[med-svn] r18733 - in trunk/packages/bowtie/tags: . 1.1.1-2/debian 1.1.1-2/debian/upstream
Charles Plessy
plessy at moszumanska.debian.org
Tue Feb 3 02:33:12 UTC 2015
Author: plessy
Date: 2015-02-03 02:33:11 +0000 (Tue, 03 Feb 2015)
New Revision: 18733
Added:
trunk/packages/bowtie/tags/1.1.1-2/
trunk/packages/bowtie/tags/1.1.1-2/debian/changelog
trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/metadata
Removed:
trunk/packages/bowtie/tags/1.1.1-2/debian/changelog
trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/edam
trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/metadata
Log:
[svn-buildpackage] Tagging bowtie 1.1.1-2
Deleted: trunk/packages/bowtie/tags/1.1.1-2/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog 2015-02-03 01:41:26 UTC (rev 18730)
+++ trunk/packages/bowtie/tags/1.1.1-2/debian/changelog 2015-02-03 02:33:11 UTC (rev 18733)
@@ -1,133 +0,0 @@
-bowtie (1.1.1-1) unstable; urgency=medium
-
- * New upstream release
- * cme fix dpkg-control
- * Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny)
- * Add Depends: python (also Build-Depends since it is used in tests)
-
- -- Andreas Tille <tille at debian.org> Thu, 02 Oct 2014 14:32:50 +0200
-
-bowtie (1.0.1-3) unstable; urgency=medium
-
- * Drop all architectures except amd64 since there was no success
- in trying to port the code to other architectures. The portability
- patch introduced in the last revision was droped again
- * debian/copyright: Drop unneeded copyright statements about code that
- was removed from upstream source
-
- -- Andreas Tille <tille at debian.org> Mon, 15 Sep 2014 11:00:25 +0200
-
-bowtie (1.0.1-2) unstable; urgency=medium
-
- * Do not use copy of outdated gcc header file which destroys portability
- to other architectures
- Closes: #756780
- * Add README.Debian informing users about the fact that we ignore copy
- of cpuid.h
- * Add unit tests for build time and autopkgtest
- * Add debian/README.test to explain how to test the package
- Attention: Please take notice of /usr/share/bowtie/README.Debian about
- "Test suite for bowtie created and potential issue with sorting"
-
- -- Andreas Tille <tille at debian.org> Wed, 03 Sep 2014 09:50:22 +0200
-
-bowtie (1.0.1-1) unstable; urgency=medium
-
- * New upstream version (adapted patches)
- * drop debian/get-orig-source but rather remove the SeqAn-1.1 code
- copy via Files-Excluded
- * debian/control: Priority: optional
-
- -- Andreas Tille <tille at debian.org> Wed, 30 Jul 2014 13:38:25 +0200
-
-bowtie (1.0.0-6) unstable; urgency=low
-
- * debian/patches/seqan-popcount.patch: New patch. (Closes: #733398)
- * Version 1.4 of seqan-dev is required now.
- * Standards-Version: 3.9.5 (no changes needed).
- * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy.
-
- -- Ognyan Kulev <ogi at debian.org> Sat, 08 Mar 2014 15:13:16 +0200
-
-bowtie (1.0.0-5) unstable; urgency=low
-
- * Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target
- instead of override_dh_fixperms in debian/rules.
-
- -- Ognyan Kulev <ogi at debian.org> Thu, 30 May 2013 09:41:25 +0300
-
-bowtie (1.0.0-4) unstable; urgency=low
-
- * Lintian fixes:
- - Removed DM-Upload-Allowed field.
- - Standards Version 3.9.4 (no changes needed).
- - Remove execute bits on some files in bowtie-examples.
- * Don't compress *.ebwt index files in bowtie-examples package.
- * Package description now starts with a capital letter.
-
- -- Ognyan Kulev <ogi at debian.org> Wed, 29 May 2013 22:53:13 +0300
-
-bowtie (1.0.0-3) unstable; urgency=low
-
- * New patch no_hash_style_both_for_mips.patch.
- This fixes build errors on mips and mipsel.
-
- -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 15:15:37 +0300
-
-bowtie (1.0.0-2) unstable; urgency=low
-
- * Requires version 1.3 of SeqAn.
- * Updated README.source about using Debian's SeqAn library.
- * Removed machine_bits_detection.patch and added disable_bits_flag.patch.
-
- -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 10:49:47 +0300
-
-bowtie (1.0.0-1) unstable; urgency=low
-
- * New upstream version. (Closes: #705616)
- * Refreshed patches: use_debian_seqan.patch, use-dpkg-buildflags.patch.
- * Removed patch gcc-4.7.patch (fixed upstream).
- * New patch machine_bits_detection.patch.
- * Added build dependancy on seqan-dev.
- * Activated use_debian_seqan.patch and added the following patches:
- - seqan-fix-setBegin-call.patch
- - seqan-rename-ChunkPool.patch
- - seqan-rename-fill-to-resize.patch
- * Added myself to Uploaders control field.
-
- -- Ognyan Kulev <ogi at debian.org> Tue, 23 Apr 2013 16:43:49 +0300
-
-bowtie (0.12.7-3) unstable; urgency=low
-
- * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
- hardening flags (thanks for the patch to Simon Ruderich
- <simon at ruderich.org>)
- Closes: #670230
-
- -- Andreas Tille <tille at debian.org> Tue, 24 Apr 2012 13:21:32 +0200
-
-bowtie (0.12.7-2) unstable; urgency=low
-
- * Do not give a pointer to non existing info pages in manpages
- * debian/control:
- - fixed Vcs fields
- - Standards-Version: 3.9.3 (no changes needed)
- * debian/upstream: Add citation information
- * debian/rules: calculate pkg name instead of setting it
- * debian/copyright: DEP5 verified using
- cme fix dpkg-copyright
- * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
- the function is used
- Thanks to Rodolfo García Peñas <kix at kix.es> and
- gregor herrmann <gregoa at debian.org>
- Closes: #667120
- * debhelper 9 (control+compat)
- Hardening flags were explicitly tested but not enforced in debian/rules
-
- -- Andreas Tille <tille at debian.org> Sun, 22 Apr 2012 21:09:05 +0200
-
-bowtie (0.12.7-1) unstable; urgency=low
-
- * Initial release (Closes: #604940)
-
- -- Andreas Tille <tille at debian.org> Wed, 02 Feb 2011 13:47:12 +0100
Copied: trunk/packages/bowtie/tags/1.1.1-2/debian/changelog (from rev 18732, trunk/packages/bowtie/trunk/debian/changelog)
===================================================================
--- trunk/packages/bowtie/tags/1.1.1-2/debian/changelog (rev 0)
+++ trunk/packages/bowtie/tags/1.1.1-2/debian/changelog 2015-02-03 02:33:11 UTC (rev 18733)
@@ -0,0 +1,140 @@
+bowtie (1.1.1-2) unstable; urgency=high
+
+ * Team upload.
+ * Install missing commands. Closes: #776881.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 03 Feb 2015 10:44:39 +0900
+
+bowtie (1.1.1-1) unstable; urgency=medium
+
+ * New upstream release
+ * cme fix dpkg-control
+ * Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny)
+ * Add Depends: python (also Build-Depends since it is used in tests)
+
+ -- Andreas Tille <tille at debian.org> Thu, 02 Oct 2014 14:32:50 +0200
+
+bowtie (1.0.1-3) unstable; urgency=medium
+
+ * Drop all architectures except amd64 since there was no success
+ in trying to port the code to other architectures. The portability
+ patch introduced in the last revision was droped again
+ * debian/copyright: Drop unneeded copyright statements about code that
+ was removed from upstream source
+
+ -- Andreas Tille <tille at debian.org> Mon, 15 Sep 2014 11:00:25 +0200
+
+bowtie (1.0.1-2) unstable; urgency=medium
+
+ * Do not use copy of outdated gcc header file which destroys portability
+ to other architectures
+ Closes: #756780
+ * Add README.Debian informing users about the fact that we ignore copy
+ of cpuid.h
+ * Add unit tests for build time and autopkgtest
+ * Add debian/README.test to explain how to test the package
+ Attention: Please take notice of /usr/share/bowtie/README.Debian about
+ "Test suite for bowtie created and potential issue with sorting"
+
+ -- Andreas Tille <tille at debian.org> Wed, 03 Sep 2014 09:50:22 +0200
+
+bowtie (1.0.1-1) unstable; urgency=medium
+
+ * New upstream version (adapted patches)
+ * drop debian/get-orig-source but rather remove the SeqAn-1.1 code
+ copy via Files-Excluded
+ * debian/control: Priority: optional
+
+ -- Andreas Tille <tille at debian.org> Wed, 30 Jul 2014 13:38:25 +0200
+
+bowtie (1.0.0-6) unstable; urgency=low
+
+ * debian/patches/seqan-popcount.patch: New patch. (Closes: #733398)
+ * Version 1.4 of seqan-dev is required now.
+ * Standards-Version: 3.9.5 (no changes needed).
+ * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy.
+
+ -- Ognyan Kulev <ogi at debian.org> Sat, 08 Mar 2014 15:13:16 +0200
+
+bowtie (1.0.0-5) unstable; urgency=low
+
+ * Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target
+ instead of override_dh_fixperms in debian/rules.
+
+ -- Ognyan Kulev <ogi at debian.org> Thu, 30 May 2013 09:41:25 +0300
+
+bowtie (1.0.0-4) unstable; urgency=low
+
+ * Lintian fixes:
+ - Removed DM-Upload-Allowed field.
+ - Standards Version 3.9.4 (no changes needed).
+ - Remove execute bits on some files in bowtie-examples.
+ * Don't compress *.ebwt index files in bowtie-examples package.
+ * Package description now starts with a capital letter.
+
+ -- Ognyan Kulev <ogi at debian.org> Wed, 29 May 2013 22:53:13 +0300
+
+bowtie (1.0.0-3) unstable; urgency=low
+
+ * New patch no_hash_style_both_for_mips.patch.
+ This fixes build errors on mips and mipsel.
+
+ -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 15:15:37 +0300
+
+bowtie (1.0.0-2) unstable; urgency=low
+
+ * Requires version 1.3 of SeqAn.
+ * Updated README.source about using Debian's SeqAn library.
+ * Removed machine_bits_detection.patch and added disable_bits_flag.patch.
+
+ -- Ognyan Kulev <ogi at debian.org> Wed, 24 Apr 2013 10:49:47 +0300
+
+bowtie (1.0.0-1) unstable; urgency=low
+
+ * New upstream version. (Closes: #705616)
+ * Refreshed patches: use_debian_seqan.patch, use-dpkg-buildflags.patch.
+ * Removed patch gcc-4.7.patch (fixed upstream).
+ * New patch machine_bits_detection.patch.
+ * Added build dependancy on seqan-dev.
+ * Activated use_debian_seqan.patch and added the following patches:
+ - seqan-fix-setBegin-call.patch
+ - seqan-rename-ChunkPool.patch
+ - seqan-rename-fill-to-resize.patch
+ * Added myself to Uploaders control field.
+
+ -- Ognyan Kulev <ogi at debian.org> Tue, 23 Apr 2013 16:43:49 +0300
+
+bowtie (0.12.7-3) unstable; urgency=low
+
+ * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
+ hardening flags (thanks for the patch to Simon Ruderich
+ <simon at ruderich.org>)
+ Closes: #670230
+
+ -- Andreas Tille <tille at debian.org> Tue, 24 Apr 2012 13:21:32 +0200
+
+bowtie (0.12.7-2) unstable; urgency=low
+
+ * Do not give a pointer to non existing info pages in manpages
+ * debian/control:
+ - fixed Vcs fields
+ - Standards-Version: 3.9.3 (no changes needed)
+ * debian/upstream: Add citation information
+ * debian/rules: calculate pkg name instead of setting it
+ * debian/copyright: DEP5 verified using
+ cme fix dpkg-copyright
+ * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
+ the function is used
+ Thanks to Rodolfo García Peñas <kix at kix.es> and
+ gregor herrmann <gregoa at debian.org>
+ Closes: #667120
+ * debhelper 9 (control+compat)
+ Hardening flags were explicitly tested but not enforced in debian/rules
+
+ -- Andreas Tille <tille at debian.org> Sun, 22 Apr 2012 21:09:05 +0200
+
+bowtie (0.12.7-1) unstable; urgency=low
+
+ * Initial release (Closes: #604940)
+
+ -- Andreas Tille <tille at debian.org> Wed, 02 Feb 2011 13:47:12 +0100
Deleted: trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/edam
===================================================================
--- trunk/packages/bowtie/trunk/debian/upstream/edam 2015-02-03 01:41:26 UTC (rev 18730)
+++ trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/edam 2015-02-03 02:33:11 UTC (rev 18733)
@@ -1,47 +0,0 @@
-topic: topic_0622 Genomics
-scope: summary
- function: operation_3212 Genome indexing (Burrows-Wheeler)
- function: operation_0292 Sequence alignment generation
- input: data_2975 Nucleic acid sequence (raw)
- input: format_1929 FASTA
- input: format_1930 FASTQ
- output: data_1383 Sequence alignment (nucleic acid)
- output: format_2573 SAM
-scope: bowtie-build
- function: operation_3212 Genome indexing (Burrows-Wheeler)
- input: data_2975 Nucleic acid sequence (raw)
- input: format_1929 FASTA
- output: data_3210 Genome index
- output: ??? Bowtie index format EBWT
- output: ??? Bowtie long index format EBTWL
-scope: bowtie-inspect
- function: operation_1813 Sequence retrieval
- function: operation_0304 Metadata retrieval
- function: operation_0228 Data index analysis
- input: data_3210 Genome index
- input: ??? Bowtie index format EBWT
- input: ??? Bowtie long index format EBTWL
- output: data_2975 Nucleic acid sequence (raw)
- output: format_1929 FASTA
- output: format_1964 plain text format (unformatted)
-scope: bowtie
- function: operation_0350 Sequence database search (by sequence using word-based methods)
- function: operation_0292 Sequence alignment generation
- input: data_3210 Genome index
- input: data_2975 Nucleic acid sequence (raw)
- input: format_1964 plain text format (unformatted)
- input: format_1929 FASTA
- input: format_1930 FASTQ
- output: data_1383 Sequence alignment (nucleic acid)
- output: data_0867 Sequence alignment report
- output: format_2573 SAM
- output: ??? Bowtie alignment report format
-
-topic: topic_0622 Genomics
-function: operation_3212 Genome indexing (Burrows-Wheeler)
-function: operation_0292 Sequence alignment generation
-input: data_2975 Nucleic acid sequence (raw)
-input: format_1929 FASTA
-input: format_1930 FASTQ
-output: data_1383 Sequence alignment (nucleic acid)
-output: format_2573 SAM
Deleted: trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/metadata
===================================================================
--- trunk/packages/bowtie/trunk/debian/upstream/metadata 2015-02-03 01:41:26 UTC (rev 18730)
+++ trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/metadata 2015-02-03 02:33:11 UTC (rev 18733)
@@ -1,10 +0,0 @@
-Reference:
- author: Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg
- title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- journal: Genome Biology
- volume: 10
- pages: R25
- year: 2009
- DOI: 10.1186/gb-2009-10-3-r25
- URL: http://genomebiology.com/2009/10/3/R25
- eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf
Copied: trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/metadata (from rev 18731, trunk/packages/bowtie/trunk/debian/upstream/metadata)
===================================================================
--- trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/metadata (rev 0)
+++ trunk/packages/bowtie/tags/1.1.1-2/debian/upstream/metadata 2015-02-03 02:33:11 UTC (rev 18733)
@@ -0,0 +1,10 @@
+Reference:
+ author: Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg
+ title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
+ journal: Genome Biology
+ volume: 10
+ pages: R25
+ year: 2009
+ DOI: 10.1186/gb-2009-10-3-r25
+ URL: http://genomebiology.com/2009/10/3/R25
+ eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf
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