[med-svn] [bwa] 01/01: bwa (0.7.12-2) unstable; urgency=medium
Charles Plessy
plessy at moszumanska.debian.org
Sat Jul 4 04:41:33 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch meta
in repository bwa.
commit fece35372605e63a9700f670a5112d409cf0212e
Author: Charles Plessy <plessy at debian.org>
Date: Sat Jul 4 13:40:26 2015 +0900
bwa (0.7.12-2) unstable; urgency=medium
* Upload to Unstable.
* Install bash completion script in /usr/share/bash-completion/completions.
* Also distribute README-alt.md.
* Watch GitHub instead of SourceForge.
-- Charles Plessy <plessy at debian.org> Sat, 04 Jul 2015 13:00:50 +0900
---
amd64.log | 924 +++++++++++++++++++++++++++++++++++++-------------------------
changes | 77 +++---
dsc | 67 +++--
upload | 5 +
4 files changed, 621 insertions(+), 452 deletions(-)
diff --git a/amd64.log b/amd64.log
index 9c67ddf..111decf 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,31 +1,58 @@
-sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on anx191
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ bwa 0.6.1-1 (amd64) 30 Nov 2011 19:40 ║
+║ bwa 0.7.12-2 (amd64) 04 juil. 2015 13:03 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: bwa
-Version: 0.6.1-1
-Source Version: 0.6.1-1
+Version: 0.7.12-2
+Source Version: 0.7.12-2
Distribution: unstable
-Architecture: amd64
+Machine Architecture: amd64
+Host Architecture: amd64
+Build Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/bwa-9cq9vY/bwa-0.6.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/bwa-9cq9vY' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-4a5a6503-97c4-4a9c-b5c3-63f1e70d95e6' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/bwa-zIKBoR/bwa-0.7.12' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/bwa-zIKBoR' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-65fa37fe-90ae-43d8-8bda-2ed8a63f24ed' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Hit http://ftp.jp.debian.org sid InRelease
-Hit http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
-Hit http://ftp.jp.debian.org sid/main TranslationIndex
+Get:1 http://ftp.jp.debian.org unstable InRelease [204 kB]
+Get:2 http://ftp.jp.debian.org unstable/main Sources/DiffIndex [7876 B]
+Get:3 http://ftp.jp.debian.org unstable/main amd64 Packages/DiffIndex [7876 B]
+Get:4 http://ftp.jp.debian.org unstable/main Translation-en/DiffIndex [7876 B]
+Get:5 http://ftp.jp.debian.org unstable/main 2015-07-04-0246.30.pdiff [7778 B]
+Get:6 http://ftp.jp.debian.org unstable/main 2015-07-04-0246.30.pdiff [7778 B]
+Get:7 http://ftp.jp.debian.org unstable/main amd64 2015-07-04-0246.30.pdiff [7014 B]
+Get:8 http://ftp.jp.debian.org unstable/main 2015-07-04-0246.30.pdiff [252 B]
+Get:9 http://ftp.jp.debian.org unstable/main amd64 2015-07-04-0246.30.pdiff [7014 B]
+Get:10 http://ftp.jp.debian.org unstable/main 2015-07-04-0246.30.pdiff [252 B]
+Fetched 242 kB in 5s (42.2 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+The following packages will be upgraded:
+ liblzma5 xz-utils
+2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
+Need to get 413 kB of archives.
+After this operation, 61.4 kB disk space will be freed.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main liblzma5 amd64 5.1.1alpha+20120614-2.1 [194 kB]
+Get:2 http://ftp.jp.debian.org/debian/ unstable/main xz-utils amd64 5.1.1alpha+20120614-2.1 [219 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 413 kB in 0s (1125 kB/s)
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 100%
(Reading database ... 11518 files and directories currently installed.)
+Preparing to unpack .../liblzma5_5.1.1alpha+20120614-2.1_amd64.deb ...
+Unpacking liblzma5:amd64 (5.1.1alpha+20120614-2.1) over (5.1.1alpha+20120614-2+b3) ...
+Setting up liblzma5:amd64 (5.1.1alpha+20120614-2.1) ...
+Processing triggers for libc-bin (2.19-18) ...
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11517 files and directories currently installed.)
+Preparing to unpack .../xz-utils_5.1.1alpha+20120614-2.1_amd64.deb ...
+Unpacking xz-utils (5.1.1alpha+20120614-2.1) over (5.1.1alpha+20120614-2+b3) ...
+Setting up xz-utils (5.1.1alpha+20120614-2.1) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -35,15 +62,24 @@ Reading state information...
Local sources
─────────────
-bwa_0.6.1-1.dsc exists in .; copying to chroot
+bwa_0.7.12-2.dsc exists in .; copying to chroot
+
+Check architectures
+───────────────────
+
-Check arch
-──────────
+Check dependencies
+──────────────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-88Ackj/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-k9eWij/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -54,12 +90,26 @@ Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-sbuild-build-depends-core-dummy is already the newest version.
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
-Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.9.4~), zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-bwa-dummy' in `/«BUILDDIR»/resolver-Bg3e5F/apt_archive/sbuild-build-depends-bwa-dummy.deb'.
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/772 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11516 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), zlib1g-dev
+dpkg-deb: building package 'sbuild-build-depends-bwa-dummy' in '/«BUILDDIR»/resolver-jPqOqh/apt_archive/sbuild-build-depends-bwa-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -71,90 +121,122 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- debhelper file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0
- libxml2 man-db po-debconf zlib1g-dev
+ bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian
+ libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libicu52 libmagic1
+ libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
- dh-make gettext-doc groff less www-browser 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
+ curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
+ libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
- debhelper file gettext gettext-base groff-base html2text intltool-debian
- libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-bwa-dummy zlib1g-dev
+ bsdmainutils debhelper file gettext gettext-base groff-base intltool-debian
+ libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libicu52 libmagic1
+ libpipeline1 libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-bwa-dummy zlib1g-dev
+0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded.
+Need to get 3278 kB/16.0 MB of archives.
+After this operation, 56.6 MB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main libglib2.0-0 amd64 2.44.1-1.1 [2461 kB]
+Get:2 http://ftp.jp.debian.org/debian/ unstable/main debhelper all 9.20150628 [817 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/9380 kB of archives.
-After this operation, 25.7 MB of additional disk space will be used.
-Selecting previously unselected package libpipeline1.
-(Reading database ... 10818 files and directories currently installed.)
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ...
-Selecting previously unselected package libpcre3.
-Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
-Selecting previously unselected package libffi5.
-Unpacking libffi5 (from .../libffi5_3.0.10-3_amd64.deb) ...
-Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ...
-Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_amd64.deb) ...
-Selecting previously unselected package libcroco3.
-Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ...
-Selecting previously unselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ...
-Selecting previously unselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../archives/file_5.09-2_amd64.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-5_amd64.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
-Selecting previously unselected package zlib1g-dev.
-Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
-Selecting previously unselected package sbuild-build-depends-bwa-dummy.
-Unpacking sbuild-build-depends-bwa-dummy (from .../sbuild-build-depends-bwa-dummy.deb) ...
-Setting up libpipeline1 (1.2.0-5) ...
-Setting up libpcre3 (8.12-4) ...
-Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
-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) ...
-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 (8.9.11) ...
-Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
-Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ...
+Fetched 3278 kB in 4s (773 kB/s)
+Selecting previously unselected package libpipeline1:amd64.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11516 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.4.0-1_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.4.0-1) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.0.2-5_amd64.deb ...
+Unpacking man-db (2.7.0.2-5) ...
+Selecting previously unselected package libasprintf0c2:amd64.
+Preparing to unpack .../libasprintf0c2_0.19.4-1_amd64.deb ...
+Unpacking libasprintf0c2:amd64 (0.19.4-1) ...
+Selecting previously unselected package libmagic1:amd64.
+Preparing to unpack .../libmagic1_1%3a5.22+15-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.22+15-2) ...
+Selecting previously unselected package libicu52:amd64.
+Preparing to unpack .../libicu52_52.1-9_amd64.deb ...
+Unpacking libicu52:amd64 (52.1-9) ...
+Selecting previously unselected package libxml2:amd64.
+Preparing to unpack .../libxml2_2.9.2+dfsg1-3_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.2+dfsg1-3) ...
+Selecting previously unselected package libffi6:amd64.
+Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ...
+Unpacking libffi6:amd64 (3.1-2+b2) ...
+Selecting previously unselected package libglib2.0-0:amd64.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.44.1-1.1) ...
+Selecting previously unselected package libcroco3:amd64.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:amd64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ...
+Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.22+15-2_amd64.deb ...
+Unpacking file (1:5.22+15-2) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.4-1_amd64.deb ...
+Unpacking gettext-base (0.19.4-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.4-1_amd64.deb ...
+Unpacking gettext (0.19.4-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.2_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.2) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150628_all.deb ...
+Unpacking debhelper (9.20150628) ...
+Selecting previously unselected package zlib1g-dev:amd64.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Selecting previously unselected package sbuild-build-depends-bwa-dummy.
+Preparing to unpack .../sbuild-build-depends-bwa-dummy.deb ...
+Unpacking sbuild-build-depends-bwa-dummy (0.invalid.0) ...
+Setting up libpipeline1:amd64 (1.4.0-1) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up man-db (2.7.0.2-5) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libasprintf0c2:amd64 (0.19.4-1) ...
+Setting up libmagic1:amd64 (1:5.22+15-2) ...
+Setting up libicu52:amd64 (52.1-9) ...
+Setting up libxml2:amd64 (2.9.2+dfsg1-3) ...
+Setting up libffi6:amd64 (3.1-2+b2) ...
+Setting up libglib2.0-0:amd64 (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:amd64 (0.6.8-3+b1) ...
+Setting up libunistring0:amd64 (0.9.3-5.2+b1) ...
+Setting up file (1:5.22+15-2) ...
+Setting up gettext-base (0.19.4-1) ...
+Setting up gettext (0.19.4-1) ...
+Setting up intltool-debian (0.35.0+20060710.2) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150628) ...
+Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-bwa-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-18) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 2.6.39-bpo.2-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-5 gcc-4.6_4.6.2-5 libc6-dev_2.13-21 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 linux-libc-dev_3.1.4-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.2-1 cpp-4.6_4.6.2-5 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.2-1 g++-4.6_4.6.2-5 [...]
+Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25-9 dpkg-dev_1.18.1 g++-4.9_4.9.3-1 gcc-4.9_4.9.3-1 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.3-1 libstdc++6_5.1.1-12 linux-libc-dev_4.0.5-1
+Package versions: apt_1.0.9.10 base-files_9.2 base-passwd_3.5.37 bash_4.3-12 binutils_2.25-9 bsdmainutils_9.0.6 bsdutils_1:2.26.2-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:4.9.2-4 cpp-4.9_4.9.3-1 dash_0.5.7-4+b1 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150628 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dpkg_1.18.1 dpkg-dev_1.18.1 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 eatmydata_82-6 fakeroot_1.20.2-1 file_1:5.22+15-2 find [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -164,10 +246,10 @@ Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (bwa_0.6.1-1.dsc)
-dpkg-source: info: extracting bwa in bwa-0.6.1
-dpkg-source: info: unpacking bwa_0.6.1.orig.tar.bz2
-dpkg-source: info: unpacking bwa_0.6.1-1.debian.tar.gz
+dpkg-source: warning: extracting unsigned source package (bwa_0.7.12-2.dsc)
+dpkg-source: info: extracting bwa in bwa-0.7.12
+dpkg-source: info: unpacking bwa_0.7.12.orig.tar.bz2
+dpkg-source: info: unpacking bwa_0.7.12-2.debian.tar.xz
Check disc space
────────────────
@@ -180,175 +262,118 @@ User Environment
HOME=/sbuild-nonexistent
LOGNAME=charles
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_CHROOT_NAME=sid-amd64-sbuild
+SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
+SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-4a5a6503-97c4-4a9c-b5c3-63f1e70d95e6
-SCHROOT_UID=31051
+SCHROOT_SESSION_ID=unstable-amd64-sbuild-65fa37fe-90ae-43d8-8bda-2ed8a63f24ed
+SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
-TERM=xterm
+TERM=xterm-256color
USER=charles
-USERNAME=charles
+XDG_RUNTIME_DIR=/run/user/1000
+XDG_SESSION_ID=2875
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package bwa
-dpkg-buildpackage: source version 0.6.1-1
+dpkg-buildpackage: source version 0.7.12-2
+dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build bwa-0.6.1
+ dpkg-source --before-build bwa-0.7.12
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
-make[1]: Entering directory `/«PKGBUILDDIR»'
+ make -j1 clean
+make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f gmon.out *.o a.out bwa *~ *.a
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean
- dpkg-source -b bwa-0.6.1
-dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building bwa using existing ./bwa_0.6.1.orig.tar.bz2
-dpkg-source: info: building bwa in bwa_0.6.1-1.debian.tar.gz
-dpkg-source: info: building bwa in bwa_0.6.1-1.dsc
+ dpkg-source -b bwa-0.7.12
+dpkg-source: info: using source format '3.0 (quilt)'
+dpkg-source: info: building bwa using existing ./bwa_0.7.12.orig.tar.bz2
+dpkg-source: info: building bwa in bwa_0.7.12-2.debian.tar.xz
+dpkg-source: info: building bwa in bwa_0.7.12-2.dsc
debian/rules build
dh build
dh_testdir
dh_auto_configure
debian/rules override_dh_auto_build
-make[1]: Entering directory `/«PKGBUILDDIR»'
-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" DFLAGS="-DHAVE_PTHREAD"
-make[2]: Entering directory `/«PKGBUILDDIR»'
-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
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- CFLAGS="-Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro" DFLAGS="-DHAVE_PTHREAD"
+ make -j1 "CFLAGS=-Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro" DFLAGS=-DHAVE_PTHREAD
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD utils.c -o utils.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD kthread.c -o kthread.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD kstring.c -o kstring.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD ksw.c -o ksw.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwt.c -o bwt.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bntseq.c -o bntseq.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwa.c -o bwa.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwamem.c -o bwamem.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwamem_extra.c -o bwamem_extra.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD malloc_wrap.c -o malloc_wrap.o
+ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
+ar: `u' modifier ignored since `D' is the default (see `U')
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -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:873:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+bwt_gen.c:878:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable]
+ bgint_t oldInverseSa0RelativeRank = 0;
+ ^
bwt_gen.c: In function 'BWTIncMergeBwt':
-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:99:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
-bntseq.c:107:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
-bntseq.c:115:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
-bntseq.c:124:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
-bntseq.c:130:10: 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 -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:74:15: warning: variable 'k' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_print_sam1':
-bwase.c:445:17: warning: variable 'm_is_N' set but not used [-Wunused-but-set-variable]
-bwase.c: In function 'bwa_sai2sam_se_core':
-bwase.c:601:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bwase.c:617:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bwase.c:622:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bwase.c: In function 'bwa_refine_gapped':
-bwase.c:308:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bwase.c:314:8: 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:686:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bwape.c:689:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bwape.c:700:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bwape.c: In function 'bwa_paired_sw':
-bwape.c:530:8: 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:186:7: warning: variable 'score' set but not used [-Wunused-but-set-variable]
-bwtsw2_aux.c: In function 'bsw2_aln':
-bwtsw2_aux.c:758:7: 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 `/«PKGBUILDDIR»'
-make[1]: Leaving directory `/«PKGBUILDDIR»'
+bwt_gen.c:952:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable]
+ unsigned int bitsInWordMinusBitPerChar;
+ ^
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwashm.c -o bwashm.o
+bwashm.c: In function 'bwa_shm_stage':
+bwashm.c:29:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
+ ftruncate(shmid, BWA_CTL_SIZE);
+ ^
+bwashm.c:66:2: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
+ ftruncate(shmid, idx->l_mem);
+ ^
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwase.c -o bwase.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bamlite.c -o bamlite.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD is.c -o is.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwape.c -o bwape.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD kopen.c -o kopen.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD pemerge.c -o pemerge.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -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-strong -Wformat -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -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-strong -Wformat -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD fastmap.c -o fastmap.o
+gcc -c -Wall -g -O2 -fstack-protector-strong -Wformat -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD main.c -o main.o
+gcc -Wall -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro -DHAVE_PTHREAD QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_auto_test
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
- dh_installdirs
dh_auto_install
dh_install
dh_installdocs
- dh_installchangelogs
- dh_installexamples
+ debian/rules override_dh_installchangelogs
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_installchangelogs NEWS.md
+make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installman
- dh_installcatalogs
- dh_installcron
- dh_installdebconf
- dh_installemacsen
- dh_installifupdown
- dh_installinfo
- dh_installinit
- dh_installmenu
- dh_installmime
- dh_installmodules
- dh_installlogcheck
- dh_installlogrotate
- dh_installpam
- dh_installppp
- dh_installudev
- dh_installwm
- dh_installxfonts
- dh_installgsettings
- dh_bugfiles
- dh_ucf
- dh_lintian
- dh_gconf
- dh_icons
dh_perl
- dh_usrlocal
dh_link
dh_compress
dh_fixperms
@@ -357,16 +382,17 @@ dh binary
dh_shlibdeps
dh_installdeb
dh_gencontrol
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package bwa: unused substitution variable ${perl:Depends}
dh_md5sums
dh_builddeb
-dpkg-deb: building package `bwa' in `../bwa_0.6.1-1_amd64.deb'.
- dpkg-genchanges >../bwa_0.6.1-1_amd64.changes
-dpkg-genchanges: including full source code in upload
- dpkg-source --after-build bwa-0.6.1
-dpkg-buildpackage: full upload (original source is included)
+dpkg-deb: building package 'bwa' in '../bwa_0.7.12-2_amd64.deb'.
+ dpkg-genchanges >../bwa_0.7.12-2_amd64.changes
+dpkg-genchanges: not including original source code in upload
+ dpkg-source --after-build bwa-0.7.12
+dpkg-buildpackage: binary and diff upload (original source NOT included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111130-1942
+Build finished at 20150704-1304
Finished
────────
@@ -374,97 +400,304 @@ Finished
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+lintian
+───────
+
+Merged Build-Depends: lintian
+Filtered Build-Depends: lintian
+dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/«BUILDDIR»/resolver-AVzM6W/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
+OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install lintian build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
+ libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
+ libexporter-tiny-perl libfile-basedir-perl libio-pty-perl
+ libio-socket-inet6-perl libio-socket-ssl-perl libio-string-perl
+ libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl
+ libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl
+ libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl
+ libsocket6-perl libssl1.0.0 libsub-name-perl libtext-levenshtein-perl
+ lintian netbase patchutils t1utils
+Suggested packages:
+ ca-certificates libhtml-template-perl libxml-simple-perl binutils-multiarch
+ libyaml-perl
+Recommended packages:
+ libauthen-sasl-perl libperlio-gzip-perl ifupdown
+The following NEW packages will be installed:
+ diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
+ libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
+ libexporter-tiny-perl libfile-basedir-perl libio-pty-perl
+ libio-socket-inet6-perl libio-socket-ssl-perl libio-string-perl
+ libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl
+ libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl
+ libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl
+ libsocket6-perl libssl1.0.0 libsub-name-perl libtext-levenshtein-perl
+ lintian netbase patchutils sbuild-build-depends-lintian-dummy t1utils
+0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded.
+Need to get 1295 kB/3937 kB of archives.
+After this operation, 12.8 MB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main libarchive-zip-perl all 1.48-1 [96.8 kB]
+Get:2 http://ftp.jp.debian.org/debian/ unstable/main libnet-ssleay-perl amd64 1.70-1 [283 kB]
+Get:3 http://ftp.jp.debian.org/debian/ unstable/main libemail-valid-perl all 1.196-1 [22.1 kB]
+Get:4 http://ftp.jp.debian.org/debian/ unstable/main liblist-moreutils-perl amd64 0.413-1 [76.7 kB]
+Get:5 http://ftp.jp.debian.org/debian/ unstable/main lintian all 2.5.32 [816 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 1295 kB in 0s (1564 kB/s)
+Selecting previously unselected package libssl1.0.0:amd64.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13016 files and directories currently installed.)
+Preparing to unpack .../libssl1.0.0_1.0.2c-1_amd64.deb ...
+Unpacking libssl1.0.0:amd64 (1.0.2c-1) ...
+Selecting previously unselected package netbase.
+Preparing to unpack .../archives/netbase_5.3_all.deb ...
+Unpacking netbase (5.3) ...
+Selecting previously unselected package diffstat.
+Preparing to unpack .../diffstat_1.58-1_amd64.deb ...
+Unpacking diffstat (1.58-1) ...
+Selecting previously unselected package hardening-includes.
+Preparing to unpack .../hardening-includes_2.7_all.deb ...
+Unpacking hardening-includes (2.7) ...
+Selecting previously unselected package libapt-pkg-perl.
+Preparing to unpack .../libapt-pkg-perl_0.1.29+b2_amd64.deb ...
+Unpacking libapt-pkg-perl (0.1.29+b2) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.48-1_all.deb ...
+Unpacking libarchive-zip-perl (1.48-1) ...
+Selecting previously unselected package libsub-name-perl.
+Preparing to unpack .../libsub-name-perl_0.12-1_amd64.deb ...
+Unpacking libsub-name-perl (0.12-1) ...
+Selecting previously unselected package libclass-accessor-perl.
+Preparing to unpack .../libclass-accessor-perl_0.34-1_all.deb ...
+Unpacking libclass-accessor-perl (0.34-1) ...
+Selecting previously unselected package libclone-perl.
+Preparing to unpack .../libclone-perl_0.38-1_amd64.deb ...
+Unpacking libclone-perl (0.38-1) ...
+Selecting previously unselected package libdigest-hmac-perl.
+Preparing to unpack .../libdigest-hmac-perl_1.03+dfsg-1_all.deb ...
+Unpacking libdigest-hmac-perl (1.03+dfsg-1) ...
+Selecting previously unselected package libnet-ssleay-perl.
+Preparing to unpack .../libnet-ssleay-perl_1.70-1_amd64.deb ...
+Unpacking libnet-ssleay-perl (1.70-1) ...
+Selecting previously unselected package libio-socket-ssl-perl.
+Preparing to unpack .../libio-socket-ssl-perl_2.016-1_all.deb ...
+Unpacking libio-socket-ssl-perl (2.016-1) ...
+Selecting previously unselected package libnet-smtp-ssl-perl.
+Preparing to unpack .../libnet-smtp-ssl-perl_1.01-3_all.deb ...
+Unpacking libnet-smtp-ssl-perl (1.01-3) ...
+Selecting previously unselected package libmailtools-perl.
+Preparing to unpack .../libmailtools-perl_2.13-1_all.deb ...
+Unpacking libmailtools-perl (2.13-1) ...
+Selecting previously unselected package libsocket6-perl.
+Preparing to unpack .../libsocket6-perl_0.25-1+b1_amd64.deb ...
+Unpacking libsocket6-perl (0.25-1+b1) ...
+Selecting previously unselected package libio-socket-inet6-perl.
+Preparing to unpack .../libio-socket-inet6-perl_2.72-2_all.deb ...
+Unpacking libio-socket-inet6-perl (2.72-2) ...
+Selecting previously unselected package libnet-ip-perl.
+Preparing to unpack .../libnet-ip-perl_1.26-1_all.deb ...
+Unpacking libnet-ip-perl (1.26-1) ...
+Selecting previously unselected package libnet-dns-perl.
+Preparing to unpack .../libnet-dns-perl_0.81-2_amd64.deb ...
+Unpacking libnet-dns-perl (0.81-2) ...
+Selecting previously unselected package libnet-domain-tld-perl.
+Preparing to unpack .../libnet-domain-tld-perl_1.73-1_all.deb ...
+Unpacking libnet-domain-tld-perl (1.73-1) ...
+Selecting previously unselected package libemail-valid-perl.
+Preparing to unpack .../libemail-valid-perl_1.196-1_all.deb ...
+Unpacking libemail-valid-perl (1.196-1) ...
+Selecting previously unselected package libexporter-tiny-perl.
+Preparing to unpack .../libexporter-tiny-perl_0.042-1_all.deb ...
+Unpacking libexporter-tiny-perl (0.042-1) ...
+Selecting previously unselected package libipc-system-simple-perl.
+Preparing to unpack .../libipc-system-simple-perl_1.25-2_all.deb ...
+Unpacking libipc-system-simple-perl (1.25-2) ...
+Selecting previously unselected package libfile-basedir-perl.
+Preparing to unpack .../libfile-basedir-perl_0.07-1_all.deb ...
+Unpacking libfile-basedir-perl (0.07-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libio-string-perl.
+Preparing to unpack .../libio-string-perl_1.08-3_all.deb ...
+Unpacking libio-string-perl (1.08-3) ...
+Selecting previously unselected package libipc-run-perl.
+Preparing to unpack .../libipc-run-perl_0.94-1_all.deb ...
+Unpacking libipc-run-perl (0.94-1) ...
+Selecting previously unselected package liblist-moreutils-perl.
+Preparing to unpack .../liblist-moreutils-perl_0.413-1_amd64.deb ...
+Unpacking liblist-moreutils-perl (0.413-1) ...
+Selecting previously unselected package libparse-debianchangelog-perl.
+Preparing to unpack .../libparse-debianchangelog-perl_1.2.0-4_all.deb ...
+Unpacking libparse-debianchangelog-perl (1.2.0-4) ...
+Selecting previously unselected package libtext-levenshtein-perl.
+Preparing to unpack .../libtext-levenshtein-perl_0.12-1_all.deb ...
+Unpacking libtext-levenshtein-perl (0.12-1) ...
+Selecting previously unselected package patchutils.
+Preparing to unpack .../patchutils_0.3.4-1_amd64.deb ...
+Unpacking patchutils (0.3.4-1) ...
+Selecting previously unselected package t1utils.
+Preparing to unpack .../t1utils_1.38-4_amd64.deb ...
+Unpacking t1utils (1.38-4) ...
+Selecting previously unselected package lintian.
+Preparing to unpack .../lintian_2.5.32_all.deb ...
+Unpacking lintian (2.5.32) ...
+Selecting previously unselected package sbuild-build-depends-lintian-dummy.
+Preparing to unpack .../sbuild-build-depends-lintian-dummy.deb ...
+Unpacking sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Processing triggers for man-db (2.7.0.2-5) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libssl1.0.0:amd64 (1.0.2c-1) ...
+Setting up netbase (5.3) ...
+Setting up diffstat (1.58-1) ...
+Setting up hardening-includes (2.7) ...
+Setting up libapt-pkg-perl (0.1.29+b2) ...
+Setting up libarchive-zip-perl (1.48-1) ...
+Setting up libsub-name-perl (0.12-1) ...
+Setting up libclass-accessor-perl (0.34-1) ...
+Setting up libclone-perl (0.38-1) ...
+Setting up libdigest-hmac-perl (1.03+dfsg-1) ...
+Setting up libnet-ssleay-perl (1.70-1) ...
+Setting up libio-socket-ssl-perl (2.016-1) ...
+Setting up libnet-smtp-ssl-perl (1.01-3) ...
+Setting up libmailtools-perl (2.13-1) ...
+Setting up libsocket6-perl (0.25-1+b1) ...
+Setting up libio-socket-inet6-perl (2.72-2) ...
+Setting up libnet-ip-perl (1.26-1) ...
+Setting up libnet-dns-perl (0.81-2) ...
+Setting up libnet-domain-tld-perl (1.73-1) ...
+Setting up libemail-valid-perl (1.196-1) ...
+Setting up libexporter-tiny-perl (0.042-1) ...
+Setting up libipc-system-simple-perl (1.25-2) ...
+Setting up libfile-basedir-perl (0.07-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libio-string-perl (1.08-3) ...
+Setting up libipc-run-perl (0.94-1) ...
+Setting up liblist-moreutils-perl (0.413-1) ...
+Setting up libparse-debianchangelog-perl (1.2.0-4) ...
+Setting up libtext-levenshtein-perl (0.12-1) ...
+Setting up patchutils (0.3.4-1) ...
+Setting up t1utils (1.38-4) ...
+Setting up lintian (2.5.32) ...
+Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-18) ...
+P: bwa source: debian-watch-may-check-gpg-signature
+I: bwa: spelling-error-in-binary usr/bin/bwa overriden overridden
+
+I: Lintian run was successful.
+
+┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.6.1-1_amd64.changes:
-──────────────────────────
+bwa_0.7.12-2_amd64.changes:
+───────────────────────────
Format: 1.8
-Date: Wed, 30 Nov 2011 19:36:04 +0900
+Date: Sat, 04 Jul 2015 13:00:50 +0900
Source: bwa
Binary: bwa
Architecture: source amd64
-Version: 0.6.1-1
+Version: 0.7.12-2
Distribution: unstable
-Urgency: low
+Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
-Description:
+Description:
bwa - Burrows-Wheeler Aligner
-Closes: 648803
-Changes:
- bwa (0.6.1-1) unstable; urgency=low
+Changes:
+ bwa (0.7.12-2) unstable; urgency=medium
.
- [b794564] New upstream release.
- [fc9894b] Pass -D_NO_SSE2 everywhere except on amd64 (Closes: #648803).
- [52312b6] Corrected changelog: 0.6.0-1 was actually uploaded to unstable.
-Checksums-Sha1:
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- 89b0bebb5d8b1839bb2b146e9bdd520733a98d38 129994 bwa_0.6.1.orig.tar.bz2
- e7e57d76613dbd6611ea14e4702463d48f6f5e7c 4469 bwa_0.6.1-1.debian.tar.gz
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-Checksums-Sha256:
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- 9accd7de0f9ca52c357b53cfe2f7ceb265163f726b01ccce995f34e0227ad562 152934 bwa_0.6.1-1_amd64.deb
-Files:
- 1b579d0644bd4410f281d87f4bed7dbf 1041 science optional bwa_0.6.1-1.dsc
- d9bfc7ffaa3268ca12faa8a664a4f575 129994 science optional bwa_0.6.1.orig.tar.bz2
- fcfb7764a26ef404020a1b60c57f167f 4469 science optional bwa_0.6.1-1.debian.tar.gz
- ccfc8470a8d468b1870830d8898d9c8d 152934 science optional bwa_0.6.1-1_amd64.deb
+ * Upload to Unstable.
+ * Install bash completion script in /usr/share/bash-completion/completions.
+ * Also distribute README-alt.md.
+ * Watch GitHub instead of SourceForge.
+Checksums-Sha1:
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+ e6854029fa5dcd4630bd0c3d1322ddf42c748d13 6012 bwa_0.7.12-2.debian.tar.xz
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+Checksums-Sha256:
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+ ce60e2caa5cf30ee10e2268b342cba1e122d25236a50971f30365de97039dc87 183802 bwa_0.7.12-2_amd64.deb
+Files:
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+ 845fb3412e665d245ad518ce52ccfb14 6012 science optional bwa_0.7.12-2.debian.tar.xz
+ d4d4b693d0902ce16c101d43b1a81b85 183802 science optional bwa_0.7.12-2_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-bwa_0.6.1-1_amd64.deb
-─────────────────────
+bwa_0.7.12-2_amd64.deb
+──────────────────────
new debian package, version 2.0.
- size 152934 bytes: control archive= 990 bytes.
- 774 bytes, 17 lines control
- 610 bytes, 10 lines md5sums
+ size 183802 bytes: control archive=1125 bytes.
+ 967 bytes, 21 lines control
+ 705 bytes, 11 lines md5sums
Package: bwa
- Version: 0.6.1-1
+ Version: 0.7.12-2
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 296
- Depends: libc6 (>= 2.7), zlib1g (>= 1:1.1.4)
+ Installed-Size: 393
+ Depends: libc6 (>= 2.15), 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 2011-11-30 19:42 ./
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/bin/
--rwxr-xr-x root/root 219752 2011-11-30 19:42 ./usr/bin/bwa
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/share/man/man1/
--rw-r--r-- root/root 7755 2011-11-30 19:42 ./usr/share/man/man1/bwa.1.gz
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/share/bwa/
--rwxr-xr-x root/root 616 2011-11-28 23:55 ./usr/share/bwa/qualfa2fq.pl
--rwxr-xr-x root/root 3176 2011-11-28 23:55 ./usr/share/bwa/solid2fastq.pl
--rwxr-xr-x root/root 730 2011-11-28 23:55 ./usr/share/bwa/xa2multi.pl
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/share/doc/bwa/
--rw-r--r-- root/root 17912 2011-11-28 23:55 ./usr/share/doc/bwa/changelog.gz
--rw-r--r-- root/root 6942 2011-11-28 23:55 ./usr/share/doc/bwa/NEWS.gz
--rw-r--r-- root/root 2785 2011-11-30 19:29 ./usr/share/doc/bwa/copyright
--rw-r--r-- root/root 814 2011-11-28 23:55 ./usr/share/doc/bwa/README
--rw-r--r-- root/root 1389 2011-11-30 19:36 ./usr/share/doc/bwa/changelog.Debian.gz
+ BWA is a software package for mapping low-divergent sequences against
+ a large reference genome, such as the human genome. It consists of
+ three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first
+ algorithm is designed for Illumina sequence reads up to 100bp, while
+ the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM
+ and BWA-SW share similar features such as long-read support and split
+ alignment, but BWA-MEM, which is the latest, is generally recommended
+ for high-quality queries as it is faster and more accurate. BWA-MEM
+ also has better performance than BWA-backtrack for 70-100bp Illumina
+ reads.
+
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/bin/
+-rwxr-xr-x root/root 343480 2015-07-04 13:04 ./usr/bin/bwa
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/bash-completion/
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/bash-completion/completions/
+-rw-r--r-- root/root 384 2015-07-04 12:26 ./usr/share/bash-completion/completions/bwa
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/bwa/
+-rwxr-xr-x root/root 616 2014-02-26 06:20 ./usr/share/bwa/qualfa2fq.pl
+-rwxr-xr-x root/root 730 2014-02-26 06:20 ./usr/share/bwa/xa2multi.pl
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/doc/bwa/
+-rw-r--r-- root/root 225 2015-07-04 12:26 ./usr/share/doc/bwa/NEWS.Debian.gz
+-rw-r--r-- root/root 4216 2014-12-24 05:35 ./usr/share/doc/bwa/README-alt.md.gz
+-rw-r--r-- root/root 3526 2014-12-24 05:35 ./usr/share/doc/bwa/README.md.gz
+-rw-r--r-- root/root 2267 2015-07-04 13:00 ./usr/share/doc/bwa/changelog.Debian.gz
+-rw-r--r-- root/root 13409 2014-12-29 05:45 ./usr/share/doc/bwa/changelog.gz
+-rw-r--r-- root/root 4384 2015-07-04 12:26 ./usr/share/doc/bwa/copyright
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-07-04 13:04 ./usr/share/man/man1/
+-rw-r--r-- root/root 10160 2015-07-04 13:04 ./usr/share/man/man1/bwa.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -472,97 +705,32 @@ drwxr-xr-x root/root 0 2011-11-30 19:42 ./usr/share/doc/bwa/
└──────────────────────────────────────────────────────────────────────────────┘
-lintian
-───────
-
-Subroutine IO::Socket::INET6::sockaddr_in6 redefined at /usr/share/perl/5.14/Exporter.pm line 67.
- at /usr/share/perl5/IO/Socket/INET6.pm line 21
-W: bwa source: package-needs-versioned-debhelper-build-depends 9
-P: bwa source: unversioned-copyright-format-uri http://dep.debian.net/deps/dep5/
-W: bwa source: debian-watch-file-should-use-sf-redirector line 4
-W: bwa: manpage-has-errors-from-man usr/share/man/man1/bwa.1.gz around line 328: table wider than line width
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:7
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:49
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:81
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:82
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:83
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:107
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:108
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:119
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:177
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz:178
-I: bwa: hyphen-used-as-minus-sign usr/share/man/man1/bwa.1.gz 9 more occurrences not shown
-
-I: Lintian run was successful.
-
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- debhelper* file* gettext* gettext-base* groff-base* html2text*
- intltool-debian* libcroco3* libffi5* libglib2.0-0* libmagic1* libpcre3*
- libpipeline1* libunistring0* libxml2* man-db* po-debconf*
- sbuild-build-depends-bwa-dummy* zlib1g-dev*
-0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
-After this operation, 25.7 MB disk space will be freed.
-(Reading database ... 12058 files and directories currently installed.)
-Removing sbuild-build-depends-bwa-dummy ...
-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 ...
-Purging configuration files for libcroco3 ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libffi5 ...
-Purging configuration files for libffi5 ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Architecture: amd64
-Build-Space: 3524
-Build-Time: 14
+Build Architecture: amd64
+Build-Space: 6140
+Build-Time: 26
Distribution: unstable
-Install-Time: 107
-Job: bwa_0.6.1-1.dsc
+Host Architecture: amd64
+Install-Time: 24
+Job: bwa_0.7.12-2.dsc
Lintian: pass
+Machine Architecture: amd64
Package: bwa
-Package-Time: 125
-Source-Version: 0.6.1-1
-Space: 3524
+Package-Time: 64
+Source-Version: 0.7.12-2
+Space: 6140
Status: successful
-Version: 0.6.1-1
+Version: 0.7.12-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111130-1942
-Build needed 00:02:05, 3524k disc space
+Finished at 20150704-1304
+Build needed 00:01:04, 6140k disc space
diff --git a/changes b/changes
index fb97c51..fb1f1ea 100644
--- a/changes
+++ b/changes
@@ -1,55 +1,52 @@
-----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
Format: 1.8
-Date: Wed, 30 Nov 2011 19:36:04 +0900
+Date: Sat, 04 Jul 2015 13:00:50 +0900
Source: bwa
Binary: bwa
Architecture: source amd64
-Version: 0.6.1-1
+Version: 0.7.12-2
Distribution: unstable
-Urgency: low
+Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
-Description:
+Description:
bwa - Burrows-Wheeler Aligner
-Closes: 648803
-Changes:
- bwa (0.6.1-1) unstable; urgency=low
+Changes:
+ bwa (0.7.12-2) unstable; urgency=medium
.
- [b794564] New upstream release.
- [fc9894b] Pass -D_NO_SSE2 everywhere except on amd64 (Closes: #648803).
- [52312b6] Corrected changelog: 0.6.0-1 was actually uploaded to unstable.
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- ccfc8470a8d468b1870830d8898d9c8d 152934 science optional bwa_0.6.1-1_amd64.deb
+ * Upload to Unstable.
+ * Install bash completion script in /usr/share/bash-completion/completions.
+ * Also distribute README-alt.md.
+ * Watch GitHub instead of SourceForge.
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-Hash: SHA256
+Hash: SHA512
Format: 3.0 (quilt)
Source: bwa
Binary: bwa
-Architecture: any
-Version: 0.6.1-1
+Architecture: amd64 kfreebsd-amd64
+Version: 0.7.12-2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>, Andreas Tille <tille at debian.org>
-Dm-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>, Andreas Tille <tille at debian.org>, Carlos Borroto <carlos.borroto at gmail.com>, Ognyan Kulev <ogi at debian.org>
Homepage: http://bio-bwa.sourceforge.net/
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+Vcs-Git: git://anonscm.debian.org/debian-med/bwa.git
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+Package-List:
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-----END PGP SIGNATURE-----
diff --git a/upload b/upload
new file mode 100644
index 0000000..c5d5859
--- /dev/null
+++ b/upload
@@ -0,0 +1,5 @@
+u bwa_0.7.12-2.debian.tar.xz ftp.upload.debian.org Sat Jul 4 13:38:12 2015
+u bwa_0.7.12-2_amd64.deb ftp.upload.debian.org Sat Jul 4 13:38:14 2015
+u bwa_0.7.12-2.dsc ftp.upload.debian.org Sat Jul 4 13:38:15 2015
+u bwa_0.7.12-2_amd64.changes ftp.upload.debian.org Sat Jul 4 13:38:16 2015
+s bwa_0.7.12-2_amd64.changes ftp.upload.debian.org Sat Jul 4 13:38:16 2015
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bwa.git
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