[med-svn] r4582 - in trunk/packages/velvet/trunk/debian: . patches

Charles Plessy plessy at alioth.debian.org
Mon Jan 25 04:58:09 UTC 2010 

Author: plessy
Date: 2010-01-25 04:58:06 +0000 (Mon, 25 Jan 2010)
New Revision: 4582

Added:
   trunk/packages/velvet/trunk/debian/README.source
   trunk/packages/velvet/trunk/debian/patches/
   trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch
   trunk/packages/velvet/trunk/debian/upstream-metadata.yaml
Removed:
   trunk/packages/velvet/trunk/debian/reference
Modified:
   trunk/packages/velvet/trunk/debian/changelog
   trunk/packages/velvet/trunk/debian/copyright
   trunk/packages/velvet/trunk/debian/rules
Log:
New upstream release. Zlib convenience copy removed from Debian source package.


Added: trunk/packages/velvet/trunk/debian/README.source
===================================================================
--- trunk/packages/velvet/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/README.source	2010-01-25 04:58:06 UTC (rev 4582)
@@ -0,0 +1,21 @@
+Repacked source package.
+────────────────────────
+
+The original sources were downloaded from
+http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.56.tgz and repacked after
+removing the third-party directory and renaming the main directory
+velvet-0.7.56~nozlibcopy, in order to not have to document all copyright
+notices in third-party/zlib-1.2.3.
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 25 Jan 2010 13:03:06 +0900
+
+
+This package uses a patch system.
+─────────────────────────────────
+
+A patch, placed in the ‘debian/patches’ directory is applied and unapplied at
+build time (but not at unpack time) using the ‘simple-patchsys’ system of CDBS.
+The ‘patch’ and ‘unpatch’ targets of debian/rules allow to apply and unapply
+the patch. Please refer to the documentation of CDBS for more information.
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 25 Jan 2010 13:03:06 +0900 

Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog	2010-01-24 16:31:56 UTC (rev 4581)
+++ trunk/packages/velvet/trunk/debian/changelog	2010-01-25 04:58:06 UTC (rev 4582)
@@ -1,3 +1,18 @@
+velvet (0.7.56~nozlibcopy-1) unstable; urgency=low
+
+  * New upstream version.
+  * Repackaged the upstream directory to remove the convenience copy
+    of the zlib. Documented this in ‘debian/README.source’.
+    Closes: #561433.
+  * Updated debian/copyright.
+  * Added ‘include_debians_zlib.patch’ to enforce the use of
+    /usr/include/zlib.h. This patch is applied using CDBS, see
+    ‘debian/rules’ and ‘debian/README.source’.
+  * Renamed ‘debian/reference’ ‘debian/upstream-metadata.yaml’ and
+    centralised upstream-specific information there.
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 25 Jan 2010 13:03:06 +0900
+
 velvet (0.7.55-1) unstable; urgency=low
 
   * New upstream version

Modified: trunk/packages/velvet/trunk/debian/copyright
===================================================================
--- trunk/packages/velvet/trunk/debian/copyright	2010-01-24 16:31:56 UTC (rev 4581)
+++ trunk/packages/velvet/trunk/debian/copyright	2010-01-25 04:58:06 UTC (rev 4582)
@@ -2,9 +2,9 @@
 
 Name    :  Velvet
 Contact :  Daniel Zerbino <zerbino at ebi.ac.uk>
-Source  :  http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.53.tgz
+Source  :  http://www.ebi.ac.uk/~zerbino/velvet/velvet_0.7.56.tgz
 
-Copyright: © 2006-2009 Daniel Zerbino <zerbino at ebi.ac.uk>
+Copyright: © 2006-2010 Daniel Zerbino <zerbino at ebi.ac.uk>
            © 2000-2005 Guy St.C. Slater <guy at ebi.ac.uk>
            ©   2009    John Marshall <jm18 at sanger.ac.uk>
            ©   2009    David Studholme <david.studholme at tsl.ac.uk>
@@ -77,38 +77,16 @@
  SUCH DAMAGE.
 
 Files: contrib/afg_handling/*, contrib/VelvetOptimiser/*
-Copyright: © 2008 Simon Gladman <simon.gladman at csiro.au>
+Copyright: © 2008,2009 Simon Gladman <simon.gladman at csiro.au>
 License: GPL-2+
 
-Files: third-party/z-lib-1.2.3
-Name: zlib
-Copyright: © 1995-1998 Jean-loup Gailly and Mark Adler
-License:
- This software is provided 'as-is', without any express or implied
- warranty.  In no event will the authors be held liable for any damages
- arising from the use of this software.
- 
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
- 
- 1. The origin of this software must not be misrepresented; you must not
-    claim that you wrote the original software. If you use this software
-    in a product, an acknowledgment in the product documentation would be
-    appreciated but is not required.
- 2. Altered source versions must be plainly marked as such, and must not be
-    misrepresented as being the original software.
- 3. This notice may not be removed or altered from any source distribution.
- 
- Jean-loup Gailly        Mark Adler
- jloup at gzip.org          madler at alumni.caltech.edu
-
 Files: contrib/layout/*
 Copyright: © 2008 Paul Harrison (pfh at logarithmic.net)
 License: GPL-2+
 
 Files: contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl,
-       contrib/observed-insert-length.pl/observed-insert-length.pl
+       contrib/observed-insert-length.pl/observed-insert-length.pl,
+       contrib/show_repeats/show_repeats.pl
 Copyright: 2009, Torsten Seemann
            2009, Daniel Zerbino
 License: GPL-3+

Added: trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch	2010-01-25 04:58:06 UTC (rev 4582)
@@ -0,0 +1,14 @@
+Description: Use the zlib distributed by Debian, not the one in third-party/zlib-1.2.3/.
+Author: Charles Plessy <plessy at debian.org>
+Forwarded: no
+--- src/readSet.c.orig	2010-01-25 13:27:24.000000000 +0900
++++ src/readSet.c	2010-01-25 13:28:00.000000000 +0900
+@@ -32,7 +32,7 @@
+ #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+ #include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
+ #else
+-#include "../third-party/zlib-1.2.3/zlib.h"
++#include <zlib.h>
+ #endif
+ 
+ #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)

Deleted: trunk/packages/velvet/trunk/debian/reference
===================================================================
--- trunk/packages/velvet/trunk/debian/reference	2010-01-24 16:31:56 UTC (rev 4581)
+++ trunk/packages/velvet/trunk/debian/reference	2010-01-25 04:58:06 UTC (rev 4582)
@@ -1,12 +0,0 @@
- at article{Daniel R.Zerbino052008,
-author = {Zerbino, Daniel R. and Birney, Ewan},
-title={{Velvet: Algorithms for de novo short read assembly using de Bruijn graphs}},
-journal = {Genome Research},
-volume = {18},
-number = {5},
-pages = {821-829},
-doi = {10.1101/gr.074492.107},
-year = {2008},
-URL = {http://genome.cshlp.org/content/18/5/821.abstract},
-eprint = {http://genome.cshlp.org/content/18/5/821.full.pdf+html}
-}

Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules	2010-01-24 16:31:56 UTC (rev 4581)
+++ trunk/packages/velvet/trunk/debian/rules	2010-01-25 04:58:06 UTC (rev 4582)
@@ -7,6 +7,7 @@
 
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/makefile.mk
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
 
 clean::
 	$(RM) zlib

Copied: trunk/packages/velvet/trunk/debian/upstream-metadata.yaml (from rev 4581, trunk/packages/velvet/trunk/debian/reference)
===================================================================
--- trunk/packages/velvet/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/upstream-metadata.yaml	2010-01-25 04:58:06 UTC (rev 4582)
@@ -0,0 +1,17 @@
+Contact: Daniel Zerbino <zerbino at ebi.ac.uk>
+DOI: 10.1101/gr.074492.107
+Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
+Name: Velvet
+PMID: 18349386
+Reference:
+  author: Zerbino, Daniel R. and Birney, Ewan
+  title: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
+  journal: Genome Research
+  volume: 18
+  number: 5
+  pages: 821-829
+  year: 2008
+  URL: http://genome.cshlp.org/content/18/5/821.abstract
+  eprint: http://genome.cshlp.org/content/18/5/821.full.pdf+html
+Repository: http://github.com/dzerbino/velvet
+Watch: http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz

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