[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.2-50-g2f9a947

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 6100a2bc07daff52813c24228e7b83580c572ebb
Merge: 4f34207a61c9f02bce9668ce6704b03ceebd738d 6795cc21e62f2dce3ac02beae06bdb8f73559232
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 27 17:14:34 2012 +0100

    Merge tag 'upstream/2.0.4'
    
    Upstream version 2.0.4

diff --combined debian/changelog
index e5cc9dd,0000000..7baa66f
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,77 -1,0 +1,83 @@@
++bowtie2 (2.0.4-1) UNRELEASED; urgency=low
++
++  * Imported Upstream version 2.0.4
++
++ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 27 Dec 2012 17:33:36 +0100
++
 +bowtie2 (2.0.2-1) unstable; urgency=low
 +
 +  [ Carlos Borroto ]
 +  * Imported Upstream version 2.0.2
 +  * bowtie2_gcc4.7.patch no longer needed
 +
 +  [ Alexandre Mestiashvili ]
 +  * added autopkgtest testsuite
 +  * updated Uploaders field
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Mon, 19 Nov 2012 16:31:02 +0100
 +
 +bowtie2 (2.0.0-beta7-1) unstable; urgency=low
 +
 +  [ Alexandre Mestiashvili ]
 +  * debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and 
 +    hurd-i386 SSE is not availbale on others. Closes: #668123 
 +  * debhelper version 9
 +  * debian/rules forced hardening flags
 +  * hardening.patch to inject hardening CPPFLAGS
 +  * Imported Upstream version 2.0.0-beta7
 +  * debian/bowtie2.lintian-overrides to avoid lintian's waring
 +    to be fixed by using epochs and tilda in upstream version 
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Mon, 30 Jul 2012 13:51:31 +0200
 +
 +bowtie2 (2.0.0-beta6-3) unstable; urgency=low
 +
 +  * normalized architecture detection.
 +    For example kfreebsd-amd64 is detected as an amd64 architecture 
 +    and msse flag is set.(Previous commit was wrong) (Closes: #673159)
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Fri, 01 Jun 2012 21:58:49 +0200
 +
 +bowtie2 (2.0.0-beta6-2) unstable; urgency=low
 +
 +  * debian/rules normalized output of dpkg-architecture,  
 +    so for example kfreebsd-amd64 is detected as an amd64 architecture 
 +    and sse flags are enabled for it.
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 31 May 2012 19:22:56 +0200
 +
 +bowtie2 (2.0.0-beta6-1) unstable; urgency=low
 +
 +  * updated debian/watch and get-orig-source to track -source suffix
 +  * Imported Upstream version 2.0.0-beta6
 +  * debian/patches/fix_makefile_machine_detection.patch
 +    use -msse2 only for Intel architectures, Closes: #672526
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Fri, 11 May 2012 08:41:59 +0200
 +
 +bowtie2 (2.0.0-beta5-2) unstable; urgency=low
 +
 +  [ Alexandre Mestiashvili ]
 +  * file sse_util.h has missing copyright header. 
 +    The Author (Benjamin Langmead) has
 +    confirmed that the file is distributed under GPL3 license.
 +
 +  [ Andreas Tille ]
 +  * debian/upstream: Added publication
 +  * debian/patches/fix_makefile_machine_detection.patch + debian/rules:
 +    prevent -mXX and -msse2 switches for non Intel architectures
 +
 +  [ Alexandre Mestiashvili ]
 +  * debian/patches/bowtie2_gcc4.7.patch Closes: #672090
 +  * updated DEP3 headers
 +  * bumperd Standards-Version to 3.9.3
 +  * uname -m doesn't detect 32 bit chroot env - updated patcH
 +
 + -- Andreas Tille <tille at debian.org>  Thu, 26 Apr 2012 13:59:54 +0200
 +
 +bowtie2 (2.0.0-beta5-1) unstable; urgency=low
 +
 +  [ Alexandre Mestiashvili ]
 +  * Initial release (Closes: #660762)
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Wed, 22 Feb 2012 11:03:03 +0100

-- 
ultrafast memory-efficient short read aligner