc
-Get:1 http://debian.carnet.hr unstable InRelease [227 kB]
-Get:2 http://incoming.debian.org unstable InRelease [227 kB]
-Get:3 http://debian.carnet.hr unstable/main Sources [6458 kB]
-Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://incoming.debian.org unstable/main Sources [6458 kB]
-Get:6 http://debian.carnet.hr unstable/contrib Sources [53.0 kB]
-Get:7 http://debian.carnet.hr unstable/non-free Sources [101 kB]
-Get:8 http://debian.carnet.hr unstable/main sparc Packages [6099 kB]
-Get:9 http://debian.carnet.hr unstable/contrib sparc Packages [36.6 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [53.0 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:12 http://incoming.debian.org unstable/main sparc Packages [6099 kB]
-Get:13 http://incoming.debian.org unstable/contrib sparc Packages [36.6 kB]
-Get:14 http://incoming.debian.org Release [1141 B]
-Get:15 http://incoming.debian.org Sources [14.0 kB]
-Get:16 http://incoming.debian.org Packages [118 kB]
-Fetched 26.1 MB in 59s (435 kB/s)
+Get:1 http://debian.carnet.hr unstable Release.gpg [836 B]
+Get:2 http://incoming.debian.org unstable Release.gpg [836 B]
+Get:3 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
+Get:4 http://debian.carnet.hr unstable Release [235 kB]
+Get:5 http://incoming.debian.org unstable Release [235 kB]
+Get:6 http://debian.carnet.hr unstable/main Sources [6484 kB]
+Get:7 http://incoming.debian.org buildd-unstable Release [109 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
+Get:9 http://debian.carnet.hr unstable/contrib Sources [51.0 kB]
+Get:10 http://debian.carnet.hr unstable/non-free Sources [101 kB]
+Get:11 http://debian.carnet.hr unstable/main sparc Packages [6115 kB]
+Get:12 http://debian.carnet.hr unstable/contrib sparc Packages [35.6 kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
+Get:15 http://incoming.debian.org unstable/main sparc Packages [6115 kB]
+Get:16 http://incoming.debian.org unstable/contrib sparc Packages [35.6 kB]
+Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
+Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
+Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
+Get:20 http://incoming.debian.org buildd-unstable/main sparc Packages [12.7 kB]
+Get:21 http://incoming.debian.org buildd-unstable/contrib sparc Packages [14 B]
+Fetched 26.2 MB in 60s (435 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -76,12 +80,12 @@ Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://git.debian.org/debian-med/samtools.git
-Need to get 391 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (dsc) [1446 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (tar) [379 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.18-4 (diff) [9920 B]
-Fetched 391 kB in 1s (256 kB/s)
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 570 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
+Fetched 570 kB in 1s (368 kB/s)
Download complete and in download only mode
Check arch
@@ -94,57 +98,58 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
-build-essential: already installed (11.5)
+build-essential: already installed (11.6)
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 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.12)
+base-files: already installed (7.1)
base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5)
+bash: already installed (4.2+dfsg-0.1)
+bsdutils: already installed (1:2.20.1-5.3)
coreutils: already installed (8.13-3.3)
dash: already installed (0.5.7-3)
debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-7)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
+diffutils: already installed (1:3.2-8)
+dpkg: already installed (1.16.10)
+e2fsprogs: already installed (1.42.5-1.1)
findutils: already installed (4.4.2-5)
grep: already installed (2.14-1)
gzip: already installed (1.5-1.1)
-hostname: already installed (3.11)
+hostname: already installed (3.12)
+libc-bin: already installed (2.13-38)
+login: already installed (1:4.1.5.1-1)
+mount: already installed (2.20.1-5.3)
ncurses-base: already installed (5.9-10)
ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-15)
+perl-base: already installed (5.14.2-20)
sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-34)
-sysvinit: already installed (2.88dsf-34)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.2)
-mount: already installed (2.20.1-5.2)
-util-linux: already installed (2.20.1-5.2)
-libc6-dev: already installed (2.13-37)
-libc6-dev-sparc64: already installed (2.13-37)
+sysvinit: already installed (2.88dsf-41)
+sysvinit-utils: already installed (2.88dsf-41)
+tar: already installed (1.26+dfsg-0.1)
+util-linux: already installed (2.20.1-5.3)
+libc6-dev: already installed (2.13-38)
+libc6-dev-sparc64: already installed (2.13-38)
gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 9.20120909
bash-completion: missing
@@ -175,26 +180,26 @@ The following NEW packages will be installed:
libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 20 not upgraded.
-Need to get 10.3 MB of archives.
-After this operation, 29.2 MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.2-1 [36.2 kB]
-Get:2 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-9 [1133 kB]
-Get:3 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 9.0.3 [206 kB]
+0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
+Need to get 9825 kB of archives.
+After this operation, 29.1 MB of additional disk space will be used.
+Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.2-2 [36.3 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.22.2-1 [693 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 9.0.4 [203 kB]
Get:4 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.3-3 [865 kB]
Get:5 http://debian.carnet.hr/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
Get:6 http://debian.carnet.hr/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-10 [26.9 kB]
-Get:7 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.11-2 [197 kB]
-Get:8 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 1:8.31-1 [252 kB]
-Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-7 [826 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 1:5.11-2.1 [197 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 1:8.31-2 [252 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-7+nmu1 [826 kB]
Get:10 http://debian.carnet.hr/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
-Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.33.12+really2.32.4-3 [1645 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.33.12+really2.32.4-5 [1645 kB]
Get:12 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.6-2 [114 kB]
Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
Get:14 http://debian.carnet.hr/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-10 [130 kB]
-Get:15 http://debian.carnet.hr/debian/ unstable/main file sparc 5.11-2 [51.1 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main file sparc 1:5.11-2.1 [51.1 kB]
Get:16 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-10 [148 kB]
-Get:17 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.119 [80.4 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
Get:18 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
Get:19 http://debian.carnet.hr/debian/ unstable/main libasprintf-dev sparc 0.18.1.1-10 [26.6 kB]
Get:20 http://debian.carnet.hr/debian/ unstable/main libgettextpo-dev sparc 0.18.1.1-10 [172 kB]
@@ -205,17 +210,17 @@ Get:24 http://debian.carnet.hr/debian/ unstable/main debhelper all 9.20120909 [7
Get:25 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
Get:26 http://debian.carnet.hr/debian/ unstable/main libtinfo-dev sparc 5.9-10 [97.5 kB]
Get:27 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-10 [204 kB]
-Get:28 http://debian.carnet.hr/debian/ unstable/main quilt all 0.60-2 [377 kB]
+Get:28 http://debian.carnet.hr/debian/ unstable/main quilt all 0.60-8 [381 kB]
Get:29 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.7.dfsg-13 [211 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.3 MB in 11s (876 kB/s)
+Fetched 9825 kB in 14s (659 kB/s)
Selecting previously unselected package libpipeline1:sparc.
-(Reading database ... 11141 files and directories currently installed.)
-Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.2-1_sparc.deb) ...
+(Reading database ... 11151 files and directories currently installed.)
+Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.2-2_sparc.deb) ...
Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-9_sparc.deb) ...
+Unpacking groff-base (from .../groff-base_1.22.2-1_sparc.deb) ...
Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_sparc.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_sparc.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-3_sparc.deb) ...
Selecting previously unselected package bash-completion.
@@ -223,15 +228,15 @@ Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
Selecting previously unselected package libasprintf0c2:sparc.
Unpacking libasprintf0c2:sparc (from .../libasprintf0c2_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package libmagic1:sparc.
-Unpacking libmagic1:sparc (from .../libmagic1_5.11-2_sparc.deb) ...
+Unpacking libmagic1:sparc (from .../libmagic1_1%3a5.11-2.1_sparc.deb) ...
Selecting previously unselected package libpcre3:sparc.
-Unpacking libpcre3:sparc (from .../libpcre3_1%3a8.31-1_sparc.deb) ...
+Unpacking libpcre3:sparc (from .../libpcre3_1%3a8.31-2_sparc.deb) ...
Selecting previously unselected package libxml2:sparc.
-Unpacking libxml2:sparc (from .../libxml2_2.8.0+dfsg1-7_sparc.deb) ...
+Unpacking libxml2:sparc (from .../libxml2_2.8.0+dfsg1-7+nmu1_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_2.33.12+really2.32.4-3_sparc.deb) ...
+Unpacking libglib2.0-0:sparc (from .../libglib2.0-0_2.33.12+really2.32.4-5_sparc.deb) ...
Selecting previously unselected package libcroco3:sparc.
Unpacking libcroco3:sparc (from .../libcroco3_0.6.6-2_sparc.deb) ...
Selecting previously unselected package libunistring0:sparc.
@@ -239,11 +244,11 @@ Unpacking libunistring0:sparc (from .../libunistring0_0.9.3-5_sparc.deb) ...
Selecting previously unselected package libgettextpo0:sparc.
Unpacking libgettextpo0:sparc (from .../libgettextpo0_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.11-2_sparc.deb) ...
+Unpacking file (from .../file_1%3a5.11-2.1_sparc.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_sparc.deb) ...
Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.119_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
Selecting previously unselected package libasprintf-dev:sparc.
@@ -265,30 +270,30 @@ 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) ...
+Unpacking quilt (from .../archives/quilt_0.60-8_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 (1.2.2-1) ...
-Setting up groff-base (1.21-9) ...
-Setting up bsdmainutils (9.0.3) ...
+Setting up libpipeline1:sparc (1.2.2-2) ...
+Setting up groff-base (1.22.2-1) ...
+Setting up bsdmainutils (9.0.4) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-3) ...
Building database of manual pages ...
Setting up bash-completion (1:2.0-1) ...
Setting up libasprintf0c2:sparc (0.18.1.1-10) ...
-Setting up libmagic1:sparc (5.11-2) ...
-Setting up libpcre3:sparc (1:8.31-1) ...
-Setting up libxml2:sparc (2.8.0+dfsg1-7) ...
+Setting up libmagic1:sparc (1:5.11-2.1) ...
+Setting up libpcre3:sparc (1:8.31-2) ...
+Setting up libxml2:sparc (2.8.0+dfsg1-7+nmu1) ...
Setting up libffi5:sparc (3.0.10-3) ...
-Setting up libglib2.0-0:sparc (2.33.12+really2.32.4-3) ...
+Setting up libglib2.0-0:sparc (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:sparc (0.6.6-2) ...
Setting up libunistring0:sparc (0.9.3-5) ...
Setting up libgettextpo0:sparc (0.18.1.1-10) ...
-Setting up file (5.11-2) ...
+Setting up file (1:5.11-2.1) ...
Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.119) ...
+Setting up cdbs (0.4.120) ...
Setting up html2text (1.3.2a-15) ...
Setting up libasprintf-dev:sparc (0.18.1.1-10) ...
Setting up libgettextpo-dev:sparc (0.18.1.1-10) ...
@@ -299,17 +304,17 @@ Setting up debhelper (9.20120909) ...
Setting up diffstat (1.55-3) ...
Setting up libtinfo-dev:sparc (5.9-10) ...
Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-2) ...
+Setting up quilt (0.60-8) ...
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 20 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.32-1
-Package versions: apt_0.9.7.6 base-files_6.12 base-passwd_3.5.26 bash_4.2-5 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.2 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.119 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.46 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_5.11-2 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-14 gcc_4:4.6.3-8 gcc-4.6_4.6.3-14 gcc-4.6-base_4.6.3-14 gcc-4.7-base_4.7.2-4 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-6 gpgv_1.4.12-6 grep_2.14-1 groff-base_1.21-9 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-34 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.6 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.2 libbz2-1.0_1.0.6-4 libc-bin_2.13-37 libc-dev-bin_2.13-37 libc6_2.13-37 libc6-dev_2.13-37 libc6-dev-sparc64_2.13-37 libc6-sparc64_2.13-37 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.9 libffi5_3.0.10-3 libgc1c2_1:7.1-9 libgcc1_1:4.7.2-4 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-3 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-4 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2 libmount1_2.20.1-5.2 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.31-1 libpipeline1_1.2.2-1 libreadline6_6.2-9 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libss2_1.42.5-1 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.2 libxml2_2.8.0+dfsg1-7 linux-libc-dev_3.2.32-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.2 multiarch-support_2.13-37 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-15 perl-base_5.14.2-15 perl-modules_5.14.2-15 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-9 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1 sysv-rc_2.88dsf-34 sysvinit_2.88dsf-34 sysvinit-utils_2.88dsf-34 tar_1.26-4 tzdata_2012j-1 util-linux_2.20.1-5.2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
+Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
+Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1.18.4-2 file_1:5.11-2.1 findutils_4.4.2-5 g++_4:4.6.3-8 g++-4.6_4.6.3-15 gcc_4:4.6.3-8 gcc-4.6_4.6.3-15 gcc-4.6-base_4.6.3-15 gcc-4.7-base_4.7.2-5 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-1 groff-base_1.22.2-1 gzip_1.5-1.1 hostname_3.12 html2text_1.3.2a-15 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38 libc-dev-bin_2.13-38 libc6_2.13-38 libc6-dev_2.13-38 libc6-dev-sparc64_2.13-38 libc6-sparc64_2.13-38 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.6-2 libdb5.1_5.1.29-5 libdpkg-perl_1.16.10 libffi5_3.0.10-3 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.11-2.1 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.1-1 libncurses5_5.9-10 libncurses5-dev_5.9-10 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.2-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libss2_1.42.5-1.1 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9-10 libtinfo5_5.9-10 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+nmu1 linux-libc-dev_3.2.39-2 login_1:4.1.5.1-1 lsb-base_4.1+Debian9 make_3.81-8.2 man-db_2.6.3-3 mawk_1.3.3-17 mount_2.20.1-5.3 multiarch-support_2.13-38 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-20 perl-base_5.14.2-20 perl-modules_5.14.2-20 po-debconf_1.0.16+nmu2 quilt_0.60-8 readline-common_6.2+dfsg-0.1 sed_4.2.1-10 sensible-utils_0.0.7 sudo_1.8.5p2-1+nmu1 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tzdata_2013b-1 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -320,16 +325,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sun Dec 23 04:34:30 2012 UTC using DSA key ID B351A900
+gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.18-4.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.18
-dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.18-4.debian.tar.gz
-dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.19
+dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
+dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
+dpkg-source: info: applying fix_example_makefile.patch
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying fix_coverage_cap.patch
-dpkg-source: info: applying fix_float_tag.patch
Check disc space
────────────────
@@ -339,44 +343,41 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.18-4
- dpkg-source --before-build samtools-0.1.18
+dpkg-buildpackage: source version 0.1.19-1
+ dpkg-source --before-build samtools-0.1.19
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
rm -f debian/stamp-makefile-check
dh_clean
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
fi
-Removing patch fix_float_tag.patch
-Restoring bam.h
-
Removing patch fix_coverage_cap.patch
Restoring bam2depth.c
Removing patch fix_segfault_with_small_ref.patch
Restoring bam_plcmd.c
-Removing patch no-pileup-tests.patch
+Removing patch fix_example_makefile.patch
Restoring examples/Makefile
No patches applied
@@ -389,11 +390,11 @@ mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch no-pileup-tests.patch
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+Applying patch fix_example_makefile.patch
patching file examples/Makefile
Applying patch fix_segfault_with_small_ref.patch
@@ -402,152 +403,189 @@ patching file bam_plcmd.c
Applying patch fix_coverage_cap.patch
patching file bam2depth.c
-Applying patch fix_float_tag.patch
-patching file bam.h
-
-Now at patch fix_float_tag.patch
+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_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
+bgzf.c: In function 'worker_aux':
+bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
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
+bgzf.c:572:11: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 3 has type 'uint32_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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
+bam_index.c: In function 'bam_index_load_core':
+bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
+razf.c: In function 'razf_close':
+razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_end_flush':
+razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function '_razf_write':
+razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'save_zindex':
+razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c: In function 'razf_flush':
+razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
+knetfile.c: In function 'khttp_connect_file':
+knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+knetfile.c: In function 'kftp_send_cmd':
+knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+bam_reheader.c:12:16: 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
+bcf.c: In function 'bcf_fmt_core':
+bcf.c:233:9: warning: variable 'iPL' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
+bcfutils.c: In function 'bcf_fit_alt':
+bcfutils.c:119:9: warning: variable 'ipl' 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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-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
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
+padding.c: In function 'bam_pad2unpad':
+padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-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_0.1.18-4-sparc-obycZR/samtools-0.1.18/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
+make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -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 -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
+ace2sam.c: In function 'main':
+ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
+make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
+gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
+razip.c: In function 'main':
+razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
+razip.c: In function 'write_open':
+razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/samtools-0.1.18'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.18-4-sparc-obycZR/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 -Wl,-z,relro -D_FORTIFY_SOURCE=2" 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_0.1.19-1-sparc-XTmM23/samtools-0.1.19/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_0.1.18-4-sparc-obycZR/samtools-0.1.18/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/examples'
make: *** [debian/stamp-makefile-check] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20121223-0500
+Build finished at 20130330-0919
FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-aca2bf8d-dc86-41b0-aa8b-47a9cdd0557a/build/buildd-samtools_0.1.18-4-sparc-obycZR
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-a9e2fc50-8623-4453-ba1c-9450161e0f4b/build/buildd-samtools_0.1.19-1-sparc-XTmM23
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -555,18 +593,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 6840
-Build-Time: 140
+Build-Space: 8216
+Build-Time: 151
Distribution: sid
Fail-Stage: build
Install-Time: 85
-Job: samtools_0.1.18-4
+Job: samtools_0.1.19-1
Package: samtools
-Package-Time: 307
-Source-Version: 0.1.18-4
-Space: 6840
+Package-Time: 319
+Source-Version: 0.1.19-1
+Space: 8216
Status: attempted
-Version: 0.1.18-4
+Version: 0.1.19-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20121223-0500
-Build needed 00:05:07, 6840k disc space
+Finished at 20130330-0919
+Build needed 00:05:19, 8216k disc space
--
Processing of sequence alignments in SAM and BAM formats.
More information about the debian-med-commit
mailing list