[med-svn] r3483 - in trunk/packages/wise/trunk/debian: . patches

Charles Plessy plessy at alioth.debian.org
Mon Jun 15 12:48:43 UTC 2009 

Author: plessy
Date: 2009-06-15 12:48:42 +0000 (Mon, 15 Jun 2009)
New Revision: 3483

Modified:
   trunk/packages/wise/trunk/debian/changelog
   trunk/packages/wise/trunk/debian/compat
   trunk/packages/wise/trunk/debian/control
   trunk/packages/wise/trunk/debian/copyright
   trunk/packages/wise/trunk/debian/patches/glib2.patch
   trunk/packages/wise/trunk/debian/rules
Log:
Uploaded with Barry's patch installed by Steffen. Other polishing changes follow:

  * debian/control:
    - Added myself to the Uploaders.
    - Added ${misc:Depends} to the package dependencies.
    - Using Debhelper 7 (also debian/compat).
    - Eliminated redundancy between the long descriptions of wise and wise-doc.
  * Replaced ?\226?\128?\152dh_clean -k?\226?\128?\153 by ?\226?\128?\152dh_prep?\226?\128?\153 in debian/rules.


Modified: trunk/packages/wise/trunk/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog	2009-06-13 02:41:29 UTC (rev 3482)
+++ trunk/packages/wise/trunk/debian/changelog	2009-06-15 12:48:42 UTC (rev 3483)
@@ -1,11 +1,20 @@
-wise (2.4.1-7) UNRELEASED; urgency=low
+wise (2.4.1-7) unstable; urgency=low
 
-  * Now builds with glib-2.0   (Closes: #523715). [ Special thank to Barry deFreese ]
-  * Updated policy to 3.8.1 (no changes required).  (Steffen)
-  * fixed api->API lintian warnin. (Steffen)
+  [ Steffen Moeller ]
+  * Now builds with glib-2. (Closes: #523715). Special thank to Barry deFreese.
+  * Updated policy to 3.8.1 (no changes required).
+  * fixed api->API lintian warning.
 
- -- Steffen Moeller <moeller at debian.org>  Thu, 16 Apr 2009 14:16:50 +0200
+  [ Charles Plessy ]
+  * debian/control:
+    - Added myself to the Uploaders.
+    - Added ${misc:Depends} to the package dependencies.
+    - Using Debhelper 7 (also debian/compat).
+    - Eliminated redundancy between the long descriptions of wise and wise-doc.
+  * Replaced ‘dh_clean -k’ by ‘dh_prep’ in debian/rules.
 
+ -- Charles Plessy <plessy at debian.org>  Mon, 15 Jun 2009 20:49:27 +0900
+
 wise (2.4.1-6) unstable; urgency=low
 
   * Updated policy to 3.8.0 (no changes required).

Modified: trunk/packages/wise/trunk/debian/compat
===================================================================
--- trunk/packages/wise/trunk/debian/compat	2009-06-13 02:41:29 UTC (rev 3482)
+++ trunk/packages/wise/trunk/debian/compat	2009-06-15 12:48:42 UTC (rev 3483)
@@ -1 +1 @@
-5
+7

Modified: trunk/packages/wise/trunk/debian/control
===================================================================
--- trunk/packages/wise/trunk/debian/control	2009-06-13 02:41:29 UTC (rev 3482)
+++ trunk/packages/wise/trunk/debian/control	2009-06-15 12:48:42 UTC (rev 3483)
@@ -2,9 +2,9 @@
 Section: science
 Priority: optional
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Philipp Benner <pbenner at uni-osnabrueck.de>, Steffen Moeller <moeller at debian.org>
+Uploaders: Philipp Benner <pbenner at uni-osnabrueck.de>, Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
 DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 5), quilt, texlive-latex-base,
+Build-Depends: debhelper (>= 7), quilt, texlive-latex-base,
  texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
 Standards-Version: 3.8.1
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/?rev=0&sc=0
@@ -13,7 +13,7 @@
 
 Package: wise
 Architecture: any
-Depends: ${shlibs:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}
 Suggests: wise-doc (= ${source:Version})
 Description: comparison of biopolymers, commonly DNA and protein sequences
  Wise2 is a package focused on comparisons of biopolymers, commonly DNA
@@ -42,27 +42,8 @@
 Package: wise-doc
 Architecture: all
 Section: doc
+Depends: ${misc:Depends}
 Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer
 Description: documentation for the wise package
- Wise2 is a package focused on comparisons of biopolymers, commonly DNA
- and protein sequences. There are many other packages which do
- this, probably the best known being BLAST package (from NCBI) and the 
- Fasta package (from Bill Pearson). There are other packages, such as
- the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
- on hidden Markov models (HMMs) of biopolymers.
- .
- Wise2's particular forte is the comparison of DNA sequence at the level
- of its protein translation. This comparison allows the simultaneous
- prediction of say gene structure with homology based alignment.
- .
- Wise2 also contains other algorithms, such as the venerable Smith-Waterman
- algorithm, or more modern ones such as Stephen Altschul's generalised
- gap penalties, or even experimental ones developed in house, such as
- dba. The development of these algorithms is due to the ease of developing
- such algorithms in the enviroment used by Wise2. 
- .
- Wise2 has also been written with an eye for reuse and maintainability. 
- Although it is a pure C package you can access its functionality 
- directly in Perl. Parts of the package (or the entire package) can
- be used by other C or C++ programs without namespace clashes as all
- externally linked variables have the unique identifier Wise2 prepended.
+ This package contains the documentation for Wise2, a package focused on
+ comparisons of biopolymers, commonly DNA and protein sequences.

Modified: trunk/packages/wise/trunk/debian/copyright
===================================================================
--- trunk/packages/wise/trunk/debian/copyright	2009-06-13 02:41:29 UTC (rev 3482)
+++ trunk/packages/wise/trunk/debian/copyright	2009-06-15 12:48:42 UTC (rev 3483)
@@ -1,9 +1,9 @@
-This package was downloaded from http://www.ebi.ac.uk/~birney/wise2/
+Name: Wise2
+Source: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz
 
-Files: *
 Copyright: © 1996-2001 Genome Research Limited (GRL) and
  Ewan Birney <birney at sanger.ac.uk> and Sean Eddy
-License: Other
+License:
  All of the documentation and software included in the dyc directory of the
  Wise2 package directory is copyrighted by Genome Research Limited
  (GRL) and other individuals where appropriate. This license is modelled
@@ -51,18 +51,20 @@
  GNULICENSE for details.
 
 Files:
- src/dynlibsrc/histogram.dy, src/dynlibsrc/histogram.pod,
+ src/dynlibsrc/histogram.dy src/dynlibsrc/histogram.pod
  src/dynlibsrc/histogram.tex
 Copyright: © 1996-1999 Genome Research Limited (GRL) and Sean Eddy
 License: LGPL-any
 
 Files: debian/*
 Copyright: © 2006-2007 Philipp Benner <pbenner at uni-osnabrueck.de>
+           © 2009 Steffen Moeller <moeller at debian.org>
+           © 2009 Charles Plessy <plessy at debian.org>
+           © 2009 Barry deFreese <bdefreese at debian.org>
 License: GPL-2+
- The Debian packaging information is under the GPL, version 2 or later.
- This package was debianized by Philipp Benner on Sun, 23 Jul 2006.
+This package was debianized by Philipp Benner on Sun, 23 Jul 2006.
 
-On Debian GNU/Linux systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL' and the
+On Debian GNU/Linux systems, the complete text of the GNU General Public
+License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the
 complete text of the GNU Lesser General Public License can be found in
 `/usr/share/common-licenses/LGPL'.

Modified: trunk/packages/wise/trunk/debian/patches/glib2.patch
===================================================================
--- trunk/packages/wise/trunk/debian/patches/glib2.patch	2009-06-13 02:41:29 UTC (rev 3482)
+++ trunk/packages/wise/trunk/debian/patches/glib2.patch	2009-06-15 12:48:42 UTC (rev 3483)
@@ -1,3 +1,6 @@
+Author: Barry deFreese <bdefreese at debian.org>
+Description: To build wise2 with the Glib version 2.0 instead of 1.2.
+Forwarded: birney at sanger.ac.uk
 diff -u wise-2.4.1/debian/control wise-2.4.1/debian/control
 --- wise-2.4.1.orig/src/makefile
 +++ wise-2.4.1/src/makefile

Modified: trunk/packages/wise/trunk/debian/rules
===================================================================
--- trunk/packages/wise/trunk/debian/rules	2009-06-13 02:41:29 UTC (rev 3482)
+++ trunk/packages/wise/trunk/debian/rules	2009-06-15 12:48:42 UTC (rev 3483)
@@ -105,7 +105,7 @@
 install: build
 	dh_testdir
 	dh_testroot
-	dh_clean -k 
+	dh_prep 
 	dh_installdirs
 
 #	$(MAKE) install DESTDIR=$(CURDIR)/debian/wise

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