[med-svn] [SCM] bwa branch, meta, updated. meta/0.5.9-2-9-gb329b15
Charles Plessy
plessy at debian.org
Tue Nov 15 08:44:04 UTC 2011
The following commit has been merged in the meta branch:
commit b329b1546a0ea42c33443f8379821153e56633eb
Author: Charles Plessy <plessy at debian.org>
Date: Tue Nov 15 17:39:30 2011 +0900
Build logs for 0.6.0-1.
diff --git a/armel.log b/armel.log
index f52a66e..0f173c2 100644
--- a/armel.log
+++ b/armel.log
@@ -1,67 +1,67 @@
-From buildd at ancina.debian.org Mon Nov 14 04:41:28 2011
-Return-path: <buildd at ancina.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at arnold.debian.org Mon Nov 14 11:06:27 2011
+Return-path: <buildd at arnold.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
- id 1RPoMJ-0000Uf-T9
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:41:28 +0000
-Received: from ancina.ugent.be ([157.193.39.13] helo=ancina.debian.org)
+ (Exim 4.72) (envelope-from <buildd at arnold.debian.org>)
+ id 1RPuMs-0008BO-Jz
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:06:27 +0000
+Received: from arnold.islands.arm.com ([217.140.96.57] helo=arnold.debian.org)
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=ancina.debian.org, EMAIL=hostmaster at ancina.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at ancina.debian.org>)
- id 1RPoMJ-0006Mz-3m
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:41:27 +0000
-Received: from buildd by ancina.debian.org with local (Exim 4.69)
- (envelope-from <buildd at ancina.debian.org>)
- id 1RPoMH-0003TV-Ui; Mon, 14 Nov 2011 04:41:25 +0000
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.021 (F2.76; B3.07_01; Q3.07)
-Date: Mon, 14 Nov 2011 04:41:25 +0000
-From: Build Daemon <buildd at ancina.debian.org>
-To: buildd-porters at ancina.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on armel (dist=sid)
-Key-Id: 82E89EDA
-Message-Id: <E1RPoMH-0003TV-Ui at ancina.debian.org>
+ CN=arnold.debian.org, EMAIL=hostmaster at arnold.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at arnold.debian.org>)
+ id 1RPuMq-0001R0-IM
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:06:24 +0000
+Received: from buildd by arnold.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at arnold.debian.org>)
+ id 1RPuMm-00059s-0e; Mon, 14 Nov 2011 11:06:20 +0000
+Date: Mon, 14 Nov 2011 11:06:20 +0000
+Message-Id: <E1RPuMm-00059s-0e at arnold.debian.org>
+From: buildd on arnold <buildd at arnold.debian.org>
+To: buildd-porters at arnold.debian.org,logs at buildd.debian.org
+Subject: Log for attempted build of bwa_0.6.0-1 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 ancina.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on arnold.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (armel) 14 Nov 2011 04:38 ║
+║ bwa 0.6.0-1 (armel) 14 Nov 2011 11:01 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: armel
-Hit http://ftp.de.debian.org sid InRelease
-Hit http://incoming.debian.org sid InRelease
+Get:1 http://incoming.debian.org unstable InRelease [146 kB]
Ign http://incoming.debian.org InRelease
-Get:1 http://incoming.debian.org Release.gpg [836 B]
-Get:2 http://incoming.debian.org Release [1604 B]
-Hit http://ftp.de.debian.org sid/main Sources/DiffIndex
-Hit http://ftp.de.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.de.debian.org sid/main armel Packages/DiffIndex
-Hit http://ftp.de.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib TranslationIndex
-Hit http://ftp.de.debian.org sid/main TranslationIndex
-Hit http://incoming.debian.org sid/main Sources/DiffIndex
-Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
-Hit http://incoming.debian.org sid/main armel Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib armel Packages/DiffIndex
-Ign http://ftp.de.debian.org sid/contrib Translation-en
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Hit http://incoming.debian.org sid/main TranslationIndex
-Get:3 http://incoming.debian.org Sources [37.6 kB]
-Get:4 http://incoming.debian.org Packages [341 kB]
+Get:2 http://incoming.debian.org Release.gpg [836 B]
+Get:3 http://incoming.debian.org Release [1604 B]
+Get:4 http://incoming.debian.org unstable/main Sources [5932 kB]
+Get:5 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
+Get:6 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:7 http://incoming.debian.org unstable/main armel Packages [7674 kB]
+Get:8 http://ftp.uk.debian.org unstable InRelease [146 kB]
+Get:9 http://incoming.debian.org unstable/contrib armel Packages [55.6 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:10 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:11 http://incoming.debian.org Sources [46.0 kB]
+Get:12 http://incoming.debian.org Packages [374 kB]
Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org sid/contrib Translation-en
-Fetched 381 kB in 12s (29.3 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:13 http://ftp.uk.debian.org unstable/main Sources [5923 kB]
+Get:14 http://ftp.uk.debian.org unstable/contrib Sources [57.2 kB]
+Get:15 http://ftp.uk.debian.org unstable/non-free Sources [103 kB]
+Get:16 http://ftp.uk.debian.org unstable/main armel Packages [7673 kB]
+Get:17 http://ftp.uk.debian.org unstable/contrib armel Packages [55.6 kB]
+Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
+Get:18 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Fetched 28.4 MB in 1min 6s (425 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (175 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 0s (213 kB/s)
Download complete and in download only mode
Check arch
@@ -106,19 +106,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 27 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 27 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa 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), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -131,16 +131,16 @@ dpkg: already installed (1.16.1.1)
e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-3)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.12)
-sysvinit: already installed (2.88dsf-13.12)
-tar: already installed (1.26-2)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
bsdutils: already installed (1:2.19.1-5)
mount: already installed (2.19.1-5)
util-linux: already installed (2.19.1-5)
@@ -149,23 +149,119 @@ gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
-debhelper: already installed (8.9.8 >= 8 is satisfied)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+debhelper: missing
+Using default version 8.9.9
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies:
+Installing positive dependencies: debhelper zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
+The following extra packages will be installed:
+ bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
+Suggested packages:
+ wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
+ libmail-box-perl
+Recommended packages:
+ curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
+ libmail-sendmail-perl
+The following NEW packages will be installed:
+ bsdmainutils debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded.
+Need to get 8915 kB of archives.
+After this operation, 24.7 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.2.0-5 [34.2 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armel 8.12-4 [223 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.28.8-1 [1552 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.7.8.dfsg-5 [815 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.2-2 [110 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5 [406 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 8.2.3 [207 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.21-6 [1072 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.6.0.2-3 [987 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 5.09-2 [247 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main file armel 5.09-2 [51.8 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.18.1.1-5 [138 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main html2text armel 1.3.2a-15 [97.0 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.18.1.1-5 [1980 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.3.4.dfsg-3 [190 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 8915 kB in 35s (251 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10559 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_armel.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_armel.deb) ...
+Selecting previously unselected package libglib2.0-0.
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_armel.deb) ...
+Selecting previously unselected package libxml2.
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_armel.deb) ...
+Selecting previously unselected package libcroco3.
+Unpacking libcroco3 (from .../libcroco3_0.6.2-2_armel.deb) ...
+Selecting previously unselected package libunistring0.
+Unpacking libunistring0 (from .../libunistring0_0.9.3-5_armel.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_armel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_armel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-3_armel.deb) ...
+Selecting previously unselected package libmagic1.
+Unpacking libmagic1 (from .../libmagic1_5.09-2_armel.deb) ...
+Selecting previously unselected package file.
+Unpacking file (from .../archives/file_5.09-2_armel.deb) ...
+Selecting previously unselected package gettext-base.
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_armel.deb) ...
+Selecting previously unselected package html2text.
+Unpacking html2text (from .../html2text_1.3.2a-15_armel.deb) ...
+Selecting previously unselected package gettext.
+Unpacking gettext (from .../gettext_0.18.1.1-5_armel.deb) ...
+Selecting previously unselected package intltool-debian.
+Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
+Selecting previously unselected package po-debconf.
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Selecting previously unselected package debhelper.
+Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
+Selecting previously unselected package zlib1g-dev.
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_armel.deb) ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libpcre3 (8.12-4) ...
+Setting up libglib2.0-0 (2.28.8-1) ...
+No schema files found: doing nothing.
+Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libcroco3 (0.6.2-2) ...
+Setting up libunistring0 (0.9.3-5) ...
+Setting up bsdmainutils (8.2.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-3) ...
+Building database of manual pages ...
+Setting up libmagic1 (5.09-2) ...
+Setting up file (5.09-2) ...
+Setting up gettext-base (0.18.1.1-5) ...
+Setting up html2text (1.3.2a-15) ...
+Setting up gettext (0.18.1.1-5) ...
+Setting up intltool-debian (0.35.0+20060710.1) ...
+Setting up po-debconf (1.0.16+nmu1) ...
+Setting up debhelper (8.9.9) ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
-Kernel: Linux 2.6.31-rc9 armel (armv5tel)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-5
-Package versions: apex-nslu2_1.6.10 apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 bc_1.06.95-2 bf-utf-source_0.05-0.1 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20111022 cmake_2.8.5-1 cmake-data_2.8.5-1 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 cramfsprogs_1.1-6 dash_0.5.7-2 dctrl-tools_2.19 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debiandoc-sgml_1.2.25 debianutils_4.0.4 devio_1.2-1+b1 diffutils_1:3.2-1 dmsetup_2:1.02.67-1 dns323-firmware-tools_0.3-2 docbook-xml_4.5-7 docbook-xsl_1.75.2+dfsg-5 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 emacsen-common_1.4.22 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gawk_1:3.1.8+dfsg-0.1 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 generatorrunner_0.6.14-2 genext2fs_1.4.1-3 genisoimage_9:1.1.11-2 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libapiextractor-dev_0.10.8-1 libapiextractor0.10_0.10.8-1 libarchive1_2.8.5-3+b1 libattr1_1:2.4.46-3 libaudio2_1.9.3-1 libblkid1_2.19.1-5 libbogl-dev_0.1.18-5 libbogl0_0.1.18-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libc6-pic_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libcurl3_7.21.7-3 libcurl3-gnutls_7.21.7-3 libdb4.8_4.8.30-10 libdb5.1_5.1.25-11 libdbus-1-3_1.4.16-1 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7 libexpat1-dev_2.0.1-7 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgcrypt11_1.5.0-3 libgd2-noxpm_2.0.36~rc1~dfsg-6 libgdbm3_1.8.3-10 libgenrunner-dev_0.6.14-2 libgenrunner0.6_0.6.14-2 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.14-2 libgomp1_4.6.2-4 libgpg-error0_1.10-1 libgpm2_1.20.4-4 libgssapi-krb5-2_1.9.1+dfsg-3 libhtml-parser-perl_3.69-1 libhtml-tagset-perl_3.20-2 libice6_2:1.0.7-2 libidn11_1.22-3 libjpeg8_8c-2 libk5crypto3_1.9.1+dfsg-3 libkeyutils1_1.5.2-2 libkrb5-3_1.9.1+dfsg-3 libkrb5support0_1.9.1+dfsg-3 liblcms1_1.19.dfsg-1+b1 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmng1_1.0.10-3 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libnewt-dev_0.52.11-2.1 libnewt-pic_0.52.11-2.1 libnewt0.52_0.52.11-2.1 libp11-kit0_0.8-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-5 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpng12-dev_1.2.46-3 libpython2.6_2.6.7-4 libpython2.7_2.7.2-7 libqt4-dbus_4:4.7.3-8 libqt4-declarative_4:4.7.3-8 libqt4-designer_4:4.7.3-8 libqt4-dev_4:4.7.3-8 libqt4-help_4:4.7.3-8 libqt4-network_4:4.7.3-8 libqt4-qt3support_4:4.7.3-8 libqt4-script_4:4.7.3-8 libqt4-scripttools_4:4.7.3-8 libqt4-sql_4:4.7.3-8 libqt4-svg_4:4.7.3-8 libqt4-test_4:4.7.3-8 libqt4-xml_4:4.7.3-8 libqt4-xmlpatterns_4:4.7.3-8 libqtcore4_4:4.7.3-8 libqtgui4_4:4.7.3-8 libreadline5_5.2-11 libreadline6_6.2-7 libroman-perl_1.23-1 librtmp0_2.4~20110711.gitc28f1bab-1 libruby1.8_1.8.7.352-2 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libsgmls-perl_1.03ii-32 libsigsegv2_2.9-4 libslang2_2.2.4-3 libslang2-dev_2.2.4-3 libslang2-pic_2.2.4-3 libsm6_2:1.2.0-2 libsp1c2_1.3.4-1.2.1-47.1 libsparsehash-dev_1.10-1 libsqlite3-0_3.7.9-2 libss2_1.42~WIP-2011-10-16-1 libssh2-1_1.2.8-2 libssl-dev_1.0.0e-2.1 libssl1.0.0_1.0.0e-2.1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libtasn1-3_2.10-1 libtext-format-perl_0.53-1 libtiff4_3.9.5-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_172-1 libunistring0_0.9.3-4 liburi-perl_1.59-1 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libvolume-id1_0.141-2 libx11-6_2:1.4.4-4 libx11-data_2:1.4.4-2 libxau6_1:1.0.6-4+b1 libxcb1_1.7-4+b1 libxdmcp6_1:1.1.0-4 libxext6_2:1.3.0-3 libxml2_2.7.8.dfsg-5 libxmlrpc-core-c3_1.16.33-3.1 libxrender1_1:0.9.6-2 libxslt1.1_1.1.26-8 libxt6_1:1.1.1-2 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 mime-support_3.51-1 mklibs_0.1.33 mklibs-copy_0.1.33 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 netbase_4.46 nullmailer_1:1.05-1 openssl_1.0.0e-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.14-1 python_2.7.2-9 python-all_2.7.2-9 python-all-dbg_2.7.2-9 python-all-dev_2.7.2-9 python-dbg_2.7.2-9 python-dev_2.7.2-9 python-minimal_2.7.2-9 python2.6_2.6.7-4 python2.6-dbg_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.2-7 python2.7-dbg_2.7.2-7 python2.7-dev_2.7.2-7 python2.7-minimal_2.7.2-7 qt4-linguist-tools_4:4.7.3-8 qt4-qmake_4:4.7.3-8 readline-common_6.2-7 ruby1.8_1.8.7.352-2 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sgmlspl_1.03ii-32 slugimage_1:0.0+r104-5 sp_1.3.4-1.2.1-47.1 sudo_1.8.3-1 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 ttf-dejavu-core_2.33-2 tzdata_2011n-1 u-boot-tools_2011.09-1 uboot-mkimage_2011.09-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 wget_1.13.4-1 x11-common_1:7.6+9 xml-core_0.13 xsltproc_1.1.26-8 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 2.6.32 armel (armv5tel)
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-6
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-6 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -176,12 +272,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -191,254 +287,103 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture armel
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-armel-Ih7NSm/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org> >../bwa_0.5.10-1_armel.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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0441
-
-bwa_0.5.10-1_armel.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: armel
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: armel Build Daemon (ancina) <buildd_armel-ancina at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 5e5b84b28c09e0a1cb51db5e77a5dcbad15d47fe 138288 bwa_0.5.10-1_armel.deb
-Checksums-Sha256:
- c98aceeb9ccb708d8e4d4709e0a6cfa3d9797fe14f291fa8b2191962767b87f6 138288 bwa_0.5.10-1_armel.deb
-Files:
- 0b93acf76c4a2f26242077b1544a1de8 138288 science optional bwa_0.5.10-1_armel.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_armel.deb
-──────────────────────
-
- new debian package, version 2.0.
- size 138288 bytes: control archive= 995 bytes.
- 775 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: armel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 274
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/bin/
--rwxr-xr-x root/root 198360 2011-11-14 04:41 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:40 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/bwa/
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1106
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-armel-sbuild-2b189384-b91f-4db1-83ee-d01065ae0b59/build/buildd-bwa_0.5.10-1-armel-Ih7NSm
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 27 not upgraded.
+Purging /var/lib/schroot/mount/sid-armel-sbuild-7d77921b-1d84-4000-a672-ca117312854e/build/buildd-bwa_0.6.0-1-armel-HDdcYb
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: armel
-Build-Space: 2632
-Build-Time: 139
+Build-Space: 1152
+Build-Time: 56
Distribution: sid
-Install-Time: 19
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 112
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 197
-Source-Version: 0.5.10-1
-Space: 2632
-Status: successful
-Version: 0.5.10-1
+Package-Time: 266
+Source-Version: 0.6.0-1
+Space: 1152
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0441
-Build needed 00:03:17, 2632k disc space
-Signature with key '82E89EDA' requested:
+Finished at 20111114-1106
+Build needed 00:04:26, 1152k disc space
+
diff --git a/hurd-i386.log b/hurd-i386.log
index a28cf5c..319e189 100644
--- a/hurd-i386.log
+++ b/hurd-i386.log
@@ -1,90 +1,69 @@
-From buildd at bach.debian.net Mon Nov 14 04:46:43 2011
-Return-path: <buildd at bach.debian.net>
+From buildd at mozart.debian.net Mon Nov 14 11:23:22 2011
+Return-path: <buildd at mozart.debian.net>
Received: from callisto.debian.net ([80.87.129.151])
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at bach.debian.net>)
- id 1RPoRO-0001GT-Gw
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:46:43 +0000
-Received: from bach.debian.net ([10.3.0.1])
+ (Exim 4.72) (envelope-from <buildd at mozart.debian.net>)
+ id 1RPudF-0003UN-C6
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:23:22 +0000
+Received: from mozart.debian.net ([10.1.0.1])
by callisto.debian.net with esmtp (Exim 4.69)
- (envelope-from <buildd at bach.debian.net>)
- id 1RPoRM-0006Me-OA; Mon, 14 Nov 2011 04:46:40 +0000
-Received: from buildd by bach.debian.net with local (Exim 4.72)
- (envelope-from <buildd at bach.debian.net>)
- id 1RPoRO-0006VA-CE; Mon, 14 Nov 2011 04:46:42 +0000
-Date: Mon, 14 Nov 2011 04:46:42 +0000
-Message-Id: <E1RPoRO-0006VA-CE at bach.debian.net>
-From: Build Daemon <buildd at bach.debian.net>
-To: samuel.thibault at ens-lyon.org,mbanck at gmx.net,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on hurd-i386 (dist=unstable)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1RPud8-0005pa-F6; Mon, 14 Nov 2011 11:23:14 +0000
+Received: from buildd by mozart.debian.net with local (Exim 4.76)
+ (envelope-from <buildd at mozart.debian.net>)
+ id 1RPud7-0000IT-P8; Mon, 14 Nov 2011 11:23:13 +0000
+From: Build Daemon <buildd at mozart.debian.net>
+To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian-ports.org,
+ logs at buildd.debian.org
+Subject: Log for attempted build of bwa_0.6.0-1 on hurd-i386 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
+Message-Id: <E1RPud7-0000IT-P8 at mozart.debian.net>
+Date: Mon, 14 Nov 2011 11:23:13 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on bach.debian.net
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mozart.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (hurd-i386) 14 nov. 2011 04:42 ║
+║ bwa 0.6.0-1 (hurd-i386) 14 nov. 2011 11:13 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: hurd-i386
-Get:1 http://ftp.uk.debian.org sid InRelease [146 kB]
-Get:2 http://ftp.fr.debian.org sid InRelease [146 kB]
Ign http://incoming.debian.org InRelease
+Hit http://ftp.fr.debian.org sid InRelease
Ign http://ftp.debian-ports.org unreleased InRelease
-Get:3 http://incoming.debian.org Release.gpg [836 B]
-Get:4 http://ftp.uk.debian.org sid/main Sources/DiffIndex [2038 B]
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://ftp.fr.debian.org sid/main Sources/DiffIndex
Hit http://ftp.debian-ports.org unreleased Release.gpg
-Get:5 http://incoming.debian.org Release [1604 B]
-Get:6 http://ftp.fr.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://ftp.uk.debian.org sid/contrib Sources/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free Sources/DiffIndex
-Get:7 http://ftp.uk.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
-Hit http://ftp.uk.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/non-free hurd-i386 Packages/DiffIndex
-Ign http://ftp.uk.debian.org sid/contrib TranslationIndex
-Get:8 http://ftp.uk.debian.org sid/main TranslationIndex [2045 B]
-Ign http://ftp.uk.debian.org sid/non-free TranslationIndex
-Hit http://ftp.debian-ports.org unreleased Release
-Get:9 http://incoming.debian.org Sources [37.6 kB]
Hit http://ftp.fr.debian.org sid/contrib Sources/DiffIndex
Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
-Get:10 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [2038 B]
+Get:3 http://incoming.debian.org Sources [46.0 kB]
+Hit http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex
Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
Hit http://ftp.fr.debian.org sid/non-free hurd-i386 Packages/DiffIndex
Ign http://ftp.fr.debian.org sid/contrib TranslationIndex
-Get:11 http://ftp.uk.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:12 http://ftp.uk.debian.org sid/main hurd-i386 2011-11-14-0212.51.pdiff [13.4 kB]
-Hit http://ftp.uk.debian.org sid/main Translation-fr
-Get:13 http://ftp.fr.debian.org sid/main TranslationIndex [2045 B]
+Hit http://ftp.debian-ports.org unreleased Release
+Hit http://ftp.fr.debian.org sid/main TranslationIndex
Ign http://ftp.fr.debian.org sid/non-free TranslationIndex
-Get:14 http://ftp.fr.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:15 http://ftp.fr.debian.org sid/main hurd-i386 2011-11-14-0212.51.pdiff [13.4 kB]
-Hit http://ftp.fr.debian.org sid/main Translation-fr
-Get:16 http://ftp.uk.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:17 http://incoming.debian.org Packages [341 kB]
-Ign http://ftp.uk.debian.org sid/contrib Translation-en
-Ign http://ftp.uk.debian.org sid/contrib Translation-fr
-Ign http://ftp.uk.debian.org sid/non-free Translation-en
-Ign http://ftp.uk.debian.org sid/non-free Translation-fr
+Get:4 http://incoming.debian.org Packages [377 kB]
Hit http://ftp.debian-ports.org unreleased/main hurd-i386 Packages
Ign http://ftp.debian-ports.org unreleased/main TranslationIndex
Ign http://ftp.fr.debian.org sid/contrib Translation-en
-Ign http://ftp.fr.debian.org sid/contrib Translation-fr
Ign http://ftp.fr.debian.org sid/non-free Translation-en
-Ign http://ftp.fr.debian.org sid/non-free Translation-fr
-Ign http://incoming.debian.org Translation-en
-Ign http://incoming.debian.org Translation-fr
Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Ign http://ftp.debian-ports.org unreleased/main Translation-fr
-Get:18 http://ftp.uk.debian.org sid/main hurd-i386 2011-11-14-0212.51.pdiff [13.4 kB]
-Get:19 http://ftp.fr.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:20 http://ftp.fr.debian.org sid/main hurd-i386 2011-11-14-0212.51.pdiff [13.4 kB]
-Fetched 730 kB in 2min 27s (4961 B/s)
+Ign http://incoming.debian.org Translation-en
+Ign http://ftp.uk.debian.org sid InRelease
+Err http://ftp.uk.debian.org sid Release.gpg
+ Could not connect to ftp.uk.debian.org:80 (83.142.228.128), connection timed out
+Fetched 425 kB in 8min 22s (847 B/s)
Reading package lists...
+W: Failed to fetch http://ftp.uk.debian.org/debian/dists/sid/Release.gpg Could not connect to ftp.uk.debian.org:80 (83.142.228.128), connection timed out
+
+W: Some index files failed to download. They have been ignored, or old ones used instead.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -104,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (153 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 0s (148 kB/s)
Download complete and in download only mode
Check arch
@@ -128,66 +107,90 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 77 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 77 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
-base-files: already installed (6.4)
-base-passwd: already installed (3.5.22)
+base-files: already installed (6.5)
+base-passwd: already installed (3.5.23)
bash: already installed (4.1-3+hurd.1)
-coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.4)
-debianutils: already installed (4.0.2)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.0.3)
-e2fsprogs: already installed (1.42~WIP-2011-07-02-1)
+coreutils: already installed (8.13-3)
+dash: already installed (0.5.7-2)
+debianutils: already installed (4.0.4)
+diffutils: already installed (1:3.2-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
-grep: already installed (2.9-1)
+grep: already installed (2.9-2)
gzip: already installed (1.3.12-9)
hostname: already installed (3.06)
hurd: already installed (20111106-1)
-ncurses-base: already installed (5.9-1)
+ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
perl-base: already installed (5.14.2-3)
sed: already installed (4.2.1-9)
-sysvinit-utils: already installed (2.88dsf-13.10)
-sysvinit: already installed (2.88dsf-13.10)
-tar: already installed (1.25-2)
-bsdutils: already installed (1:2.16.2-0)
-util-linux: already installed (2.16.2-0)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-2)
+bsdutils: already installed (1:2.19.1-5)
+util-linux: already installed (2.19.1-5)
libc0.3-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.0-6 >= 4:4.4.3 is satisfied)
+g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
hurd-dev: already installed (20111106-1)
-debhelper: already installed (8.9.8 >= 8 is satisfied)
-zlib1g-dev: already installed (1:1.2.3.4.dfsg-3)
+debhelper: already installed (8.9.9 >= 8.9.4~ is satisfied)
+zlib1g-dev: missing
Checking for dependency conflicts...
-Installing positive dependencies:
+Installing positive dependencies: zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 77 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+The following NEW packages will be installed:
+ zlib1g-dev
+0 upgraded, 1 newly installed, 0 to remove and 16 not upgraded.
+Need to get 0 B/186 kB of archives.
+After this operation, 418 kB of additional disk space will be used.
+WARNING: The following packages cannot be authenticated!
+ zlib1g-dev
+Authentication warning overridden.
+Selecting previously unselected package zlib1g-dev.
+(Reading database ... 14514 files and directories currently installed.)
+Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_hurd-i386.deb) ...
+Processing triggers for man-db ...
+Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 77 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Checking correctness of dependencies...
Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 hurd-dev_20111106-1 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1
-Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 autopoint_0.18.1.1-4 base-files_6.4 base-passwd_3.5.22 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsd-mailx_8.1.2-0.20100314cvs-1 bsdmainutils_8.2.3 bsdutils_1:2.16.2-0 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20110502+nmu1 coreutils_8.5-1 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.4_4.4.6-10 cpp-4.5_4.5.3-8 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-118 dash_0.5.5.1-7.4 debconf_1.5.40 debfoster_2.6-2 debhelper_8.9.8 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.2 deborphan_1.7.28.5 dialog_1.1-20110707-1 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-07-02-1 e2fsprogs_1.42~WIP-2011-07-02-1 exim4-base_4.76-2+b3 exim4-config_4.76-2 exim4-daemon-light_4.76-2+b3 fakeroot_1.15.1-1 file_5.08-1 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.0-6 g++-4.5_4.5.3-8 g++-4.6_4.6.1-9+hurd.1 gawk_1:3.1.7.dfsg-5 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6+b1 gcc-4.4_4.4.6-10 gcc-4.4-base_4.4.6-10 gcc-4.5_4.5.3-8 gcc-4.5-base_4.5.3-8 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gfortran_4:4.6.1-3 gfortran-4.6_4.6.1-9+hurd.1 git_1:1.7.6.3-1 git-man_1:1.7.6.3-1 gnumach-dev_2:1.3.99.dfsg.git20110609-1 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-1 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20111106-1 hurd-dev_20111106-1 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-6 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libapt-pkg-dev_0.8.15.8 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-1 libcurl3-gnutls_7.21.7-3 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libelfg0_0.8.13-3 libept-dev_1.0.5 libept1_1.0.5 liberror-perl_0.17-1 libexpat1_2.0.1-7.2 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.8-1 libglib2.0-data_2.28.6-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libidn11_1.22-3 libldap-2.4-2_2.4.25-4 liblockfile-bin_1.09-3 liblockfile1_1.09-3 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.08-1 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.7-2 libpam-modules_1.1.3-2 libpam-modules-bin_1.1.3-2 libpam-runtime_1.1.3-2 libpam0g_1.1.3-6 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-7 librtmp0_2.4~20110711.gitc28f1bab-1 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2.1 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-8 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1 libtagcoll2-dev_2.0.13-1 libtasn1-3_2.10-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4p_2:0.1.12-13+hurd.1 libuuid1_2.19.1-5 libwibble-dev_0.1.26-1 libxapian-dev_1.2.7-1 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-5 lsb-base_3.2-27 lynx-cur_2.8.8dev.9-2+b1 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mime-support_3.51-1 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-4 netbase_4.46 netcat-traditional_1.10-39 openssl_1.0.0e-2 original-awk_2011-05-06-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 pkg-config_0.26-1 po-debconf_1.0.16+nmu1 procps_1:3.2.8-10 psmisc_22.3-1 readline-common_6.2-2 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-2 ttf-bitstream-vera_1.10-8 ttf-freefont_20100919-1 type-handling_0.2.23 tzdata_2011h-3 ucf_3.0025+nmu2 util-linux_2.16.2-0 xml-core_0.13 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.53.20110823-3+hurd.1 dpkg-dev_1.16.1.1 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gcc-4.4_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gnumach-dev_2:1.3.99.dfsg.git20111010-1 hurd-dev_20111106-1 libc0.3-dev_2.13-21 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1
+Package versions: adduser_3.113 apt_0.8.15.8 apt-utils_0.8.15.8 autopoint_0.18.1.1-5 base-files_6.5 base-passwd_3.5.23 bash_4.1-3+hurd.1 binutils_2.21.53.20110823-3+hurd.1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 ca-certificates_20111025 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.4_4.4.6-11 cpp-4.5_4.5.3-9 cpp-4.6_4.6.1-9+hurd.1 cron_3.0pl1-120 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debian-ports-archive-keyring_2011.01.12 debianutils_4.0.4 deborphan_1.7.28.5 dialog_1.1-20111020-1 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.15.1-1 file_5.09-2 findutils_4.4.2-1+b1 fontconfig_2.8.0-3 fontconfig-config_2.8.0-3 g++_4:4.6.1-3 g++-4.5_4.5.3-9 g++-4.6_4.6.1-9+hurd.1 gcc_4:4.6.1-3 gcc-4.4_4.4.6-11 gcc-4.4-base_4.4.6-11 gcc-4.5_4.5.3-9 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.1-9+hurd.1 gcc-4.6-base_4.6.1-9+hurd.1 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gfortran_4:4.6.1-3 gfortran-4.6_4.6.1-9+hurd.1 git_1:1.7.7-2 git-man_1:1.7.7-2 gnumach-dev_2:1.3.99.dfsg.git20111010-1 gnupg_1.4.11-3 gobjc-4.4_4.4.6-11 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15+b1 hurd_20111106-1 hurd-dev_20111106-1 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libboost-iostreams1.46.1_1.46.1-7 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.3_2.13-21 libc0.3-dev_2.13-21 libc0.3-xen_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libcurl3-gnutls_7.21.7-3 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libelfg0_0.8.13-3 libept1_1.0.5 liberror-perl_0.17-1 libexpat1_2.0.1-7.2 libfontconfig1_2.8.0-3 libfreetype6_2.4.7-2 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9+hurd.1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgfortran3_4.6.1-9+hurd.1 libglib2.0-0_2.28.8-1 libglib2.0-data_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.10-2 libgomp1_4.6.1-9+hurd.1 libgpg-error0_1.10-1 libidn11_1.22-3 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libobjc2_4.5.3-9 libp11-kit0_0.7-2 libpam-modules_1.1.3-5 libpam-modules-bin_1.1.3-5 libpam-runtime_1.1.3-5 libpam0g_1.1.3-6 libparted0debian1_2.3-3+hurd.1 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libpopt0_1.16-1 libpthread-stubs0_0.3-2.1+hurd.1 libpthread-stubs0-dev_0.3-2.1+hurd.1 libquadmath0_4.6.1-9+hurd.1 libreadline6_6.2-7 librtmp0_2.4~20110711.gitc28f1bab-1 libsasl2-2_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libsasl2-modules_2.1.24~rc1.dfsg1+cvs2011-05-23-6 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libssl0.9.8_0.9.8o-7+b1 libssl1.0.0_1.0.0e-2.1 libstdc++6_4.6.1-9+hurd.1 libstdc++6-4.5-dev_4.5.3-9 libstdc++6-4.6-dev_4.6.1-9+hurd.1 libswitch-perl_2.16-2 libsysfs2_2.1.0+repack-1 libtasn1-3_2.10-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libuuid1_2.19.1-5 libxapian22_1.2.7-1 libxml2_2.7.8.dfsg-5 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 openssl_1.0.0e-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.3-1 readline-common_6.2-7 rsync_3.0.9-1 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 shared-mime-info_0.90-1 sudo_1.7.2p7-1 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-2 ttf-dejavu-core_2.33-2 type-handling_0.2.23 tzdata_2011n-1 ucf_3.0025+nmu2 util-linux_2.19.1-5 xml-core_0.13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -198,12 +201,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -212,260 +215,151 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -fstack-protector --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture hurd-i386
/usr/bin/fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-hurd-i386-QaeTwo/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-hurd-i386-QaeTwo/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-hurd-i386-QaeTwo/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-hurd-i386-QaeTwo/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm/bwa-0.5.10'
- dh_auto_test
- /usr/bin/fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+In file included from ksw.c:28:0:
+/usr/lib/gcc/i486-gnu/4.6.1/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
+ksw.c:42:2: error: unknown type name '__m128i'
+ksw.c: In function 'ksw_qinit':
+ksw.c:54:11: error: '__m128i' undeclared (first use in this function)
+ksw.c:54:11: note: each undeclared identifier is reported only once for each function it appears in
+ksw.c:54:19: error: expected expression before ')' token
+ksw.c: In function 'ksw_sse2_16':
+ksw.c:97:2: error: unknown type name '__m128i'
+ksw.c:109:2: warning: implicit declaration of function '_mm_set1_epi32' [-Wimplicit-function-declaration]
+ksw.c:110:2: warning: implicit declaration of function '_mm_set1_epi8' [-Wimplicit-function-declaration]
+ksw.c:116:3: warning: implicit declaration of function '_mm_store_si128' [-Wimplicit-function-declaration]
+ksw.c:123:3: error: unknown type name '__m128i'
+ksw.c:124:3: warning: implicit declaration of function '_mm_load_si128' [-Wimplicit-function-declaration]
+ksw.c:125:3: warning: implicit declaration of function '_mm_slli_si128' [-Wimplicit-function-declaration]
+ksw.c:133:4: warning: implicit declaration of function '_mm_adds_epu8' [-Wimplicit-function-declaration]
+ksw.c:134:4: warning: implicit declaration of function '_mm_subs_epu8' [-Wimplicit-function-declaration]
+ksw.c:136:4: warning: implicit declaration of function '_mm_max_epu8' [-Wimplicit-function-declaration]
+ksw.c:160:5: warning: implicit declaration of function '_mm_movemask_epi8' [-Wimplicit-function-declaration]
+ksw.c:160:5: warning: implicit declaration of function '_mm_cmpeq_epi8' [-Wimplicit-function-declaration]
+ksw.c:166:3: warning: implicit declaration of function '_mm_srli_si128' [-Wimplicit-function-declaration]
+ksw.c:166:3: warning: implicit declaration of function '_mm_extract_epi16' [-Wimplicit-function-declaration]
+ksw.c: In function 'ksw_sse2_8':
+ksw.c:207:2: error: unknown type name '__m128i'
+ksw.c:219:2: warning: implicit declaration of function '_mm_set1_epi16' [-Wimplicit-function-declaration]
+ksw.c:231:3: error: unknown type name '__m128i'
+ksw.c:235:4: warning: implicit declaration of function '_mm_adds_epi16' [-Wimplicit-function-declaration]
+ksw.c:237:4: warning: implicit declaration of function '_mm_max_epi16' [-Wimplicit-function-declaration]
+ksw.c:241:4: warning: implicit declaration of function '_mm_subs_epu16' [-Wimplicit-function-declaration]
+ksw.c:257:5: warning: implicit declaration of function '_mm_cmpgt_epi16' [-Wimplicit-function-declaration]
+make[2]: *** [ksw.o] Error 1
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-hurd-i386-QaeTwo/bwa-0.6.0'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-hurd-i386-QaeTwo/bwa-0.6.0'
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0446
-
-bwa_0.5.10-1_hurd-i386.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: hurd-i386
-Version: 0.5.10-1
-Distribution: unstable
-Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-bach at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 0886e828f2d645d6a9414e3ec362b619fb0fbe2e 142682 bwa_0.5.10-1_hurd-i386.deb
-Checksums-Sha256:
- cfe6a204b0455b5f7fe615ec24c7149e19a0145a06b66bdd5d15807effb38d0e 142682 bwa_0.5.10-1_hurd-i386.deb
-Files:
- 4389e57e70fc246589076332d3864b18 142682 science optional bwa_0.5.10-1_hurd-i386.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_hurd-i386.deb
-──────────────────────────
-
- new debian package, version 2.0.
- size 142682 bytes: control archive= 1000 bytes.
- 787 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: hurd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 298
- Depends: hurd, libc0.3 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:46 ./
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:46 ./usr/bin/
--rwxr-xr-x root/root 223108 2011-11-14 04:46 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:46 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:46 ./usr/share/doc/bwa/
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-14 04:46 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:46 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:46 ./usr/share/man/man1/bwa.1.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1123
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /home/buildd/build/chroot-unstable/build/buildd-bwa_0.5.10-1-hurd-i386-kYXFNm
+Purging /home/buildd/build/chroot-sid/build/buildd-bwa_0.6.0-1-hurd-i386-QaeTwo
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 77 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 77 not upgraded.
+The following packages were automatically installed and are no longer required:
+ libept1 libxapian22 libboost-iostreams1.46.1 libsysfs2
+Use 'apt-get autoremove' to remove them.
+The following packages will be REMOVED:
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 1 to remove and 16 not upgraded.
+After this operation, 418 kB disk space will be freed.
+(Reading database ... 14544 files and directories currently installed.)
+Removing zlib1g-dev ...
+Processing triggers for man-db ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: hurd-i386
-Build-Space: 2704
-Build-Time: 77
-Distribution: unstable
-Install-Time: 15
-Job: bwa_0.5.10-1
+Build-Space: 1160
+Build-Time: 19
+Distribution: sid
+Fail-Stage: build
+Install-Time: 18
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 272
-Source-Version: 0.5.10-1
-Space: 2704
-Status: successful
-Version: 0.5.10-1
+Package-Time: 567
+Source-Version: 0.6.0-1
+Space: 1160
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0446
-Build needed 00:04:32, 2704k disc space
+Finished at 20111114-1123
+Build needed 00:09:27, 1160k disc space
diff --git a/i386.log b/i386.log
index 7ba390c..67d1c48 100644
--- a/i386.log
+++ b/i386.log
@@ -1,4 +1,4 @@
-From buildd at biber.debian.org Mon Nov 14 04:39:37 2011
+From buildd at biber.debian.org Mon Nov 14 11:02:06 2011
Return-path: <buildd at biber.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,43 +6,43 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1RPoKW-0008M7-Og
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:39:36 +0000
+ id 1RPuIg-0007SY-FD
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:02:06 +0000
Received: from biber.debian.org ([2001:648:2ffc:deb:214:22ff:feb2:1268])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=biber.debian.org, EMAIL=hostmaster at biber.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at biber.debian.org>)
- id 1RPoKV-0006Aa-Hs; Mon, 14 Nov 2011 04:39:35 +0000
+ id 1RPuIf-0007uY-JB; Mon, 14 Nov 2011 11:02:05 +0000
Received: from buildd by biber.debian.org with local (Exim 4.72)
(envelope-from <buildd at biber.debian.org>)
- id 1RPoKT-0000wE-EN; Mon, 14 Nov 2011 04:39:33 +0000
-Message-Id: <E1RPoKT-0000wE-EN at biber.debian.org>
+ id 1RPuIe-0007NM-RO; Mon, 14 Nov 2011 11:02:04 +0000
+Message-Id: <E1RPuIe-0007NM-RO 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: Mon, 14 Nov 2011 04:39:33 +0000
+Date: Mon, 14 Nov 2011 11:02:04 +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 bwa_0.5.10-1 on i386 (dist=sid)
+Subject: Log for attempted build of bwa_0.6.0-1 on i386 (dist=sid)
Key-Id: C83D412C
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on biber.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (i386) 14 Nov 2011 04:37 ║
+║ bwa 0.6.0-1 (i386) 14 Nov 2011 11:00 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: i386
Get:1 http://ftp.gr.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.gr.debian.org unstable/main Sources [5923 kB]
+Get:2 http://ftp.gr.debian.org unstable/main Sources [5932 kB]
Get:3 http://ftp.gr.debian.org unstable/contrib Sources [57.2 kB]
Get:4 http://ftp.gr.debian.org unstable/non-free Sources [103 kB]
-Get:5 http://ftp.gr.debian.org unstable/main i386 Packages [7853 kB]
+Get:5 http://ftp.gr.debian.org unstable/main i386 Packages [7852 kB]
Get:6 http://incoming.debian.org unstable InRelease [146 kB]
Get:7 http://ftp.gr.debian.org unstable/contrib i386 Packages [68.6 kB]
Ign http://ftp.gr.debian.org unstable/contrib TranslationIndex
@@ -50,19 +50,19 @@ Get:8 http://ftp.gr.debian.org unstable/main TranslationIndex [2045 B]
Ign http://ftp.gr.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
Get:9 http://incoming.debian.org Release.gpg [836 B]
-Get:10 http://incoming.debian.org unstable/main Sources [5923 kB]
+Get:10 http://incoming.debian.org unstable/main Sources [5932 kB]
Get:11 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main i386 Packages [7853 kB]
+Get:13 http://incoming.debian.org unstable/main i386 Packages [7852 kB]
Get:14 http://incoming.debian.org unstable/contrib i386 Packages [68.6 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [37.6 kB]
-Get:18 http://incoming.debian.org Packages [341 kB]
+Get:17 http://incoming.debian.org Sources [46.0 kB]
+Get:18 http://incoming.debian.org Packages [374 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.7 MB in 25s (1147 kB/s)
+Fetched 28.7 MB in 14s (2007 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 1s (113 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 1s (122 kB/s)
Download complete and in download only mode
Check arch
@@ -107,19 +107,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 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 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa 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), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -172,7 +172,7 @@ The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 12 not upgraded.
Need to get 9233 kB of archives.
After this operation, 25.6 MB of additional disk space will be used.
Get:1 http://ftp.gr.debian.org/debian/ unstable/main libpipeline1 i386 1.2.0-5 [37.6 kB]
@@ -194,7 +194,7 @@ Get:16 http://ftp.gr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1
Get:17 http://ftp.gr.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
Get:18 http://ftp.gr.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.3.4.dfsg-3 [186 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9233 kB in 0s (11.2 MB/s)
+Fetched 9233 kB in 0s (11.1 MB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10639 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_i386.deb) ...
@@ -258,7 +258,7 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-amd64 i386 (x86_64)
Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-6
@@ -273,12 +273,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -288,228 +288,111 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture i386
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-i386-iHJr0j/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-i386-iHJr0j/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-i386-iHJr0j/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-i386-iHJr0j/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-i386-rjrhDT/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_i386.deb'.
- dpkg-genchanges -B -mi386 Build Daemon <buildd_i386-biber at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+In file included from ksw.c:28:0:
+/usr/lib/gcc/i486-linux-gnu/4.6/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
+ksw.c:42:2: error: unknown type name '__m128i'
+ksw.c: In function 'ksw_qinit':
+ksw.c:54:11: error: '__m128i' undeclared (first use in this function)
+ksw.c:54:11: note: each undeclared identifier is reported only once for each function it appears in
+ksw.c:54:19: error: expected expression before ')' token
+ksw.c: In function 'ksw_sse2_16':
+ksw.c:97:2: error: unknown type name '__m128i'
+ksw.c:109:2: warning: implicit declaration of function '_mm_set1_epi32' [-Wimplicit-function-declaration]
+ksw.c:110:2: warning: implicit declaration of function '_mm_set1_epi8' [-Wimplicit-function-declaration]
+ksw.c:116:3: warning: implicit declaration of function '_mm_store_si128' [-Wimplicit-function-declaration]
+ksw.c:123:3: error: unknown type name '__m128i'
+ksw.c:124:3: warning: implicit declaration of function '_mm_load_si128' [-Wimplicit-function-declaration]
+ksw.c:125:3: warning: implicit declaration of function '_mm_slli_si128' [-Wimplicit-function-declaration]
+ksw.c:133:4: warning: implicit declaration of function '_mm_adds_epu8' [-Wimplicit-function-declaration]
+ksw.c:134:4: warning: implicit declaration of function '_mm_subs_epu8' [-Wimplicit-function-declaration]
+ksw.c:136:4: warning: implicit declaration of function '_mm_max_epu8' [-Wimplicit-function-declaration]
+ksw.c:160:5: warning: implicit declaration of function '_mm_movemask_epi8' [-Wimplicit-function-declaration]
+ksw.c:160:5: warning: implicit declaration of function '_mm_cmpeq_epi8' [-Wimplicit-function-declaration]
+ksw.c:166:3: warning: implicit declaration of function '_mm_srli_si128' [-Wimplicit-function-declaration]
+ksw.c:166:3: warning: implicit declaration of function '_mm_extract_epi16' [-Wimplicit-function-declaration]
+ksw.c: In function 'ksw_sse2_8':
+ksw.c:207:2: error: unknown type name '__m128i'
+ksw.c:219:2: warning: implicit declaration of function '_mm_set1_epi16' [-Wimplicit-function-declaration]
+ksw.c:231:3: error: unknown type name '__m128i'
+ksw.c:235:4: warning: implicit declaration of function '_mm_adds_epi16' [-Wimplicit-function-declaration]
+ksw.c:237:4: warning: implicit declaration of function '_mm_max_epi16' [-Wimplicit-function-declaration]
+ksw.c:241:4: warning: implicit declaration of function '_mm_subs_epu16' [-Wimplicit-function-declaration]
+ksw.c:257:5: warning: implicit declaration of function '_mm_cmpgt_epi16' [-Wimplicit-function-declaration]
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-i386-iHJr0j/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-i386-iHJr0j/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0439
-
-bwa_0.5.10-1_i386.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: i386
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: i386 Build Daemon <buildd_i386-biber at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- ca051e86f15e6d733a2714230c6fa7a106a3b530 143304 bwa_0.5.10-1_i386.deb
-Checksums-Sha256:
- 96170b68ae48d65eba19d9e8596b2d692526bd62f4b19455493221579b9830d6 143304 bwa_0.5.10-1_i386.deb
-Files:
- 446ed09e4c0d60d18d9223700989952b 143304 science optional bwa_0.5.10-1_i386.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_i386.deb
-─────────────────────
-
- new debian package, version 2.0.
- size 143304 bytes: control archive= 991 bytes.
- 774 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 298
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/bin/
--rwxr-xr-x root/root 223108 2011-11-14 04:39 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:39 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/bwa/
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1101
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-i386-sbuild-de4688c0-8ef9-40ec-bc1e-d4a3f328686f/build/buildd-bwa_0.5.10-1-i386-rjrhDT
+Purging /var/lib/schroot/mount/sid-i386-sbuild-3d73598b-a211-4f48-a5e6-a90b84eba70b/build/buildd-bwa_0.6.0-1-i386-iHJr0j
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -517,18 +400,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: i386
-Build-Space: 2704
-Build-Time: 20
+Build-Space: 1160
+Build-Time: 9
Distribution: sid
-Install-Time: 36
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 34
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 94
-Source-Version: 0.5.10-1
-Space: 2704
-Status: successful
-Version: 0.5.10-1
+Package-Time: 71
+Source-Version: 0.6.0-1
+Space: 1160
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0439
-Build needed 00:01:34, 2704k disc space
-Signature with key 'C83D412C' requested:
+Finished at 20111114-1101
+Build needed 00:01:11, 1160k disc space
diff --git a/ia64.log b/ia64.log
index e7ce66c..90ad9c8 100644
--- a/ia64.log
+++ b/ia64.log
@@ -1,4 +1,4 @@
-From buildd at alkman.debian.org Mon Nov 14 06:08:28 2011
+From buildd at alkman.debian.org Mon Nov 14 11:44:52 2011
Return-path: <buildd at alkman.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,23 +6,23 @@ Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1RPpiW-0006Uj-Hv
- for logs at buildd.debian.org; Mon, 14 Nov 2011 06:08:28 +0000
+ id 1RPuy4-0007Jx-L2
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:44:52 +0000
Received: from alkman.debian.org ([192.25.206.63])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=alkman.debian.org, EMAIL=hostmaster at alkman.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at alkman.debian.org>)
- id 1RPpiV-0001ba-2g
- for logs at buildd.debian.org; Mon, 14 Nov 2011 06:08:27 +0000
+ id 1RPuy2-0001HC-Ud
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:44:51 +0000
Received: from buildd by alkman.debian.org with local (Exim 4.72)
(envelope-from <buildd at alkman.debian.org>)
- id 1RPpiS-0004S8-8O; Mon, 14 Nov 2011 06:08:24 +0000
-Date: Mon, 14 Nov 2011 06:08:24 +0000
-Message-Id: <E1RPpiS-0004S8-8O at alkman.debian.org>
+ id 1RPuy0-00015Q-Nw; Mon, 14 Nov 2011 11:44:48 +0000
+Date: Mon, 14 Nov 2011 11:44:48 +0000
+Message-Id: <E1RPuy0-00015Q-Nw at alkman.debian.org>
From: buildd on alkman <buildd at alkman.debian.org>
To: buildd-porters at alkman.debian.org,logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on ia64 (dist=sid)
+Subject: Log for attempted build of bwa_0.6.0-1 on ia64 (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
Delivered-To: logs at buildd.debian.org
@@ -30,38 +30,38 @@ Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on alkman.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (ia64) 14 Nov 2011 06:04 ║
+║ bwa 0.6.0-1 (ia64) 14 Nov 2011 11:42 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: ia64
Get:1 http://spohr.debian.org unstable InRelease [146 kB]
-Get:2 http://spohr.debian.org unstable/main Sources [5923 kB]
+Get:2 http://spohr.debian.org unstable/main Sources [5932 kB]
Get:3 http://incoming.debian.org unstable InRelease [146 kB]
Get:4 http://spohr.debian.org unstable/contrib Sources [57.2 kB]
Get:5 http://spohr.debian.org unstable/non-free Sources [103 kB]
Get:6 http://spohr.debian.org unstable/main ia64 Packages [7546 kB]
Ign http://incoming.debian.org InRelease
Get:7 http://incoming.debian.org Release.gpg [836 B]
-Get:8 http://incoming.debian.org unstable/main Sources [5923 kB]
-Get:9 http://spohr.debian.org unstable/contrib ia64 Packages [56.3 kB]
+Get:8 http://incoming.debian.org unstable/main Sources [5932 kB]
+Get:9 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
+Get:10 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:11 http://incoming.debian.org unstable/main ia64 Packages [7546 kB]
+Get:12 http://incoming.debian.org unstable/contrib ia64 Packages [56.3 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:13 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:14 http://incoming.debian.org Release [1604 B]
+Get:15 http://incoming.debian.org Sources [46.1 kB]
+Get:16 http://incoming.debian.org Packages [381 kB]
+Get:17 http://spohr.debian.org unstable/contrib ia64 Packages [56.3 kB]
Ign http://spohr.debian.org unstable/contrib TranslationIndex
-Get:10 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
+Get:18 http://spohr.debian.org unstable/main TranslationIndex [2045 B]
Ign http://spohr.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main ia64 Packages [7546 kB]
-Get:14 http://incoming.debian.org unstable/contrib ia64 Packages [56.3 kB]
-Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [36.5 kB]
-Get:18 http://incoming.debian.org Packages [317 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.0 MB in 23s (1169 kB/s)
+Fetched 28.1 MB in 23s (1179 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (203 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 0s (206 kB/s)
Download complete and in download only mode
Check arch
@@ -124,7 +124,7 @@ Checking correctness of dependencies...
│ Install bwa build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -202,7 +202,7 @@ Get:16 http://spohr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1
Get:17 http://spohr.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
Get:18 http://spohr.debian.org/debian/ unstable/main zlib1g-dev ia64 1:1.2.3.4.dfsg-3 [224 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.0 MB in 3s (2811 kB/s)
+Fetched 11.0 MB in 0s (14.0 MB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10538 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_ia64.deb) ...
@@ -284,12 +284,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -304,228 +304,83 @@ dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIF
dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS =
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture ia64
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-ia64-k_dwhK/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-ia64-k_dwhK/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-ia64-k_dwhK/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security "
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-ia64-k_dwhK/bwa-0.6.0'
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-ia64-XQOwWM/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-ia64-k_dwhK/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-ia64-k_dwhK/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0608
-
-bwa_0.5.10-1_ia64.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: ia64
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: ia64 Build Daemon (alkman) <buildd_ia64-alkman at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 4cc31d07eab3b280f19eda8081a6b36e4db33f85 210050 bwa_0.5.10-1_ia64.deb
-Checksums-Sha256:
- 08e182a831ea19ae65c6292366dc7d632603ba2af0f4521c7c126e250cf93e65 210050 bwa_0.5.10-1_ia64.deb
-Files:
- 3ff1bc53862c3168a27184c906aed428 210050 science optional bwa_0.5.10-1_ia64.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_ia64.deb
-─────────────────────
-
- new debian package, version 2.0.
- size 210050 bytes: control archive= 993 bytes.
- 776 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: ia64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 463
- Depends: libc6.1 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 06:08 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/share/bwa/
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
-drwxr-xr-x root/root 0 2011-11-14 06:08 ./usr/bin/
--rwxr-xr-x root/root 432352 2011-11-14 06:08 ./usr/bin/bwa
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1144
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-cf34cad6-3458-4285-8519-44936c10337f/build/buildd-bwa_0.5.10-1-ia64-XQOwWM
+Purging /var/lib/schroot/mount/sid-ia64-sbuild-d7cab6a9-22a1-454d-8a11-b88379ae3c74/build/buildd-bwa_0.6.0-1-ia64-k_dwhK
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -533,19 +388,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: ia64
-Build-Space: 4932
-Build-Time: 63
+Build-Space: 2080
+Build-Time: 18
Distribution: sid
-Install-Time: 96
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 59
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 222
-Source-Version: 0.5.10-1
-Space: 4932
-Status: successful
-Version: 0.5.10-1
+Package-Time: 133
+Source-Version: 0.6.0-1
+Space: 2080
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0608
-Build needed 00:03:42, 4932k disc space
-Signature with key 'FC1E8668' requested:
+Finished at 20111114-1144
+Build needed 00:02:13, 2080k disc space
diff --git a/info b/info
index a382f45..088d45a 100644
--- a/info
+++ b/info
@@ -1,11 +1,11 @@
-i386~1321245583~sid~successful
-powerpc~1321245602~sid~successful
-kfreebsd-i386~1321245632~sid~successful
-s390~1321245640~sid~successful
-armel~1321245688~sid~successful
-kfreebsd-amd64~1321245709~sid~successful
-sparc~1321245731~sid~successful
-mips~1321245931~sid~successful
-mipsel~1321245956~sid~successful
-hurd-i386~1321246004~sid~successful
-ia64~1321250909~sid~successful
+s390~1321268358~sid~failed
+powerpc~1321268378~sid~failed
+i386~1321268527~sid~failed
+sparc~1321268561~sid~failed
+mips~1321268650~sid~failed
+mipsel~1321268667~sid~failed
+armel~1321268787~sid~failed
+kfreebsd-i386~1321269767~sid~failed
+hurd-i386~1321269813~sid~failed
+kfreebsd-amd64~1321270379~sid~successful
+ia64~1321271093~sid~failed
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 4c5624e..57d64b7 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,82 +1,74 @@
-From buildd at fano.debian.org Mon Nov 14 04:41:48 2011
-Return-path: <buildd at fano.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+From buildd at fasch.debian.org Mon Nov 14 11:32:59 2011
+Return-path: <buildd at fasch.debian.org>
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1RPoMe-0000VG-NY
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:41:48 +0000
-Received: from fano.debian.org ([206.12.19.110])
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1RPumZ-0005F2-CZ
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:32:59 +0000
+Received: from fasch.debian.org ([194.177.211.201])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at fano.debian.org>)
- id 1RPoMd-0006N5-8f; Mon, 14 Nov 2011 04:41:47 +0000
-Received: from buildd by fano.debian.org with local (Exim 4.72)
- (envelope-from <buildd at fano.debian.org>)
- id 1RPoMa-000Ded-RW; Mon, 14 Nov 2011 04:41:44 +0000
-Message-Id: <E1RPoMa-000Ded-RW at fano.debian.org>
+ CN=fasch.debian.org, EMAIL=hostmaster at fasch.debian.org (verified)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ (Exim 4.72) (envelope-from <buildd at fasch.debian.org>)
+ id 1RPumY-0002jR-8P; Mon, 14 Nov 2011 11:32:58 +0000
+Received: from buildd by fasch.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at fasch.debian.org>)
+ id 1RPumX-000EZd-M9; Mon, 14 Nov 2011 11:32:57 +0000
+Message-Id: <E1RPumX-000EZd-M9 at fasch.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Mon, 14 Nov 2011 04:41:44 +0000
-From: buildd on fano <buildd at fano.debian.org>
+Date: Mon, 14 Nov 2011 11:32:57 +0000
+From: buildd on fasch <buildd at fasch.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on kfreebsd-amd64 (dist=sid)
-Key-Id: D33FE1D8
+Subject: Log for successful build of bwa_0.6.0-1 on kfreebsd-amd64 (dist=sid)
+Key-Id: 0868AC12
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fano.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on fasch.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (kfreebsd-amd64) 14 Nov 2011 04:39 ║
+║ bwa 0.6.0-1 (kfreebsd-amd64) 14 Nov 2011 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: kfreebsd-amd64
-Get:1 http://incoming.debian.org sid InRelease [146 kB]
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
+Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Get:3 http://incoming.debian.org sid/main Sources/DiffIndex [2038 B]
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
+Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
+Get:1 http://incoming.debian.org Release.gpg [836 B]
+Ign http://ftp.gr.debian.org sid/contrib Translation-en
+Ign http://ftp.gr.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:4 http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
+Hit http://incoming.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
Hit http://incoming.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:5 http://incoming.debian.org sid/main TranslationIndex [2045 B]
+Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:6 http://mirror-ubc.debian.org sid InRelease [146 kB]
-Get:7 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
-Get:8 http://incoming.debian.org Release [1604 B]
-Get:9 http://incoming.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:10 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-14-0212.51.pdiff [7519 B]
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Get:11 http://incoming.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:12 http://incoming.debian.org Sources [37.6 kB]
-Get:13 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 Packages/DiffIndex [2038 B]
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-amd64 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-amd64 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Get:14 http://mirror-ubc.debian.org sid/main TranslationIndex [2045 B]
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:15 http://mirror-ubc.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:16 http://incoming.debian.org Packages [341 kB]
-Get:17 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-14-0212.51.pdiff [7519 B]
-Get:18 http://incoming.debian.org sid/main kfreebsd-amd64 2011-11-14-0212.51.pdiff [7519 B]
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
+Get:2 http://incoming.debian.org Release [1604 B]
+Hit http://incoming.debian.org Sources
+Get:3 http://incoming.debian.org Packages [377 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Get:19 http://mirror-ubc.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:20 http://mirror-ubc.debian.org sid/main kfreebsd-amd64 2011-11-14-0212.51.pdiff [7519 B]
-Fetched 718 kB in 9s (71.9 kB/s)
+Fetched 379 kB in 5s (74.9 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -97,11 +89,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (171 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 1s (92.0 kB/s)
Download complete and in download only mode
Check arch
@@ -121,19 +113,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -145,18 +137,18 @@ diffutils: already installed (1:3.2-1)
dpkg: already installed (1.16.1.1)
e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1)
-freebsd-utils: already installed (8.2+ds2-9)
+freebsd-utils: already installed (8.2+ds2-10)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-3)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.13)
sysvinit: already installed (2.88dsf-13.13)
-tar: already installed (1.25-3)
+tar: already installed (1.26-3)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
@@ -173,23 +165,23 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
- libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
+ file gettext gettext-base groff-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
dh-make gettext-doc groff less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
- debhelper file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
- zlib1g-dev
+ debhelper file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 15 newly installed, 0 to remove and 8 not upgraded.
-Need to get 0 B/7774 kB of archives.
-After this operation, 20.0 MB of additional disk space will be used.
+0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/8886 kB of archives.
+After this operation, 23.1 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 11669 files and directories currently installed.)
+(Reading database ... 11451 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_kfreebsd-amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-amd64.deb) ...
@@ -199,6 +191,8 @@ Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-amd64.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-amd64.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-amd64.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-3_kfreebsd-amd64.deb) ...
Selecting previously unselected package libmagic1.
@@ -225,6 +219,7 @@ No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
@@ -240,11 +235,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-amd64 kfreebsd-amd64 (x86_64)
Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-3 gcc-4.6_4.6.2-3 kfreebsd-kernel-headers_0.60 libc0.1-dev_2.13-21 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-9 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kbdcontrol_8.2+ds2-9 kfreebsd-kernel-headers_0.60 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.25-3 type-handling_0.2.23 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-3 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-10 g++_4:4.6.1-3 g++-4.6_4.6.2-3 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.2-3 gcc-4.6-base_4.6.2-3 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kbdcontrol_8.2+ds2-10 kfreebsd-kernel-headers_0.60 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-3 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libquadmath0_4.6.2-3 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-3 libstdc++6-4.6-dev_4.6.2-3 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 type-handling_0.2.23 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -255,12 +250,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -270,79 +265,116 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture kfreebsd-amd64
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-kfreebsd-amd64-e8smFP/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-kfreebsd-amd64-e8smFP/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-kfreebsd-amd64-e8smFP/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-kfreebsd-amd64-e8smFP/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD stdaln.c -o stdaln.o
stdaln.c: In function 'aln_local_core':
stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
stdaln.c: In function 'aln_extend_core':
stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwase.c -o bwase.o
bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
+bwase.c:74:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+bwase.c:447:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
+bwase.c: In function 'bwa_sai2sam_se_core':
+bwase.c:603:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwase.c:619:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwase.c:624:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwase.c: In function 'bwa_refine_gapped':
+bwase.c:310:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwase.c:316:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwape.c -o bwape.o
+bwape.c: In function 'bwa_sai2sam_pe_core':
+bwape.c:683:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwape.c:686:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwape.c:697:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwape.c: In function 'bwa_paired_sw':
+bwape.c:527:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwape.c: In function 'bwa_cal_pac_pos_pe':
+bwape.c:312:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwape.c:316:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi/bwa-0.5.10'
+bwtsw2_aux.c:186:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
+bwtsw2_aux.c: In function 'bsw2_aln':
+bwtsw2_aux.c:734:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD fastmap.c -o fastmap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD main.c -o main.o
+gcc -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.o bwt_gen.o utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o ksw.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o fastmap.o bwtsw2_pair.o main.o -o bwa -lm -lz -lpthread
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-kfreebsd-amd64-e8smFP/bwa-0.6.0'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-kfreebsd-amd64-e8smFP/bwa-0.6.0'
dh_auto_test
fakeroot debian/rules binary-arch
dh binary-arch
@@ -391,61 +423,58 @@ dh binary-arch
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../bwa_0.5.10-1_kfreebsd-amd64.changes
+dpkg-deb: building package `bwa' in `../bwa_0.6.0-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org> >../bwa_0.6.0-1_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 bwa-0.5.10
+ dpkg-source --after-build bwa-0.6.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0441
+Build finished at 20111114-1132
-bwa_0.5.10-1_kfreebsd-amd64.changes:
+bwa_0.6.0-1_kfreebsd-amd64.changes:
Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
+Date: Mon, 14 Nov 2011 19:28:44 +0900
Source: bwa
Binary: bwa
Architecture: kfreebsd-amd64
-Version: 0.5.10-1
+Version: 0.6.0-1
Distribution: sid
Urgency: low
-Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
+Maintainer: kfreebsd-amd64 Build Daemon (fasch) <buildd_kfreebsd-amd64-fasch at buildd.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
bwa - Burrows-Wheeler Aligner
Changes:
- bwa (0.5.10-1) unstable; urgency=low
+ bwa (0.6.0-1) experimental; urgency=low
.
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
+ [9ce640c] New upstream release (not to use in a production pipeline).
+ [e641dd6] Corrected the name of the file downloaded by uscan.
+ [4ada685] Pass Dpkg build flags to the compiler through Debhelper 9. Thanks, Niels Thykier!
Checksums-Sha1:
- 0f0e4580316f25a586791173e6fbc9b7e3f8f088 137840 bwa_0.5.10-1_kfreebsd-amd64.deb
+ ae72ac75c495fa6add85a536ed7d0946cba67815 151688 bwa_0.6.0-1_kfreebsd-amd64.deb
Checksums-Sha256:
- c58a41579600306d5fd5ff0419720e008304b0d940cebd249fcc783d5981c1d1 137840 bwa_0.5.10-1_kfreebsd-amd64.deb
+ e6a5eb118a5f1f8c78312ad2b539941d45cd238f277f869787cf6a9270c69e0e 151688 bwa_0.6.0-1_kfreebsd-amd64.deb
Files:
- fa8859882847a81664fc5fdcf98b1a89 137840 science optional bwa_0.5.10-1_kfreebsd-amd64.deb
+ 1e7bf632d35356660c7ab95fd4d12dfc 151688 science optional bwa_0.6.0-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.5.10-1_kfreebsd-amd64.deb
-───────────────────────────────
+bwa_0.6.0-1_kfreebsd-amd64.deb
+──────────────────────────────
new debian package, version 2.0.
- size 137840 bytes: control archive= 999 bytes.
- 786 bytes, 17 lines control
+ size 151688 bytes: control archive= 1000 bytes.
+ 785 bytes, 17 lines control
610 bytes, 10 lines md5sums
Package: bwa
- Version: 0.5.10-1
+ Version: 0.6.0-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 240
+ Installed-Size: 261
Depends: libc0.1 (>= 2.7), zlib1g (>= 1:1.1.4)
Suggests: samtools
Section: science
@@ -459,25 +488,25 @@ bwa_0.5.10-1_kfreebsd-amd64.deb
to around 100 kbp. Both algorithms do gapped alignment. They are usually more
accurate and faster on queries with low error rates.
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/bin/
--rwxr-xr-x root/root 199752 2011-11-14 04:41 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/bwa/
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/bin/
+-rwxr-xr-x root/root 219752 2011-11-14 11:32 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/share/
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/share/bwa/
-rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
-rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
-rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/doc/bwa/
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/share/doc/bwa/
-rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
+-rw-r--r-- root/root 2785 2011-11-14 10:27 ./usr/share/doc/bwa/copyright
-rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:41 ./usr/share/man/man1/bwa.1.gz
+-rw-r--r-- root/root 6680 2011-11-13 01:07 ./usr/share/doc/bwa/NEWS.gz
+-rw-r--r-- root/root 1299 2011-11-14 10:28 ./usr/share/doc/bwa/changelog.Debian.gz
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-11-14 11:32 ./usr/share/man/man1/
+-rw-r--r-- root/root 7745 2011-11-14 11:32 ./usr/share/man/man1/bwa.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -491,27 +520,31 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-ka-sbuild-1321245599-51310/build/buildd-bwa_0.5.10-1-kfreebsd-amd64-0kWugi
+Purging /var/lib/schroot/mount/sid-ka-sbuild-1321270210-54109/build/buildd-bwa_0.6.0-1-kfreebsd-amd64-e8smFP
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- debhelper* file* gettext* gettext-base* html2text* intltool-debian*
- libcroco3* libglib2.0-0* libmagic1* libpipeline1* libunistring0* libxml2*
- man-db* po-debconf* zlib1g-dev*
-0 upgraded, 0 newly installed, 15 to remove and 8 not upgraded.
-After this operation, 20.0 MB disk space will be freed.
-(Reading database ... 12704 files and directories currently installed.)
+ debhelper* file* gettext* gettext-base* groff-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
+ libunistring0* libxml2* man-db* po-debconf* zlib1g-dev*
+0 upgraded, 0 newly installed, 16 to remove and 0 not upgraded.
+After this operation, 23.1 MB disk space will be freed.
+(Reading database ... 12666 files and directories currently installed.)
Removing debhelper ...
Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
@@ -520,8 +553,6 @@ Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
-Removing man-db ...
-Purging configuration files for man-db ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
@@ -535,18 +566,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-amd64
-Build-Space: 3010
-Build-Time: 23
+Build-Space: 3258
+Build-Time: 24
Distribution: sid
-Install-Time: 32
-Job: bwa_0.5.10-1
+Install-Time: 76
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 75
-Source-Version: 0.5.10-1
-Space: 3010
+Package-Time: 121
+Source-Version: 0.6.0-1
+Space: 3258
Status: successful
-Version: 0.5.10-1
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0441
-Build needed 00:01:15, 3010k disc space
-Signature with key 'D33FE1D8' requested:
+Finished at 20111114-1132
+Build needed 00:02:01, 3258k disc space
+Signature with key '0868AC12' requested:
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 0cd2efe..848d2b8 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,46 +1,59 @@
-From buildd at finzi.debian.org Mon Nov 14 04:40:31 2011
-Return-path: <buildd at finzi.debian.org>
+From buildd at field.debian.org Mon Nov 14 11:22:46 2011
+Return-path: <buildd at field.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1RPoLP-0000A3-Fw
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:40:31 +0000
-Received: from finzi.debian.org ([206.12.19.111])
+ (Exim 4.72) (envelope-from <buildd at field.debian.org>)
+ id 1RPucg-0003L7-RS
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:22:46 +0000
+Received: from field.debian.org ([194.177.211.210])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
+ CN=field.debian.org, EMAIL=hostmaster at field.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at finzi.debian.org>)
- id 1RPoLN-0004On-J0; Mon, 14 Nov 2011 04:40:30 +0000
-Received: from buildd by finzi.debian.org with local (Exim 4.72)
- (envelope-from <buildd at finzi.debian.org>)
- id 1RPoLK-0002UZ-JI; Mon, 14 Nov 2011 04:40:26 +0000
-Message-Id: <E1RPoLK-0002UZ-JI at finzi.debian.org>
+ (Exim 4.72) (envelope-from <buildd at field.debian.org>)
+ id 1RPuce-0002HY-NS; Mon, 14 Nov 2011 11:22:44 +0000
+Received: from buildd by field.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at field.debian.org>)
+ id 1RPuce-0001wP-3B; Mon, 14 Nov 2011 11:22:44 +0000
+Message-Id: <E1RPuce-0001wP-3B at field.debian.org>
MIME-Version: 1.0
Content-Transfer-Encoding: binary
X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Mon, 14 Nov 2011 04:40:26 +0000
-From: buildd on finzi <buildd at finzi.debian.org>
+Date: Mon, 14 Nov 2011 11:22:44 +0000
+From: buildd on field <buildd at field.debian.org>
To: logs at buildd.debian.org,aurelien at aurel32.net,christoph at debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on kfreebsd-i386 (dist=sid)
-Key-Id: D859A500
+Subject: Log for attempted build of bwa_0.6.0-1 on kfreebsd-i386 (dist=sid)
+Key-Id: 65BA331C
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on finzi.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on field.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (kfreebsd-i386) 14 Nov 2011 04:38 ║
+║ bwa 0.6.0-1 (kfreebsd-i386) 14 Nov 2011 11:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: kfreebsd-i386
+Hit http://ftp.gr.debian.org sid InRelease
+Hit http://ftp.gr.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid InRelease
Ign http://incoming.debian.org InRelease
+Hit http://ftp.gr.debian.org sid/contrib Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free Sources/DiffIndex
+Hit http://ftp.gr.debian.org sid/main kfreebsd-i386 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
+Ign http://ftp.gr.debian.org sid/contrib TranslationIndex
+Hit http://ftp.gr.debian.org sid/main TranslationIndex
+Ign http://ftp.gr.debian.org sid/non-free TranslationIndex
Get:1 http://incoming.debian.org Release.gpg [836 B]
+Hit http://ftp.gr.debian.org sid/non-free kfreebsd-i386 Packages
+Ign http://ftp.gr.debian.org sid/contrib Translation-en
+Ign http://ftp.gr.debian.org sid/non-free Translation-en
Hit http://incoming.debian.org sid/main Sources/DiffIndex
Hit http://incoming.debian.org sid/contrib Sources/DiffIndex
Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
@@ -50,31 +63,14 @@ Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
Ign http://incoming.debian.org sid/contrib TranslationIndex
Hit http://incoming.debian.org sid/main TranslationIndex
Ign http://incoming.debian.org sid/non-free TranslationIndex
-Get:2 http://mirror-ubc.debian.org sid InRelease [146 kB]
-Get:3 http://incoming.debian.org Release [1604 B]
+Get:2 http://incoming.debian.org Release [1604 B]
Hit http://incoming.debian.org sid/non-free kfreebsd-i386 Packages
-Get:4 http://mirror-ubc.debian.org sid/main Sources/DiffIndex [2038 B]
-Hit http://mirror-ubc.debian.org sid/contrib Sources/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free Sources/DiffIndex
-Get:5 http://mirror-ubc.debian.org sid/main kfreebsd-i386 Packages/DiffIndex [2038 B]
-Hit http://mirror-ubc.debian.org sid/contrib kfreebsd-i386 Packages/DiffIndex
-Hit http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages/DiffIndex
-Ign http://mirror-ubc.debian.org sid/contrib TranslationIndex
-Hit http://mirror-ubc.debian.org sid/main TranslationIndex
-Ign http://mirror-ubc.debian.org sid/non-free TranslationIndex
-Get:6 http://mirror-ubc.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:7 http://incoming.debian.org Sources [37.6 kB]
-Get:8 http://incoming.debian.org Packages [341 kB]
-Get:9 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-11-14-0212.51.pdiff [7511 B]
-Get:10 http://mirror-ubc.debian.org sid/main 2011-11-14-0212.51.pdiff [9020 B]
-Get:11 http://mirror-ubc.debian.org sid/non-free kfreebsd-i386 Packages [87.9 kB]
-Ign http://mirror-ubc.debian.org sid/contrib Translation-en
-Ign http://mirror-ubc.debian.org sid/non-free Translation-en
+Hit http://incoming.debian.org Sources
+Get:3 http://incoming.debian.org Packages [377 kB]
Ign http://incoming.debian.org sid/contrib Translation-en
Ign http://incoming.debian.org sid/non-free Translation-en
Ign http://incoming.debian.org Translation-en
-Get:12 http://mirror-ubc.debian.org sid/main kfreebsd-i386 2011-11-14-0212.51.pdiff [7511 B]
-Fetched 636 kB in 7s (86.6 kB/s)
+Fetched 379 kB in 5s (74.0 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -95,11 +91,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (181 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 1s (107 kB/s)
Download complete and in download only mode
Check arch
@@ -119,19 +115,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 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 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -145,16 +141,16 @@ e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1)
freebsd-utils: already installed (8.2+ds2-8)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-4)
ncurses-bin: already installed (5.9-4)
-perl-base: already installed (5.12.4-6)
+perl-base: already installed (5.14.2-3)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
sysvinit-utils: already installed (2.88dsf-13.13)
sysvinit: already installed (2.88dsf-13.13)
-tar: already installed (1.25-3)
+tar: already installed (1.26-3)
bsdutils: already installed (1:2.19.1-5)
util-linux: already installed (2.19.1-5)
libc6-dev: already installed (~*=PROVIDED=*=)
@@ -171,23 +167,23 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
- libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
+ file gettext gettext-base groff-base html2text intltool-debian libcroco3
+ libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
Suggested packages:
dh-make gettext-doc groff less www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
- debhelper file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
- zlib1g-dev
+ debhelper file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db
+ po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 15 newly installed, 0 to remove and 6 not upgraded.
-Need to get 0 B/7638 kB of archives.
-After this operation, 19.5 MB of additional disk space will be used.
+0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/8731 kB of archives.
+After this operation, 22.6 MB of additional disk space will be used.
Selecting previously unselected package libpipeline1.
-(Reading database ... 13417 files and directories currently installed.)
+(Reading database ... 11547 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_kfreebsd-i386.deb) ...
Selecting previously unselected package libglib2.0-0.
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_kfreebsd-i386.deb) ...
@@ -197,6 +193,8 @@ Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_kfreebsd-i386.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_kfreebsd-i386.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_kfreebsd-i386.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-3_kfreebsd-i386.deb) ...
Selecting previously unselected package libmagic1.
@@ -223,6 +221,7 @@ No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-3) ...
Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
@@ -238,11 +237,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: GNU/kFreeBSD 8.1-1-686-smp kfreebsd-i386 (i686)
Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 kfreebsd-kernel-headers_0.60 libc0.1-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4
-Package versions: apt_0.8.15.9 autotools-dev_20110511.1 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-8 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.2-base_4.2.4-6 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kbdcontrol_8.2+ds2-8 kfreebsd-kernel-headers_0.60 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.12-1 libgomp1_4.6.2-4 libgpg-error0_1.10-1 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 libldap-2.4-2_2.4.25-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.8-2 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libquadmath0_4.6.2-4 libreadline6_6.2-7 libsasl2-2_2.1.25.dfsg1-2 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libtasn1-3_2.10-1 libtext-charwidth-perl_0.04-7 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-1 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.25-3 tzdata_2011n-1 util-linux_2.19.1-5 vim_2:7.3.346-1 vim-common_2:7.3.346-1 vim-runtime_2:7.3.346-1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debconf-english_1.5.38 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1 freebsd-utils_8.2+ds2-8 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 kbdcontrol_8.2+ds2-8 kfreebsd-kernel-headers_0.60 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbsd0_0.3.0-1 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc0.1_2.13-21 libc0.1-dev_2.13-21 libcam0_8.2+ds1-4 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libexpat1_2.0.1-7.2 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libgeom1_8.2+ds1-4 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 libgssglue1_0.3-3.1 libjail1_8.2+ds1-4 libkiconv4_8.2+ds1-4 libkvm0_8.2+ds1-4 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libquadmath0_4.6.2-4 libreadline6_6.2-7 libsbuf0_8.2+ds1-4 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libtirpc1_0.2.2-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 lzma_4.43-14 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 psmisc_22.13-1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 type-handling_0.2.23 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -253,12 +252,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -268,248 +267,135 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture kfreebsd-i386
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-kfreebsd-i386-Inf6PD/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-kfreebsd-i386-Inf6PD/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-kfreebsd-i386-Inf6PD/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-kfreebsd-i386-Inf6PD/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+In file included from ksw.c:28:0:
+/usr/lib/gcc/i486-kfreebsd-gnu/4.6/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
+ksw.c:42:2: error: unknown type name '__m128i'
+ksw.c: In function 'ksw_qinit':
+ksw.c:54:11: error: '__m128i' undeclared (first use in this function)
+ksw.c:54:11: note: each undeclared identifier is reported only once for each function it appears in
+ksw.c:54:19: error: expected expression before ')' token
+ksw.c: In function 'ksw_sse2_16':
+ksw.c:97:2: error: unknown type name '__m128i'
+ksw.c:109:2: warning: implicit declaration of function '_mm_set1_epi32' [-Wimplicit-function-declaration]
+ksw.c:110:2: warning: implicit declaration of function '_mm_set1_epi8' [-Wimplicit-function-declaration]
+ksw.c:116:3: warning: implicit declaration of function '_mm_store_si128' [-Wimplicit-function-declaration]
+ksw.c:123:3: error: unknown type name '__m128i'
+ksw.c:124:3: warning: implicit declaration of function '_mm_load_si128' [-Wimplicit-function-declaration]
+ksw.c:125:3: warning: implicit declaration of function '_mm_slli_si128' [-Wimplicit-function-declaration]
+ksw.c:133:4: warning: implicit declaration of function '_mm_adds_epu8' [-Wimplicit-function-declaration]
+ksw.c:134:4: warning: implicit declaration of function '_mm_subs_epu8' [-Wimplicit-function-declaration]
+ksw.c:136:4: warning: implicit declaration of function '_mm_max_epu8' [-Wimplicit-function-declaration]
+ksw.c:160:5: warning: implicit declaration of function '_mm_movemask_epi8' [-Wimplicit-function-declaration]
+ksw.c:160:5: warning: implicit declaration of function '_mm_cmpeq_epi8' [-Wimplicit-function-declaration]
+ksw.c:166:3: warning: implicit declaration of function '_mm_srli_si128' [-Wimplicit-function-declaration]
+ksw.c:166:3: warning: implicit declaration of function '_mm_extract_epi16' [-Wimplicit-function-declaration]
+ksw.c: In function 'ksw_sse2_8':
+ksw.c:207:2: error: unknown type name '__m128i'
+ksw.c:219:2: warning: implicit declaration of function '_mm_set1_epi16' [-Wimplicit-function-declaration]
+ksw.c:231:3: error: unknown type name '__m128i'
+ksw.c:235:4: warning: implicit declaration of function '_mm_adds_epi16' [-Wimplicit-function-declaration]
+ksw.c:237:4: warning: implicit declaration of function '_mm_max_epi16' [-Wimplicit-function-declaration]
+ksw.c:241:4: warning: implicit declaration of function '_mm_subs_epu16' [-Wimplicit-function-declaration]
+ksw.c:257:5: warning: implicit declaration of function '_mm_cmpgt_epi16' [-Wimplicit-function-declaration]
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-kfreebsd-i386-Inf6PD/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-kfreebsd-i386-Inf6PD/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0440
-
-bwa_0.5.10-1_kfreebsd-i386.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: kfreebsd-i386
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: kfreebsd-i386 Build Daemon (finzi) <buildd_kfreebsd-i386-finzi at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 9587807d9d257e3a262d1c702831527badd9c337 142604 bwa_0.5.10-1_kfreebsd-i386.deb
-Checksums-Sha256:
- b85602978d5c6ebc5bcf16fb997843dc5e6849d90805fef2301d0700b30897b3 142604 bwa_0.5.10-1_kfreebsd-i386.deb
-Files:
- 54d95ed06964e1c64effde3328e39cd1 142604 science optional bwa_0.5.10-1_kfreebsd-i386.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_kfreebsd-i386.deb
-──────────────────────────────
-
- new debian package, version 2.0.
- size 142604 bytes: control archive= 1001 bytes.
- 785 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: kfreebsd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 263
- Depends: libc0.1 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/bin/
--rwxr-xr-x root/root 223108 2011-11-14 04:40 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/doc/bwa/
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:39 ./usr/share/man/man1/bwa.1.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1121
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-ki-sbuild-1321245533-8321/build/buildd-bwa_0.5.10-1-kfreebsd-i386-d6O4Q4
+Purging /var/lib/schroot/mount/sid-ki-sbuild-1321269613-6078/build/buildd-bwa_0.6.0-1-kfreebsd-i386-Inf6PD
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- debhelper* file* gettext* gettext-base* html2text* intltool-debian*
- libcroco3* libglib2.0-0* libmagic1* libpipeline1* libunistring0* libxml2*
- man-db* po-debconf* zlib1g-dev*
-0 upgraded, 0 newly installed, 15 to remove and 6 not upgraded.
-After this operation, 19.5 MB disk space will be freed.
-(Reading database ... 14450 files and directories currently installed.)
+ debhelper* file* gettext* gettext-base* groff-base* html2text*
+ intltool-debian* libcroco3* libglib2.0-0* libmagic1* libpipeline1*
+ libunistring0* libxml2* man-db* po-debconf* zlib1g-dev*
+0 upgraded, 0 newly installed, 16 to remove and 0 not upgraded.
+After this operation, 22.6 MB disk space will be freed.
+(Reading database ... 12762 files and directories currently installed.)
Removing debhelper ...
Removing file ...
Removing po-debconf ...
Removing intltool-debian ...
Removing gettext ...
Removing gettext-base ...
+Removing man-db ...
+Purging configuration files for man-db ...
+Removing groff-base ...
+Purging configuration files for groff-base ...
Removing html2text ...
Purging configuration files for html2text ...
Removing libcroco3 ...
@@ -518,8 +404,6 @@ Removing libglib2.0-0 ...
Purging configuration files for libglib2.0-0 ...
Removing libmagic1 ...
Purging configuration files for libmagic1 ...
-Removing man-db ...
-Purging configuration files for man-db ...
Removing libpipeline1 ...
Purging configuration files for libpipeline1 ...
Removing libunistring0 ...
@@ -533,18 +417,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: kfreebsd-i386
-Build-Space: 2540
-Build-Time: 25
+Build-Space: 1030
+Build-Time: 7
Distribution: sid
-Install-Time: 30
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 77
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 73
-Source-Version: 0.5.10-1
-Space: 2540
-Status: successful
-Version: 0.5.10-1
+Package-Time: 105
+Source-Version: 0.6.0-1
+Space: 1030
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0440
-Build needed 00:01:13, 2540k disc space
-Signature with key 'D859A500' requested:
+Finished at 20111114-1121
+Build needed 00:01:45, 1030k disc space
diff --git a/mips.log b/mips.log
index 4c5de68..5fc9c01 100644
--- a/mips.log
+++ b/mips.log
@@ -1,4 +1,4 @@
-From buildd at corelli.debian.org Mon Nov 14 04:45:30 2011
+From buildd at corelli.debian.org Mon Nov 14 11:04:09 2011
Return-path: <buildd at corelli.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
@@ -6,49 +6,49 @@ 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 corelli.debian.org>)
- id 1RPoQE-0000zH-8k
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:30 +0000
+ id 1RPuKf-0007kc-6O
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:09 +0000
Received: from corelli.debian.org ([2607:f8f0:610:4000:2e0:98ff:fe00:4489])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=corelli.debian.org, EMAIL=hostmaster at corelli.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at corelli.debian.org>)
- id 1RPoQC-0004gz-Gs
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:29 +0000
+ id 1RPuKd-0001Fg-HP
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:08 +0000
Received: from buildd by corelli.debian.org with local (Exim 4.69)
- (envelope-from <buildd at corelli.debian.org>) id 1RPoQA-0000Fm-0X
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:26 +0000
+ (envelope-from <buildd at corelli.debian.org>) id 1RPuKa-0003sY-A6
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:04 +0000
From: buildd on corelli <buildd at corelli.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on mips (dist=sid)
+Subject: Log for attempted build of bwa_0.6.0-1 on mips (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RPoQA-0000Fm-0X at corelli.debian.org>
-Date: Mon, 14 Nov 2011 04:45:26 +0000
+Message-Id: <E1RPuKa-0003sY-A6 at corelli.debian.org>
+Date: Mon, 14 Nov 2011 11:04:04 +0000
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on corelli.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (mips) 14 Nov 2011 04:38 ║
+║ bwa 0.6.0-1 (mips) 14 Nov 2011 10:59 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: mips
-Get:1 http://incoming.debian.org unstable InRelease [146 kB]
-Get:2 http://mirror-ubc.debian.org unstable InRelease [146 kB]
-Get:3 http://mirror-ubc.debian.org unstable/main Sources [5923 kB]
+Get:1 http://mirror-ubc.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://mirror-ubc.debian.org unstable/main Sources [5932 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 [5923 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5932 kB]
Get:6 http://mirror-ubc.debian.org unstable/contrib Sources [57.2 kB]
Get:7 http://mirror-ubc.debian.org unstable/non-free Sources [103 kB]
-Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7626 kB]
+Get:8 http://mirror-ubc.debian.org unstable/main mips Packages [7627 kB]
Get:9 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
Get:10 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:11 http://incoming.debian.org unstable/main mips Packages [7626 kB]
+Get:11 http://incoming.debian.org unstable/main mips Packages [7627 kB]
Get:12 http://mirror-ubc.debian.org unstable/contrib mips Packages [56.2 kB]
Ign http://mirror-ubc.debian.org unstable/contrib TranslationIndex
Get:13 http://mirror-ubc.debian.org unstable/main TranslationIndex [2045 B]
@@ -57,11 +57,11 @@ Get:14 http://incoming.debian.org unstable/contrib mips Packages [56.2 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [37.6 kB]
-Get:18 http://incoming.debian.org Packages [341 kB]
+Get:17 http://incoming.debian.org Sources [46.0 kB]
+Get:18 http://incoming.debian.org Packages [374 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.2 MB in 1min 20s (351 kB/s)
+Fetched 28.3 MB in 1min 18s (362 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -82,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (217 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 0s (220 kB/s)
Download complete and in download only mode
Check arch
@@ -106,19 +106,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 45 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 45 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa 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), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -126,21 +126,21 @@ bash: already installed (4.1-3)
coreutils: already installed (8.13-3)
dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
-diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.16.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
+diffutils: already installed (1:3.2-1)
+dpkg: already installed (1.16.1.1)
+e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
-gzip: already installed (1.4-1)
+gzip: already installed (1.4-2)
hostname: already installed (3.06)
-ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-2)
-perl-base: already installed (5.12.4-6)
+ncurses-base: already installed (5.9-4)
+ncurses-bin: already installed (5.9-4)
+perl-base: already installed (5.14.2-3)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
-sysvinit-utils: already installed (2.88dsf-13.11)
-sysvinit: already installed (2.88dsf-13.11)
-tar: already installed (1.26-2)
+sysvinit-utils: already installed (2.88dsf-13.13)
+sysvinit: already installed (2.88dsf-13.13)
+tar: already installed (1.26-3)
bsdutils: already installed (1:2.19.1-5)
mount: already installed (2.19.1-5)
util-linux: already installed (2.19.1-5)
@@ -148,7 +148,7 @@ libc6-dev: already installed (2.13-21)
gcc: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.6.1-3 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8.1)
-dpkg-dev: already installed (1.16.1 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.16.1.1 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 8.9.9
zlib1g-dev: missing
@@ -171,7 +171,7 @@ The following NEW packages will be installed:
bsdmainutils debhelper file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
libunistring0 libxml2 man-db po-debconf zlib1g-dev
-0 upgraded, 18 newly installed, 0 to remove and 45 not upgraded.
+0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded.
Need to get 9112 kB of archives.
After this operation, 26.5 MB of additional disk space will be used.
Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.0-5 [35.4 kB]
@@ -193,9 +193,9 @@ Get:16 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+
Get:17 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
Get:18 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9112 kB in 4s (2198 kB/s)
+Fetched 9112 kB in 1s (5384 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10552 files and directories currently installed.)
+(Reading database ... 10651 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_mips.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_mips.deb) ...
@@ -257,11 +257,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.35.4-dsa-octeon mips (mips64)
-Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.8 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.0-1 dpkg_1.16.1 dpkg-dev_1.16.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 netbase_4.46 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-6
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-16-1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-6 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 netbase_4.47 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-3 perl-base_5.14.2-3 perl-modules_5.14.2-3 po-debconf_1.0.16+nmu1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.3p1-2 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -272,12 +272,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -286,234 +286,84 @@ Check disc space
dpkg-buildpackage
─────────────────
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CPPFLAGS =
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): CXXFLAGS = -g -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): FFLAGS = -g -O2
-dpkg-buildpackage: dpkg-buildflags (origin: vendor): LDFLAGS = -Wl,-z,relro
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture mips
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-mips-P86njU/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-mips-P86njU/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-mips-P86njU/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-mips-P86njU/bwa-0.6.0'
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-mips-phQ91R/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (corelli) <buildd_mips-corelli at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-mips-P86njU/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-mips-P86njU/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0445
-
-bwa_0.5.10-1_mips.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: mips
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: mips Build Daemon (corelli) <buildd_mips-corelli at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 623b58ac029847066175ea91f01d34162bc3ca38 148484 bwa_0.5.10-1_mips.deb
-Checksums-Sha256:
- 7cbc14f400a1987857565fb3acf82eaf212be882c16514538880dd44d00ede5e 148484 bwa_0.5.10-1_mips.deb
-Files:
- aad9aa6083107eee9e65cef78f41417d 148484 science optional bwa_0.5.10-1_mips.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_mips.deb
-─────────────────────
-
- new debian package, version 2.0.
- size 148484 bytes: control archive= 995 bytes.
- 774 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: mips
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 297
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/share/bwa/
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:44 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
-drwxr-xr-x root/root 0 2011-11-14 04:44 ./usr/bin/
--rwxr-xr-x root/root 221876 2011-11-14 04:44 ./usr/bin/bwa
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1103
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-mips-sbuild-7073cbec-f22b-4241-8c61-209a2aac7101/build/buildd-bwa_0.5.10-1-mips-phQ91R
+Purging /var/lib/schroot/mount/sid-mips-sbuild-d8a3c0c9-e928-44b7-82fb-d1d27bcb0768/build/buildd-bwa_0.6.0-1-mips-P86njU
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -521,84 +371,86 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mips
-Build-Space: 2784
-Build-Time: 224
+Build-Space: 1180
+Build-Time: 79
Distribution: sid
+Fail-Stage: build
Install-Time: 71
-Job: bwa_0.5.10-1
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 419
-Source-Version: 0.5.10-1
-Space: 2784
-Status: successful
-Version: 0.5.10-1
+Package-Time: 273
+Source-Version: 0.6.0-1
+Space: 1180
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0445
-Build needed 00:06:59, 2784k disc space
-Signature with key '102A90D8' requested:
+Finished at 20111114-1103
+Build needed 00:04:33, 1180k disc space
-From buildd at mayer.debian.org Mon Nov 14 04:45:56 2011
-Return-path: <buildd at mayer.debian.org>
+From buildd at rem.debian.org Mon Nov 14 11:04:26 2011
+Return-path: <buildd at rem.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RPoQd-00016I-Tk
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:56 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1RPuKw-0007ln-2B
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:26 +0000
+Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RPoQc-0004ka-Iz
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:55 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1RPoQV-0004vi-Gr
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:47 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1RPuKu-0001Fp-GW
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:24 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>) id 1RPuKs-0001Di-4V
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:22 +0000
+Date: Mon, 14 Nov 2011 11:04:22 +0000
+Message-Id: <E1RPuKs-0001Di-4V at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on mipsel (dist=sid)
+Subject: Log for attempted build of bwa_0.6.0-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RPoQV-0004vi-Gr at mayer.debian.org>
-Date: Mon, 14 Nov 2011 04:45:47 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (mipsel) 14 Nov 2011 04:40 ║
+║ bwa 0.6.0-1 (mipsel) 14 Nov 2011 11:01 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
-Get:2 http://incoming.debian.org sid InRelease [146 kB]
-Get:3 http://debian.oregonstate.edu sid/main Sources [5923 kB]
+Get:1 http://mirror.ayous.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [5932 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 [5923 kB]
-Get:6 http://debian.oregonstate.edu sid/contrib Sources [57.2 kB]
-Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [7645 kB]
-Get:8 http://debian.oregonstate.edu sid/contrib mipsel Packages [56.5 kB]
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Get:9 http://debian.oregonstate.edu sid/main TranslationIndex [2045 B]
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Get:10 http://incoming.debian.org sid/contrib Sources [57.2 kB]
-Get:11 http://incoming.debian.org sid/main mipsel Packages [7645 kB]
-Get:12 http://incoming.debian.org sid/contrib mipsel Packages [56.5 kB]
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:13 http://incoming.debian.org sid/main TranslationIndex [2045 B]
-Get:14 http://incoming.debian.org Release [1604 B]
-Get:15 http://incoming.debian.org Sources [37.6 kB]
-Get:16 http://incoming.debian.org Packages [341 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:5 http://incoming.debian.org unstable/main Sources [5932 kB]
+Get:6 http://mirror.ayous.org unstable/contrib Sources [57.2 kB]
+Get:7 http://mirror.ayous.org unstable/non-free Sources [103 kB]
+Get:8 http://mirror.ayous.org unstable/main mipsel Packages [7645 kB]
+Get:9 http://mirror.ayous.org unstable/contrib mipsel Packages [56.5 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:10 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main mipsel Packages [7645 kB]
+Get:14 http://incoming.debian.org unstable/contrib mipsel Packages [56.5 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [46.0 kB]
+Get:18 http://incoming.debian.org Packages [374 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.0 MB in 1min 6s (423 kB/s)
+Fetched 28.3 MB in 50s (559 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -619,11 +471,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (190 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 0s (191 kB/s)
Download complete and in download only mode
Check arch
@@ -643,25 +495,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa 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), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -671,13 +517,13 @@ dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-4)
+ncurses-bin: already installed (5.9-2)
perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -700,26 +546,49 @@ Installing positive dependencies: debhelper zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
- libmagic1 libunistring0 libxml2 po-debconf
+ bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
- dh-make gettext-doc libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
+ libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
- debhelper file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf zlib1g-dev
+ bsdmainutils debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 18 newly installed, 0 to remove and 40 not upgraded.
+Need to get 9069 kB of archives.
+After this operation, 26.5 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-5 [35.3 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-3 [986 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 13 newly installed, 0 to remove and 21 not upgraded.
-Need to get 0 B/6470 kB of archives.
-After this operation, 19.5 MB of additional disk space will be used.
+Fetched 9069 kB in 1s (8001 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10550 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_mipsel.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0.
-(Reading database ... 11452 files and directories currently installed.)
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mipsel.deb) ...
Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mipsel.deb) ...
@@ -727,6 +596,12 @@ Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-3_mipsel.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_mipsel.deb) ...
Selecting previously unselected package file.
@@ -745,12 +620,19 @@ Selecting previously unselected package debhelper.
Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Processing triggers for man-db ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libpcre3 (8.12-4) ...
Setting up libglib2.0-0 (2.28.8-1) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up bsdmainutils (8.2.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-3) ...
+Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
@@ -764,14 +646,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.0-1 dmsetup_2:1.02.67-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libpopt0_1.16-1 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl1.0.0_1.0.0e-2.1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_172-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -782,12 +661,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -797,287 +676,103 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0445
-
-bwa_0.5.10-1_mipsel.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: mipsel
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 2f155edfa33ef066e9f2d40164e1ffdf553b19a6 149306 bwa_0.5.10-1_mipsel.deb
-Checksums-Sha256:
- 2a36f4702952e52326389db275bb78953ede7b4ab061b83644b926d87b14a1f2 149306 bwa_0.5.10-1_mipsel.deb
-Files:
- b8730fa64e8e1945bb6d28f8f289c369 149306 science optional bwa_0.5.10-1_mipsel.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_mipsel.deb
-───────────────────────
-
- new debian package, version 2.0.
- size 149306 bytes: control archive= 992 bytes.
- 776 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 298
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/bin/
--rwxr-xr-x root/root 222884 2011-11-14 04:45 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/doc/bwa/
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:45 ./usr/share/man/man1/bwa.1.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1104
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-11f08e98-ab05-426b-85ba-85ca19a3688e/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-The following packages will be REMOVED:
- debhelper* file* gettext* gettext-base* html2text* intltool-debian*
- libcroco3* libglib2.0-0* libmagic1* libunistring0* libxml2* po-debconf*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 13 to remove and 21 not upgraded.
-After this operation, 19.5 MB disk space will be freed.
-(Reading database ... 12272 files and directories currently installed.)
-Removing debhelper ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-f4d78b36-7cb7-402c-9b4a-1cd18e03feff/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 2784
-Build-Time: 121
+Build-Space: 1180
+Build-Time: 46
Distribution: sid
-Install-Time: 51
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 65
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 276
-Source-Version: 0.5.10-1
-Space: 2784
-Status: successful
-Version: 0.5.10-1
+Package-Time: 190
+Source-Version: 0.6.0-1
+Space: 1180
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0445
-Build needed 00:04:36, 2784k disc space
-Signature with key 'B0903E66' requested:
+Finished at 20111114-1104
+Build needed 00:03:10, 1180k disc space
diff --git a/mipsel.log b/mipsel.log
index 8852cde..90a9cf5 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,65 +1,67 @@
-From buildd at mayer.debian.org Mon Nov 14 04:45:56 2011
-Return-path: <buildd at mayer.debian.org>
+From buildd at rem.debian.org Mon Nov 14 11:04:26 2011
+Return-path: <buildd at rem.debian.org>
Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=merikanto.debian.org,
EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RPoQd-00016I-Tk
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:56 +0000
-Received: from mayer.debian.org ([140.211.166.78])
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1RPuKw-0007ln-2B
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:26 +0000
+Received: from rem.debian.org ([2001:41b8:202:deb:202:4cff:fefe:d06])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mayer.debian.org, EMAIL=hostmaster at mayer.debian.org (verified)
+ CN=rem.debian.org, EMAIL=hostmaster at rem.debian.org (verified)
by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1RPoQc-0004ka-Iz
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:55 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.69)
- (envelope-from <buildd at mayer.debian.org>) id 1RPoQV-0004vi-Gr
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:45:47 +0000
-From: buildd on mayer <buildd at mayer.debian.org>
+ (Exim 4.72) (envelope-from <buildd at rem.debian.org>)
+ id 1RPuKu-0001Fp-GW
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:24 +0000
+Received: from buildd by rem.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at rem.debian.org>) id 1RPuKs-0001Di-4V
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:04:22 +0000
+Date: Mon, 14 Nov 2011 11:04:22 +0000
+Message-Id: <E1RPuKs-0001Di-4V at rem.debian.org>
+From: buildd on rem <buildd at rem.debian.org>
To: logs at buildd.debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on mipsel (dist=sid)
+Subject: Log for attempted build of bwa_0.6.0-1 on mipsel (dist=sid)
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
-Message-Id: <E1RPoQV-0004vi-Gr at mayer.debian.org>
-Date: Mon, 14 Nov 2011 04:45:47 +0000
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on rem.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (mipsel) 14 Nov 2011 04:40 ║
+║ bwa 0.6.0-1 (mipsel) 14 Nov 2011 11:01 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: mipsel
-Get:1 http://debian.oregonstate.edu sid InRelease [146 kB]
-Get:2 http://incoming.debian.org sid InRelease [146 kB]
-Get:3 http://debian.oregonstate.edu sid/main Sources [5923 kB]
+Get:1 http://mirror.ayous.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://mirror.ayous.org unstable/main Sources [5932 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 [5923 kB]
-Get:6 http://debian.oregonstate.edu sid/contrib Sources [57.2 kB]
-Get:7 http://debian.oregonstate.edu sid/main mipsel Packages [7645 kB]
-Get:8 http://debian.oregonstate.edu sid/contrib mipsel Packages [56.5 kB]
-Ign http://debian.oregonstate.edu sid/contrib TranslationIndex
-Get:9 http://debian.oregonstate.edu sid/main TranslationIndex [2045 B]
-Ign http://debian.oregonstate.edu sid/contrib Translation-en
-Get:10 http://incoming.debian.org sid/contrib Sources [57.2 kB]
-Get:11 http://incoming.debian.org sid/main mipsel Packages [7645 kB]
-Get:12 http://incoming.debian.org sid/contrib mipsel Packages [56.5 kB]
-Ign http://incoming.debian.org sid/contrib TranslationIndex
-Get:13 http://incoming.debian.org sid/main TranslationIndex [2045 B]
-Get:14 http://incoming.debian.org Release [1604 B]
-Get:15 http://incoming.debian.org Sources [37.6 kB]
-Get:16 http://incoming.debian.org Packages [341 kB]
-Ign http://incoming.debian.org sid/contrib Translation-en
+Get:5 http://incoming.debian.org unstable/main Sources [5932 kB]
+Get:6 http://mirror.ayous.org unstable/contrib Sources [57.2 kB]
+Get:7 http://mirror.ayous.org unstable/non-free Sources [103 kB]
+Get:8 http://mirror.ayous.org unstable/main mipsel Packages [7645 kB]
+Get:9 http://mirror.ayous.org unstable/contrib mipsel Packages [56.5 kB]
+Ign http://mirror.ayous.org unstable/contrib TranslationIndex
+Get:10 http://mirror.ayous.org unstable/main TranslationIndex [2045 B]
+Ign http://mirror.ayous.org unstable/contrib Translation-en
+Get:11 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
+Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:13 http://incoming.debian.org unstable/main mipsel Packages [7645 kB]
+Get:14 http://incoming.debian.org unstable/contrib mipsel Packages [56.5 kB]
+Ign http://incoming.debian.org unstable/contrib TranslationIndex
+Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:16 http://incoming.debian.org Release [1604 B]
+Get:17 http://incoming.debian.org Sources [46.0 kB]
+Get:18 http://incoming.debian.org Packages [374 kB]
+Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.0 MB in 1min 6s (423 kB/s)
+Fetched 28.3 MB in 50s (559 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -80,11 +82,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (190 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 0s (191 kB/s)
Download complete and in download only mode
Check arch
@@ -104,25 +106,19 @@ Installing positive dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install bwa 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), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -132,13 +128,13 @@ dash: already installed (0.5.7-2)
debianutils: already installed (4.0.4)
diffutils: already installed (1:3.0-1)
dpkg: already installed (1.16.1.1)
-e2fsprogs: already installed (1.42~WIP-2011-10-16-1)
+e2fsprogs: already installed (1.42~WIP-2011-10-09-1)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.9-2)
gzip: already installed (1.4-1)
hostname: already installed (3.06)
ncurses-base: already installed (5.9-2)
-ncurses-bin: already installed (5.9-4)
+ncurses-bin: already installed (5.9-2)
perl-base: already installed (5.12.4-6)
sed: already installed (4.2.1-9)
login: already installed (1:4.1.4.2+svn3283-3)
@@ -161,26 +157,49 @@ Installing positive dependencies: debhelper zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
-Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
- file gettext gettext-base html2text intltool-debian libcroco3 libglib2.0-0
- libmagic1 libunistring0 libxml2 po-debconf
+ bsdmainutils file gettext gettext-base groff-base html2text intltool-debian
+ libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
+ man-db po-debconf
Suggested packages:
- dh-make gettext-doc libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
+ libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
- debhelper file gettext gettext-base html2text intltool-debian libcroco3
- libglib2.0-0 libmagic1 libunistring0 libxml2 po-debconf zlib1g-dev
+ bsdmainutils debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libcroco3 libglib2.0-0 libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
+0 upgraded, 18 newly installed, 0 to remove and 40 not upgraded.
+Need to get 9069 kB of archives.
+After this operation, 26.5 MB of additional disk space will be used.
+Get:1 http://mirror.ayous.org/debian/ unstable/main libpipeline1 mipsel 1.2.0-5 [35.3 kB]
+Get:2 http://mirror.ayous.org/debian/ unstable/main libpcre3 mipsel 8.12-4 [227 kB]
+Get:3 http://mirror.ayous.org/debian/ unstable/main libglib2.0-0 mipsel 2.28.8-1 [1561 kB]
+Get:4 http://mirror.ayous.org/debian/ unstable/main libxml2 mipsel 2.7.8.dfsg-5 [858 kB]
+Get:5 http://mirror.ayous.org/debian/ unstable/main libcroco3 mipsel 0.6.2-2 [103 kB]
+Get:6 http://mirror.ayous.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5 [407 kB]
+Get:7 http://mirror.ayous.org/debian/ unstable/main bsdmainutils mipsel 8.2.3 [208 kB]
+Get:8 http://mirror.ayous.org/debian/ unstable/main groff-base mipsel 1.21-6 [1142 kB]
+Get:9 http://mirror.ayous.org/debian/ unstable/main man-db mipsel 2.6.0.2-3 [986 kB]
+Get:10 http://mirror.ayous.org/debian/ unstable/main libmagic1 mipsel 5.09-2 [247 kB]
+Get:11 http://mirror.ayous.org/debian/ unstable/main file mipsel 5.09-2 [52.0 kB]
+Get:12 http://mirror.ayous.org/debian/ unstable/main gettext-base mipsel 0.18.1.1-5 [133 kB]
+Get:13 http://mirror.ayous.org/debian/ unstable/main html2text mipsel 1.3.2a-15 [103 kB]
+Get:14 http://mirror.ayous.org/debian/ unstable/main gettext mipsel 0.18.1.1-5 [2008 kB]
+Get:15 http://mirror.ayous.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://mirror.ayous.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://mirror.ayous.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
+Get:18 http://mirror.ayous.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.3.4.dfsg-3 [192 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 13 newly installed, 0 to remove and 21 not upgraded.
-Need to get 0 B/6470 kB of archives.
-After this operation, 19.5 MB of additional disk space will be used.
+Fetched 9069 kB in 1s (8001 kB/s)
+Selecting previously unselected package libpipeline1.
+(Reading database ... 10550 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_mipsel.deb) ...
+Selecting previously unselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_mipsel.deb) ...
Selecting previously unselected package libglib2.0-0.
-(Reading database ... 11452 files and directories currently installed.)
Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.8-1_mipsel.deb) ...
Selecting previously unselected package libxml2.
Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_mipsel.deb) ...
@@ -188,6 +207,12 @@ Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_mipsel.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_mipsel.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_mipsel.deb) ...
+Selecting previously unselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_mipsel.deb) ...
+Selecting previously unselected package man-db.
+Unpacking man-db (from .../man-db_2.6.0.2-3_mipsel.deb) ...
Selecting previously unselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.09-2_mipsel.deb) ...
Selecting previously unselected package file.
@@ -206,12 +231,19 @@ Selecting previously unselected package debhelper.
Unpacking debhelper (from .../debhelper_8.9.9_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mipsel.deb) ...
-Processing triggers for man-db ...
+Setting up libpipeline1 (1.2.0-5) ...
+Setting up libpcre3 (8.12-4) ...
Setting up libglib2.0-0 (2.28.8-1) ...
No schema files found: doing nothing.
Setting up libxml2 (2.7.8.dfsg-5) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up bsdmainutils (8.2.3) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
+Setting up groff-base (1.21-6) ...
+Setting up man-db (2.6.0.2-3) ...
+Building database of manual pages ...
Setting up libmagic1 (5.09-2) ...
Setting up file (5.09-2) ...
Setting up gettext-base (0.18.1.1-5) ...
@@ -225,14 +257,11 @@ Removing negative dependencies:
Reading package lists...
Building dependency tree...
Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
+0 upgraded, 0 newly installed, 0 to remove and 40 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.21.90.20111025-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-4 gcc-4.6_4.6.2-4 libc6-dev_2.13-21 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 linux-libc-dev_3.0.0-5
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111025-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpio_2.11-7 cpp_4:4.6.1-3 cpp-4.6_4.6.2-4 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.0-1 dmsetup_2:1.02.67-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-16-1 e2fsprogs_1.42~WIP-2011-10-16-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-4 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.5-base_4.5.3-9 gcc-4.6_4.6.2-4 gcc-4.6-base_4.6.2-4 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-16-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdevmapper1.02.1_2:1.02.67-1 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-4 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-4 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-4 libncursesw5_5.9-4 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-4 libpng12-0_1.2.46-3 libpopt0_1.16-1 libreadline6_6.2-7 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libssl1.0.0_1.0.0e-2.1 libstdc++6_4.6.2-4 libstdc++6-4.6-dev_4.6.2-4 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libudev0_172-1 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 module-init-tools_3.16-1 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 procps_1:3.2.8-11 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011n-1 udev_172-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.90.20111004-2 dpkg-dev_1.16.1.1 g++-4.6_4.6.1-15 gcc-4.6_4.6.1-15 libc6-dev_2.13-21 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 linux-libc-dev_3.0.0-5
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.90.20111004-2 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.1-15 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.9 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.0-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-10-09-1 e2fsprogs_1.42~WIP-2011-10-09-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.1-15 gcc_4:4.6.1-3 gcc-4.4-base_4.4.6-11 gcc-4.6_4.6.1-15 gcc-4.6-base_4.6.1-15 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.12 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libcomerr2_1.42~WIP-2011-10-09-1 libcroco3_0.6.2-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-15 libgdbm3_1.8.3-10 libglib2.0-0_2.28.8-1 libgmp10_2:5.0.2+dfsg-1 libgomp1_4.6.1-15 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.09-2 libmount1_2.19.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-2 libncurses5_5.9-2 libpam-modules_1.1.3-4 libpam-modules-bin_1.1.3-4 libpam-runtime_1.1.3-4 libpam0g_1.1.3-4 libpcre3_8.12-4 libpipeline1_1.2.0-5 libreadline6_6.2-7 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-10-09-1 libstdc++6_4.6.1-15 libstdc++6-4.6-dev_4.6.1-15 libtimedate-perl_1.2000-1 libtinfo5_5.9-2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.0.0-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-2 ncurses-bin_5.9-2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-6 perl-base_5.12.4-6 perl-modules_5.12.4-6 po-debconf_1.0.16+nmu1 readline-common_6.2-7 sed_4.2.1-9 sensible-utils_0.0.6 sudo_1.8.2-2 sysv-rc_2.88dsf-13.12 sysvinit_2.88dsf-13.12 sysvinit-utils_2.88dsf-13.12 tar_1.26-2 tzdata_2011l-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -243,12 +272,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -258,287 +287,103 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture mipsel
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0445
-
-bwa_0.5.10-1_mipsel.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: mipsel
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 2f155edfa33ef066e9f2d40164e1ffdf553b19a6 149306 bwa_0.5.10-1_mipsel.deb
-Checksums-Sha256:
- 2a36f4702952e52326389db275bb78953ede7b4ab061b83644b926d87b14a1f2 149306 bwa_0.5.10-1_mipsel.deb
-Files:
- b8730fa64e8e1945bb6d28f8f289c369 149306 science optional bwa_0.5.10-1_mipsel.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_mipsel.deb
-───────────────────────
-
- new debian package, version 2.0.
- size 149306 bytes: control archive= 992 bytes.
- 776 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 298
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/bin/
--rwxr-xr-x root/root 222884 2011-11-14 04:45 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/doc/bwa/
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:45 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:45 ./usr/share/man/man1/bwa.1.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1104
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-11f08e98-ab05-426b-85ba-85ca19a3688e/build/buildd-bwa_0.5.10-1-mipsel-6ezpgw
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- libpopt0 groff-base libpipeline1 man-db libssl1.0.0
-Use 'apt-get autoremove' to remove them.
-The following packages will be REMOVED:
- debhelper* file* gettext* gettext-base* html2text* intltool-debian*
- libcroco3* libglib2.0-0* libmagic1* libunistring0* libxml2* po-debconf*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 13 to remove and 21 not upgraded.
-After this operation, 19.5 MB disk space will be freed.
-(Reading database ... 12272 files and directories currently installed.)
-Removing debhelper ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
-Processing triggers for man-db ...
+Purging /var/lib/schroot/mount/sid-mipsel-sbuild-f4d78b36-7cb7-402c-9b4a-1cd18e03feff/build/buildd-bwa_0.6.0-1-mipsel-AIAOvn
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: mipsel
-Build-Space: 2784
-Build-Time: 121
+Build-Space: 1180
+Build-Time: 46
Distribution: sid
-Install-Time: 51
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 65
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 276
-Source-Version: 0.5.10-1
-Space: 2784
-Status: successful
-Version: 0.5.10-1
+Package-Time: 190
+Source-Version: 0.6.0-1
+Space: 1180
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0445
-Build needed 00:04:36, 2784k disc space
-Signature with key 'B0903E66' requested:
+Finished at 20111114-1104
+Build needed 00:03:10, 1180k disc space
diff --git a/powerpc.log b/powerpc.log
index a966605..46a89b4 100644
--- a/powerpc.log
+++ b/powerpc.log
@@ -1,69 +1,68 @@
-From buildd at porpora.debian.org Mon Nov 14 04:40:00 2011
-Return-path: <buildd at porpora.debian.org>
+From buildd at praetorius.debian.org Mon Nov 14 10:59:30 2011
+Return-path: <buildd at praetorius.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1RPoKt-0008R2-UO
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:40:00 +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 1RPuG9-0006ua-Vj
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 10:59:30 +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 kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at porpora.debian.org>)
- id 1RPoKt-0006Cy-3T; Mon, 14 Nov 2011 04:39:59 +0000
-Received: from buildd by porpora.debian.org with local (Exim 4.72)
- (envelope-from <buildd at porpora.debian.org>)
- id 1RPoKs-0008Bi-D1; Mon, 14 Nov 2011 04:39:58 +0000
-Message-Id: <E1RPoKs-0008Bi-D1 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: Mon, 14 Nov 2011 04:39:58 +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 bwa_0.5.10-1 on powerpc (dist=sid)
-Key-Id: 8CE75D05
+ (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
+ id 1RPuG8-0007hw-UU; Mon, 14 Nov 2011 10:59:29 +0000
+Received: from buildd by praetorius.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at praetorius.debian.org>)
+ id 1RPuG8-0008LY-64; Mon, 14 Nov 2011 10:59:28 +0000
+Date: Mon, 14 Nov 2011 10:59:28 +0000
+Message-Id: <E1RPuG8-0008LY-64 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 attempted build of bwa_0.6.0-1 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
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (powerpc) 14 Nov 2011 04:37 ║
+║ bwa 0.6.0-1 (powerpc) 14 Nov 2011 10:57 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: powerpc
-Get:1 http://ftp.uk.debian.org unstable InRelease [146 kB]
-Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [5923 kB]
+Get:1 http://ftp.se.debian.org unstable InRelease [146 kB]
+Get:2 http://ftp.se.debian.org unstable/main Sources [5932 kB]
+Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:4 http://ftp.se.debian.org unstable/contrib Sources [57.2 kB]
+Get:5 http://ftp.se.debian.org unstable/non-free Sources [103 kB]
+Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [7720 kB]
+Get:7 http://ftp.se.debian.org unstable/contrib powerpc Packages [55.8 kB]
+Ign http://ftp.se.debian.org unstable/contrib TranslationIndex
+Get:8 http://ftp.se.debian.org unstable/main TranslationIndex [2045 B]
+Ign http://ftp.se.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org InRelease
-Get:4 http://incoming.debian.org Release.gpg [836 B]
-Get:5 http://ftp.uk.debian.org unstable/contrib Sources [57.2 kB]
-Get:6 http://ftp.uk.debian.org unstable/non-free Sources [103 kB]
-Get:7 http://incoming.debian.org unstable/main Sources [5923 kB]
-Get:8 http://ftp.uk.debian.org unstable/main powerpc Packages [7719 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib powerpc Packages [55.8 kB]
-Ign http://ftp.uk.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.uk.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.uk.debian.org unstable/contrib Translation-en
+Get:9 http://incoming.debian.org Release.gpg [836 B]
+Get:10 http://incoming.debian.org unstable/main Sources [5932 kB]
Get:11 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main powerpc Packages [7719 kB]
+Get:13 http://incoming.debian.org unstable/main powerpc Packages [7720 kB]
Get:14 http://incoming.debian.org unstable/contrib powerpc Packages [55.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [37.6 kB]
-Get:18 http://incoming.debian.org Packages [341 kB]
+Get:17 http://incoming.debian.org Sources [46.0 kB]
+Get:18 http://incoming.debian.org Packages [374 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.4 MB in 25s (1101 kB/s)
+Fetched 28.5 MB in 13s (2101 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +83,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (129 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 0s (141 kB/s)
Download complete and in download only mode
Check arch
@@ -120,7 +119,7 @@ Checking correctness of dependencies...
│ Install bwa 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), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -176,26 +175,26 @@ The following NEW packages will be installed:
0 upgraded, 18 newly installed, 0 to remove and 28 not upgraded.
Need to get 9215 kB of archives.
After this operation, 26.1 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-5 [37.6 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-3 [1014 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
+Get:1 http://ftp.se.debian.org/debian/ unstable/main libpipeline1 powerpc 1.2.0-5 [37.6 kB]
+Get:2 http://ftp.se.debian.org/debian/ unstable/main libpcre3 powerpc 8.12-4 [222 kB]
+Get:3 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.28.8-1 [1609 kB]
+Get:4 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.7.8.dfsg-5 [837 kB]
+Get:5 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.2-2 [114 kB]
+Get:6 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
+Get:7 http://ftp.se.debian.org/debian/ unstable/main bsdmainutils powerpc 8.2.3 [207 kB]
+Get:8 http://ftp.se.debian.org/debian/ unstable/main groff-base powerpc 1.21-6 [1179 kB]
+Get:9 http://ftp.se.debian.org/debian/ unstable/main man-db powerpc 2.6.0.2-3 [1014 kB]
+Get:10 http://ftp.se.debian.org/debian/ unstable/main libmagic1 powerpc 5.09-2 [253 kB]
+Get:11 http://ftp.se.debian.org/debian/ unstable/main file powerpc 5.09-2 [52.0 kB]
+Get:12 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-5 [132 kB]
+Get:13 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
+Get:14 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-5 [2036 kB]
+Get:15 http://ftp.se.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://ftp.se.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://ftp.se.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
+Get:18 http://ftp.se.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.3.4.dfsg-3 [190 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9215 kB in 5s (1600 kB/s)
+Fetched 9215 kB in 1s (7681 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10725 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_powerpc.deb) ...
@@ -274,12 +273,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -289,228 +288,83 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture powerpc
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-powerpc-SQ4Qhk/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-powerpc-SQ4Qhk/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-powerpc-SQ4Qhk/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-powerpc-SQ4Qhk/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-powerpc-SQ4Qhk/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-powerpc-SQ4Qhk/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0439
-
-bwa_0.5.10-1_powerpc.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: powerpc
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: powerpc Build Daemon (porpora) <buildd_powerpc-porpora at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 9db6218e639f5b2551622181b3ccb2590915cb3c 148980 bwa_0.5.10-1_powerpc.deb
-Checksums-Sha256:
- 6923fce6ff233465b4b35ee04d65affb7ff54cb0ff02290e03b062aa0c085882 148980 bwa_0.5.10-1_powerpc.deb
-Files:
- 274428365168e60415bee64ebad77368 148980 science optional bwa_0.5.10-1_powerpc.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_powerpc.deb
-────────────────────────
-
- new debian package, version 2.0.
- size 148980 bytes: control archive= 994 bytes.
- 777 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: powerpc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 286
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/bin/
--rwxr-xr-x root/root 211432 2011-11-14 04:39 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:39 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
-drwxr-xr-x root/root 0 2011-11-14 04:39 ./usr/share/bwa/
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1059
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-8a27c5e1-a918-4d0b-b751-8613df03829f/build/buildd-bwa_0.5.10-1-powerpc-nMIqLx
+Purging /var/lib/schroot/mount/sid-powerpc-sbuild-7642b5e4-f0d4-4489-9f8c-d244a9fff759/build/buildd-bwa_0.6.0-1-powerpc-SQ4Qhk
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -518,18 +372,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: powerpc
-Build-Space: 2784
-Build-Time: 36
+Build-Space: 1192
+Build-Time: 12
Distribution: sid
-Install-Time: 43
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 40
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 120
-Source-Version: 0.5.10-1
-Space: 2784
-Status: successful
-Version: 0.5.10-1
+Package-Time: 86
+Source-Version: 0.6.0-1
+Space: 1192
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0439
-Build needed 00:02:00, 2784k disc space
-Signature with key '8CE75D05' requested:
+Finished at 20111114-1059
+Build needed 00:01:26, 1192k disc space
+
diff --git a/s390.log b/s390.log
index 7ec39a8..ae1177d 100644
--- a/s390.log
+++ b/s390.log
@@ -1,50 +1,50 @@
-From buildd at zandonai.debian.org Mon Nov 14 04:40:39 2011
+From buildd at zandonai.debian.org Mon Nov 14 10:59:13 2011
Return-path: <buildd at zandonai.debian.org>
-Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
+Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=kokkonen.debian.org,
- EMAIL=hostmaster at kokkonen.debian.org (verified)
+ CN=merikanto.debian.org,
+ EMAIL=hostmaster at merikanto.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RPoLX-0000C9-9H
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:40:39 +0000
+ id 1RPuFs-0006s3-M4
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 10:59:12 +0000
Received: from zandonai.debian.org ([80.245.147.46])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=zandonai.debian.org,
EMAIL=hostmaster at zandonai.debian.org (verified)
- by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
+ by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
(Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1RPoLR-0006Ge-Im; Mon, 14 Nov 2011 04:40:33 +0000
+ id 1RPuFr-00011A-6D; Mon, 14 Nov 2011 10:59:11 +0000
Received: from buildd by zandonai.debian.org with local (Exim 4.72)
(envelope-from <buildd at zandonai.debian.org>)
- id 1RPoLR-0003kH-5C; Mon, 14 Nov 2011 04:40:33 +0000
-Message-Id: <E1RPoLR-0003kH-5C at zandonai.debian.org>
+ id 1RPuFq-0000dY-Ml; Mon, 14 Nov 2011 10:59:10 +0000
+Message-Id: <E1RPuFq-0000dY-Ml 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: Mon, 14 Nov 2011 04:40:33 +0000
+Date: Mon, 14 Nov 2011 10:59:10 +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 bwa_0.5.10-1 on s390 (dist=sid)
+Subject: Log for attempted build of bwa_0.6.0-1 on s390 (dist=sid)
Key-Id: 772711F7
Delivered-To: logs at buildd.debian.org
sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (s390) 14 Nov 2011 04:39 ║
+║ bwa 0.6.0-1 (s390) 14 Nov 2011 10:57 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: s390
Get:1 http://ftp.de.debian.org unstable InRelease [146 kB]
-Get:2 http://ftp.de.debian.org unstable/main Sources [5923 kB]
-Get:3 http://incoming.debian.org unstable InRelease [146 kB]
+Get:2 http://incoming.debian.org unstable InRelease [146 kB]
+Get:3 http://ftp.de.debian.org unstable/main Sources [5932 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 [5923 kB]
+Get:5 http://incoming.debian.org unstable/main Sources [5932 kB]
Get:6 http://ftp.de.debian.org unstable/contrib Sources [57.2 kB]
Get:7 http://ftp.de.debian.org unstable/non-free Sources [103 kB]
Get:8 http://ftp.de.debian.org unstable/main s390 Packages [7631 kB]
@@ -59,11 +59,11 @@ Get:14 http://incoming.debian.org unstable/contrib s390 Packages [54.9 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [37.6 kB]
-Get:18 http://incoming.debian.org Packages [341 kB]
+Get:17 http://incoming.debian.org Sources [46.0 kB]
+Get:18 http://incoming.debian.org Packages [374 kB]
Ign http://incoming.debian.org unstable/contrib Translation-en
Ign http://incoming.debian.org Translation-en
-Fetched 28.2 MB in 27s (1035 kB/s)
+Fetched 28.3 MB in 38s (727 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -84,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 0s (146 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 1s (129 kB/s)
Download complete and in download only mode
Check arch
@@ -120,7 +120,7 @@ Checking correctness of dependencies...
│ Install bwa 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), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -195,7 +195,7 @@ Get:16 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1
Get:17 http://ftp.de.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
Get:18 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.3.4.dfsg-3 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9401 kB in 2s (3530 kB/s)
+Fetched 9401 kB in 4s (2011 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10599 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_s390.deb) ...
@@ -274,12 +274,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -289,228 +289,83 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture s390
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-s390-T70MK0/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-s390-T70MK0/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-s390-T70MK0/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-s390-T70MK0/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-s390-y6DgGz/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_s390.deb'.
- dpkg-genchanges -B -ms390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../bwa_0.5.10-1_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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-s390-T70MK0/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-s390-T70MK0/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0440
-
-bwa_0.5.10-1_s390.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: s390
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: s390 Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- edfdfa4e68784b14fd11bb64d5a397849344201a 142218 bwa_0.5.10-1_s390.deb
-Checksums-Sha256:
- 1179e3dc80b5165d8eb3f7a87ca4f40abd681a8cb26dae8033e3e13923ff2a85 142218 bwa_0.5.10-1_s390.deb
-Files:
- 7c12ca0944d19e2247bed4112c672444 142218 science optional bwa_0.5.10-1_s390.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_s390.deb
-─────────────────────
-
- new debian package, version 2.0.
- size 142218 bytes: control archive= 989 bytes.
- 774 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: s390
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 286
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/bin/
--rwxr-xr-x root/root 211336 2011-11-14 04:40 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/bwa/
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:40 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:40 ./usr/share/doc/bwa/
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1059
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-s390-sbuild-25cc7e9e-b6a5-4ff6-bb8b-19219e938783/build/buildd-bwa_0.5.10-1-s390-y6DgGz
+Purging /var/lib/schroot/mount/sid-s390-sbuild-817d8e41-13eb-4d3a-b868-f8458c4a1ebb/build/buildd-bwa_0.6.0-1-s390-T70MK0
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -518,18 +373,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: s390
-Build-Space: 2836
-Build-Time: 18
+Build-Space: 1220
+Build-Time: 8
Distribution: sid
-Install-Time: 10
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 12
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 69
-Source-Version: 0.5.10-1
-Space: 2836
-Status: successful
-Version: 0.5.10-1
+Package-Time: 72
+Source-Version: 0.6.0-1
+Space: 1220
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0440
-Build needed 00:01:09, 2836k disc space
-Signature with key '772711F7' requested:
+Finished at 20111114-1059
+Build needed 00:01:12, 1220k disc space
diff --git a/sparc.log b/sparc.log
index 68568bf..2311f0e 100644
--- a/sparc.log
+++ b/sparc.log
@@ -1,70 +1,69 @@
-From buildd at schroeder.debian.org Mon Nov 14 04:42:11 2011
-Return-path: <buildd at schroeder.debian.org>
+From buildd at lebrun.debian.org Mon Nov 14 11:02:41 2011
+Return-path: <buildd at lebrun.debian.org>
Received: from kokkonen.debian.org ([2001:41b8:202:deb:1a1a:0:52c3:4b61])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
CN=kokkonen.debian.org,
EMAIL=hostmaster at kokkonen.debian.org (verified)
by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1RPoN1-0000XJ-8h
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:42:11 +0000
-Received: from schroeder.debian.org ([193.198.184.11])
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1RPuJF-0007Xr-A4
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:02:41 +0000
+Received: from lebrun.debian.org ([193.198.184.10])
from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=schroeder.debian.org,
- EMAIL=hostmaster at schroeder.debian.org (verified)
+ CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
by kokkonen.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at schroeder.debian.org>)
- id 1RPoN0-0006NA-Bg
- for logs at buildd.debian.org; Mon, 14 Nov 2011 04:42:10 +0000
-Received: from buildd by schroeder.debian.org with local (Exim 4.72)
- (envelope-from <buildd at schroeder.debian.org>)
- id 1RPoMy-00046N-7Q; Mon, 14 Nov 2011 04:42:08 +0000
-Message-Id: <E1RPoMy-00046N-7Q at schroeder.debian.org>
+ (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
+ id 1RPuJE-0007vG-HU
+ for logs at buildd.debian.org; Mon, 14 Nov 2011 11:02:40 +0000
+Received: from buildd by lebrun.debian.org with local (Exim 4.72)
+ (envelope-from <buildd at lebrun.debian.org>)
+ id 1RPuJC-0001yb-Ih; Mon, 14 Nov 2011 11:02:38 +0000
+Message-Id: <E1RPuJC-0001yb-Ih 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: Mon, 14 Nov 2011 04:42:07 +0000
-From: buildd on schroeder <buildd at schroeder.debian.org>
-To: logs at buildd.debian.org,buildd-admin at schroeder.debian.org
-Subject: Log for successful build of bwa_0.5.10-1 on sparc (dist=sid)
-Key-Id: 2BF501AB
+Date: Mon, 14 Nov 2011 11:02:38 +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 bwa_0.6.0-1 on sparc (dist=sid)
+Key-Id: 4DF860F5
Delivered-To: logs at buildd.debian.org
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on schroeder.debian.org
+sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.5.10-1 (sparc) 14 Nov 2011 04:39 ║
+║ bwa 0.6.0-1 (sparc) 14 Nov 2011 11:00 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.5.10-1
-Source Version: 0.5.10-1
+Version: 0.6.0-1
+Source Version: 0.6.0-1
Architecture: sparc
-Get:1 http://ftp.hr.debian.org unstable InRelease [146 kB]
+Get:1 http://debian.carnet.hr unstable InRelease [146 kB]
Get:2 http://incoming.debian.org unstable InRelease [146 kB]
-Get:3 http://ftp.hr.debian.org unstable/main Sources [5923 kB]
-Get:4 http://ftp.hr.debian.org unstable/contrib Sources [57.2 kB]
-Get:5 http://ftp.hr.debian.org unstable/non-free Sources [103 kB]
+Get:3 http://debian.carnet.hr unstable/main Sources [5932 kB]
+Get:4 http://debian.carnet.hr unstable/contrib Sources [57.2 kB]
+Get:5 http://debian.carnet.hr unstable/non-free Sources [103 kB]
Ign http://incoming.debian.org InRelease
-Get:6 http://incoming.debian.org Release.gpg [836 B]
-Get:7 http://ftp.hr.debian.org unstable/main sparc Packages [7670 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [5923 kB]
-Get:9 http://ftp.hr.debian.org unstable/contrib sparc Packages [55.8 kB]
-Ign http://ftp.hr.debian.org unstable/contrib TranslationIndex
-Get:10 http://ftp.hr.debian.org unstable/main TranslationIndex [2045 B]
-Ign http://ftp.hr.debian.org unstable/contrib Translation-en
-Get:11 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
-Get:12 http://incoming.debian.org unstable/non-free Sources [103 kB]
-Get:13 http://incoming.debian.org unstable/main sparc Packages [7670 kB]
-Get:14 http://incoming.debian.org unstable/contrib sparc Packages [55.8 kB]
+Get:6 http://debian.carnet.hr unstable/main sparc Packages [7670 kB]
+Get:7 http://incoming.debian.org Release.gpg [836 B]
+Get:8 http://incoming.debian.org Release [1604 B]
+Get:9 http://incoming.debian.org unstable/main Sources [5932 kB]
+Get:10 http://debian.carnet.hr unstable/contrib sparc Packages [55.8 kB]
+Ign http://debian.carnet.hr unstable/contrib TranslationIndex
+Get:11 http://debian.carnet.hr unstable/main TranslationIndex [2045 B]
+Ign http://debian.carnet.hr unstable/contrib Translation-en
+Get:12 http://incoming.debian.org unstable/contrib Sources [57.2 kB]
+Get:13 http://incoming.debian.org unstable/non-free Sources [103 kB]
+Get:14 http://incoming.debian.org unstable/main sparc Packages [7670 kB]
+Get:15 http://incoming.debian.org unstable/contrib sparc Packages [55.8 kB]
Ign http://incoming.debian.org unstable/contrib TranslationIndex
-Get:15 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
-Get:16 http://incoming.debian.org Release [1604 B]
-Get:17 http://incoming.debian.org Sources [37.6 kB]
-Get:18 http://incoming.debian.org Packages [341 kB]
-Ign http://incoming.debian.org unstable/contrib Translation-en
+Get:16 http://incoming.debian.org unstable/main TranslationIndex [2045 B]
+Get:17 http://incoming.debian.org Sources [46.0 kB]
+Get:18 http://incoming.debian.org Packages [374 kB]
Ign http://incoming.debian.org Translation-en
-Fetched 28.3 MB in 29s (973 kB/s)
+Ign http://incoming.debian.org unstable/contrib Translation-en
+Fetched 28.4 MB in 29s (965 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -85,11 +84,11 @@ Building dependency tree...
Reading state information...
NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bwa.git
-Need to get 126 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (dsc) [1929 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (tar) [120 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.5.10-1 (diff) [4113 B]
-Fetched 126 kB in 1s (91.9 kB/s)
+Need to get 136 kB of source archives.
+Get:1 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (dsc) [1927 B]
+Get:2 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (tar) [130 kB]
+Get:3 http://incoming.debian.org/buildd-unstable/ bwa 0.6.0-1 (diff) [4313 B]
+Fetched 136 kB in 1s (121 kB/s)
Download complete and in download only mode
Check arch
@@ -121,7 +120,7 @@ Checking correctness of dependencies...
│ Install bwa build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), zlib1g-dev
+Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
Checking for already installed dependencies...
base-files: already installed (6.5)
base-passwd: already installed (3.5.23)
@@ -178,26 +177,26 @@ The following NEW packages will be installed:
0 upgraded, 18 newly installed, 0 to remove and 11 not upgraded.
Need to get 8985 kB of archives.
After this operation, 25.5 MB of additional disk space will be used.
-Get:1 http://ftp.hr.debian.org/debian/ unstable/main libpipeline1 sparc 1.2.0-5 [35.0 kB]
-Get:2 http://ftp.hr.debian.org/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
-Get:3 http://ftp.hr.debian.org/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
-Get:4 http://ftp.hr.debian.org/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
-Get:5 http://ftp.hr.debian.org/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
-Get:6 http://ftp.hr.debian.org/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:7 http://ftp.hr.debian.org/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
-Get:8 http://ftp.hr.debian.org/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
-Get:9 http://ftp.hr.debian.org/debian/ unstable/main man-db sparc 2.6.0.2-3 [997 kB]
-Get:10 http://ftp.hr.debian.org/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
-Get:11 http://ftp.hr.debian.org/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
-Get:12 http://ftp.hr.debian.org/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
-Get:13 http://ftp.hr.debian.org/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:14 http://ftp.hr.debian.org/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
-Get:15 http://ftp.hr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:16 http://ftp.hr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
-Get:17 http://ftp.hr.debian.org/debian/ unstable/main debhelper all 8.9.9 [552 kB]
-Get:18 http://ftp.hr.debian.org/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
+Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.0-5 [35.0 kB]
+Get:2 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 8.12-4 [231 kB]
+Get:3 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.28.8-1 [1508 kB]
+Get:4 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.7.8.dfsg-5 [816 kB]
+Get:5 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.2-2 [106 kB]
+Get:6 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
+Get:7 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 8.2.3 [206 kB]
+Get:8 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.21-6 [1155 kB]
+Get:9 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.0.2-3 [997 kB]
+Get:10 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 5.09-2 [245 kB]
+Get:11 http://debian.carnet.hr/debian/ unstable/main file sparc 5.09-2 [51.5 kB]
+Get:12 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-5 [140 kB]
+Get:13 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
+Get:14 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-5 [1983 kB]
+Get:15 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
+Get:16 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu1 [223 kB]
+Get:17 http://debian.carnet.hr/debian/ unstable/main debhelper all 8.9.9 [552 kB]
+Get:18 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.3.4.dfsg-3 [189 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 8985 kB in 7s (1232 kB/s)
+Fetched 8985 kB in 6s (1313 kB/s)
Selecting previously unselected package libpipeline1.
(Reading database ... 10914 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_sparc.deb) ...
@@ -276,12 +275,12 @@ Unpack source
─────────────
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Nov 14 04:21:35 2011 UTC using RSA key ID 2295D502
+gpgv: Signature made Mon Nov 14 10:30:40 2011 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./bwa_0.5.10-1.dsc
-dpkg-source: info: extracting bwa in bwa-0.5.10
-dpkg-source: info: unpacking bwa_0.5.10.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.5.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./bwa_0.6.0-1.dsc
+dpkg-source: info: extracting bwa in bwa-0.6.0
+dpkg-source: info: unpacking bwa_0.6.0.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.6.0-1.debian.tar.gz
Check disc space
────────────────
@@ -291,228 +290,83 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.5.10-1
- dpkg-source --before-build bwa-0.5.10
+dpkg-buildpackage: source version 0.6.0-1
+ dpkg-source --before-build bwa-0.6.0
dpkg-buildpackage: host architecture sparc
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-sparc-rb8v81/bwa-0.6.0'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10/bwt_gen'
-rm -f gmon.out *.o a.out *~ *.a
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10/bwt_gen'
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-sparc-rb8v81/bwa-0.6.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
- dh_auto_build
-make[1]: Entering directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
-make[2]: Entering directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
+ debian/rules override_dh_auto_build
+make[1]: Entering directory `/build/buildd-bwa_0.6.0-1-sparc-rb8v81/bwa-0.6.0'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro"
+make[2]: Entering directory `/build/buildd-bwa_0.6.0-1-sparc-rb8v81/bwa-0.6.0'
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+QSufSort.c: In function 'QSufSortSuffixSort':
+QSufSort.c:62:10: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function 'BWTIncBuildRelativeRank':
-bwt_gen.c:824:15: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function 'BWTIncMergeBwt':
-bwt_gen.c:899:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
-QSufSort.c: In function 'QSufSortSuffixSort':
-QSufSort.c:89:6: warning: variable 'maxNumInputSymbol' set but not used [-Wunused-but-set-variable]
-ar -scru libbwtgen.a bwt_gen.o QSufSort.o
-make[2]: Leaving directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10/bwt_gen'
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
-bwtmisc.c: In function 'bwa_pac_rev_core':
-bwtmisc.c:163:20: warning: variable 'j' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o
-stdaln.c: In function 'aln_local_core':
-stdaln.c:545:25: warning: variable 'b' set but not used [-Wunused-but-set-variable]
-stdaln.c: In function 'aln_extend_core':
-stdaln.c:865:16: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
-bwase.c: In function 'bwa_aln2seq_core':
-bwase.c:75:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:452:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
-bwtsw2_aux.c: In function 'gen_cigar':
-bwtsw2_aux.c:193:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
-gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
-gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
-make[1]: Leaving directory `/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0/bwa-0.5.10'
- dh_auto_test
- fakeroot debian/rules binary-arch
-dh binary-arch
- dh_testroot -a
- dh_prep -a
- dh_installdirs -a
- dh_auto_install -a
- dh_install -a
- dh_installdocs -a
- dh_installchangelogs -a
- dh_installexamples -a
- dh_installman -a
- dh_installcatalogs -a
- dh_installcron -a
- dh_installdebconf -a
- dh_installemacsen -a
- dh_installifupdown -a
- dh_installinfo -a
- dh_installinit -a
- dh_installmenu -a
- dh_installmime -a
- dh_installmodules -a
- dh_installlogcheck -a
- dh_installlogrotate -a
- dh_installpam -a
- dh_installppp -a
- dh_installudev -a
- dh_installwm -a
- dh_installxfonts -a
- dh_installgsettings -a
- dh_bugfiles -a
- dh_ucf -a
- dh_lintian -a
- dh_gconf -a
- dh_icons -a
- dh_perl -a
- dh_usrlocal -a
- dh_link -a
- dh_compress -a
- dh_fixperms -a
- dh_strip -a
- dh_makeshlibs -a
- dh_shlibdeps -a
- dh_installdeb -a
- dh_gencontrol -a
-dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
- dh_md5sums -a
- dh_builddeb -a
-dpkg-deb: building package `bwa' in `../bwa_0.5.10-1_sparc.deb'.
- dpkg-genchanges -B -msparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org> >../bwa_0.5.10-1_sparc.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 bwa-0.5.10
-dpkg-buildpackage: binary only upload (no source included)
+bwt_gen.c:947:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+bwt_gen.c: In function 'BWTIncConstructFromPacked':
+bwt_gen.c:1452:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1468:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwt_gen.c:1483:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtio.c -o bwtio.o
+bwtio.c: In function 'bwt_restore_bwt':
+bwtio.c:62:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:63:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:64:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c: In function 'bwt_restore_sa':
+bwtio.c:36:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:38:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:39:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:40:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtio.c:47:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+bntseq.c: In function 'bns_restore_core':
+bntseq.c:98:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:106:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:114:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:123:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+bntseq.c:129:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
+bwtmisc.c: In function 'bwa_pac2cspac_core':
+bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwt_pac2bwt':
+bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+bwtmisc.c: In function 'bwa_seq_len':
+bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
+compilation terminated.
+make[2]: *** [ksw.o] Error 1
+make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-sparc-rb8v81/bwa-0.6.0'
+dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
+make[1]: *** [override_dh_auto_build] Error 2
+make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-sparc-rb8v81/bwa-0.6.0'
+make: *** [build] Error 2
+dpkg-buildpackage: error: debian/rules build gave error exit status 2
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111114-0441
-
-bwa_0.5.10-1_sparc.changes:
-Format: 1.8
-Date: Mon, 14 Nov 2011 13:12:50 +0900
-Source: bwa
-Binary: bwa
-Architecture: sparc
-Version: 0.5.10-1
-Distribution: sid
-Urgency: low
-Maintainer: sparc Build Daemon (schroeder) <buildd_sparc-schroeder at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- bwa - Burrows-Wheeler Aligner
-Changes:
- bwa (0.5.10-1) unstable; urgency=low
- .
- [a01f6ca] New upstream release.
- [6d7bc7f] Conforms with Debian Policy version 3.9.2.
- [125c73d] Corrected Vcs-Git URL.
- [37f43c9] Normalised machine-readable copyright file with config-edit.
- [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’.
- [b106d64] Removed redundant ChangeLog file, already installed by Debhelper.
-Checksums-Sha1:
- 0943630080ef37c30733df589a885e4ffb3d97bc 141136 bwa_0.5.10-1_sparc.deb
-Checksums-Sha256:
- af5510c28156a8e8780e30326d95ec5226f0aea16d84eb8aa51db20916f794c8 141136 bwa_0.5.10-1_sparc.deb
-Files:
- f8e30a9ce31d77c9a17077c0ff97fc08 141136 science optional bwa_0.5.10-1_sparc.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-bwa_0.5.10-1_sparc.deb
-──────────────────────
-
- new debian package, version 2.0.
- size 141136 bytes: control archive= 991 bytes.
- 775 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
- Package: bwa
- Version: 0.5.10-1
- Architecture: sparc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 274
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
- Suggests: samtools
- Section: science
- Priority: optional
- Homepage: http://bio-bwa.sourceforge.net/
- Description: Burrows-Wheeler Aligner
- Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
- nucleotide sequences against a long reference sequence such as the human
- genome. It implements two algorithms, bwa-short and BWA-SW. The former works
- for query sequences shorter than 200 bp and the latter for longer sequences up
- to around 100 kbp. Both algorithms do gapped alignment. They are usually more
- accurate and faster on queries with low error rates.
-
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/bin/
--rwxr-xr-x root/root 199156 2011-11-14 04:41 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/man/man1/
--rw-r--r-- root/root 7554 2011-11-14 04:41 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/bwa/
--rwxr-xr-x root/root 730 2011-11-13 01:07 ./usr/share/bwa/xa2multi.pl
--rwxr-xr-x root/root 616 2011-11-13 01:07 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2011-11-13 01:07 ./usr/share/bwa/solid2fastq.pl
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-14 04:41 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17912 2011-11-13 01:07 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 2740 2011-11-14 04:09 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 634 2011-11-13 01:07 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 1159 2011-11-14 04:16 ./usr/share/doc/bwa/changelog.Debian.gz
--rw-r--r-- root/root 5857 2011-11-13 01:08 ./usr/share/doc/bwa/NEWS.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
+Build finished at 20111114-1102
+FAILED [dpkg-buildpackage died]
────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-9410175d-7016-4c1d-bc79-7a31899e6bab/build/buildd-bwa_0.5.10-1-sparc-wsjLJ0
+Purging /var/lib/schroot/mount/sid-sparc-sbuild-c53dc514-4039-4198-964b-bead9225802a/build/buildd-bwa_0.6.0-1-sparc-rb8v81
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -520,18 +374,18 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: sparc
-Build-Space: 2680
-Build-Time: 64
+Build-Space: 1180
+Build-Time: 24
Distribution: sid
-Install-Time: 52
-Job: bwa_0.5.10-1
+Fail-Stage: build
+Install-Time: 59
+Job: bwa_0.6.0-1
Package: bwa
-Package-Time: 165
-Source-Version: 0.5.10-1
-Space: 2680
-Status: successful
-Version: 0.5.10-1
+Package-Time: 133
+Source-Version: 0.6.0-1
+Space: 1180
+Status: attempted
+Version: 0.6.0-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111114-0441
-Build needed 00:02:45, 2680k disc space
-Signature with key '2BF501AB' requested:
+Finished at 20111114-1102
+Build needed 00:02:13, 1180k disc space
--
Burrows-Wheeler Aligner
More information about the debian-med-commit
mailing list