[med-svn] r7786 - in trunk/packages/wise/tags: . 2.4.1-9/debian 2.4.1-9/debian/patches

Charles Plessy plessy at alioth.debian.org
Wed Sep 14 09:35:54 UTC 2011


Author: plessy
Date: 2011-09-14 09:35:54 +0000 (Wed, 14 Sep 2011)
New Revision: 7786

Added:
   trunk/packages/wise/tags/2.4.1-9/
   trunk/packages/wise/tags/2.4.1-9/debian/changelog
   trunk/packages/wise/tags/2.4.1-9/debian/compat
   trunk/packages/wise/tags/2.4.1-9/debian/control
   trunk/packages/wise/tags/2.4.1-9/debian/copyright
   trunk/packages/wise/tags/2.4.1-9/debian/patches/series
   trunk/packages/wise/tags/2.4.1-9/debian/rules
Removed:
   trunk/packages/wise/tags/2.4.1-9/debian/changelog
   trunk/packages/wise/tags/2.4.1-9/debian/compat
   trunk/packages/wise/tags/2.4.1-9/debian/control
   trunk/packages/wise/tags/2.4.1-9/debian/copyright
   trunk/packages/wise/tags/2.4.1-9/debian/patches/series
   trunk/packages/wise/tags/2.4.1-9/debian/rules
Log:
[svn-buildpackage] Tagging wise 2.4.1-9

Deleted: trunk/packages/wise/tags/2.4.1-9/debian/changelog
===================================================================
--- trunk/packages/wise/trunk/debian/changelog	2011-09-14 00:43:42 UTC (rev 7780)
+++ trunk/packages/wise/tags/2.4.1-9/debian/changelog	2011-09-14 09:35:54 UTC (rev 7786)
@@ -1,140 +0,0 @@
-wise (2.4.1-9) UNRELEASED; urgency=low
-
-  * Correct src/models/makefile to link --as-needed (Closes: #641333).
-
- -- Charles Plessy <plessy at debian.org>  Wed, 14 Sep 2011 09:38:06 +0900
-
-wise (2.4.1-8) unstable; urgency=low
-
-  * Fixed conflicting definitions of getline(). (Closes: #552821)
-  * Added README.source.
-  * Standards version 3.8.3.
-  * Fixed spelling error in package description.
-
- -- Philipp Benner <philipp at debian.org>  Sat, 31 Oct 2009 21:25:52 +0000
-
-wise (2.4.1-7) unstable; urgency=low
-
-  [ 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.
-
-  [ 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).
-  * wise now suggests wise-doc (downgraded from 'recommends').
-  [ Steffen Moeller ]
-  * Using quilt instead of dpatch.
-  [ Philipp Benner ]
-
- -- Philipp Benner <pbenner at uni-osnabrueck.de>  Sun, 25 Jan 2009 22:57:27 +0000
-
-wise (2.4.1-5) unstable; urgency=low
-
-  * Removed a bashism in debian/rules (Closes: #478639).
-
- -- Charles Plessy <plessy at debian.org>  Sun, 04 May 2008 15:19:01 +0900
-
-wise (2.4.1-4) unstable; urgency=low
-
-  * Changed the doc-base section according to the new policy
-    [Charles Plessy].
-    
- -- Philipp Benner <pbenner at uni-osnabrueck.de>  Mon, 31 Mar 2008 10:07:35 +0200
-
-wise (2.4.1-3) unstable; urgency=low
-
-  * New maintainer e-mail address.
-  * debian/control: Added DM-Upload-Allowed: yes.
-
- -- Philipp Benner <pbenner at uni-osnabrueck.de>  Mon, 14 Jan 2008 18:33:27 +0100
-
-wise (2.4.1-2) unstable; urgency=low
-
-  * Using official Vcs-Browser and Vcs-Svn fields (debian/control).
-  * Moved the Homepage: field out from the package's description
-  + (Charles Plessy).
-  * Converted copyright file to machine interpretable format.
-  * Changed maintainer to Debian-Med Packaging Team.
-
- -- Philipp Benner <mail at philipp-benner.de>  Sun, 02 Dec 2007 16:15:50 +0100
-
-wise (2.4.1-1) unstable; urgency=low
-
-  * New upstream release.
-
- -- Philipp Benner <mail at philipp-benner.de>  Sat, 15 Sep 2007 17:18:49 +0200
-
-wise (2.4.0-3) unstable; urgency=low
-
-  * Removed debtags from debian/control.
-  * Updated package description (Closes: #435904).
-  * Excluded genewise21.eps and genewise6.eps from documentation
-  + (workaround for a bug in gs-esp).
-
- -- Philipp Benner <mail at philipp-benner.de>  Sun, 05 Aug 2007 20:21:35 +0200
-
-wise (2.4.0-2) unstable; urgency=low
-
-  * Converted wise2.tex to a pdflatex compatible latex file
-  + (workaround for a bug in dvips)
-
- -- Philipp Benner <mail at philipp-benner.de>  Fri, 27 Jul 2007 18:46:33 +0200
-
-wise (2.4.0-1) unstable; urgency=low
-
-  * New upstream release (Closes: #431392)
-  * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
-  * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
-
- -- Philipp Benner <mail at philipp-benner.de>  Tue, 24 Jul 2007 11:58:36 +0200
-
-wise (2.2.0-5) unstable; urgency=low
-
-  * Removed obsolete dependencies (Closes: #422123)
-
- -- Philipp Benner <mail at philipp-benner.de>  Sun,  6 May 2007 22:42:27 +0200
-
-wise (2.2.0-4) unstable; urgency=low
-
-  * Adapted debian-med tags
-  * Uscan support
-  * Migrating to texlive
-  * use /bin/sh instead of /bin/csh in src/welcome.csh
-
- -- Philipp Benner <mail at philipp-benner.de>  Tue, 27 Mar 2007 19:29:08 +0200
-
-wise (2.2.0-3) unstable; urgency=low
-
-  * package tags
-  * fixed typos in package description
-
- -- Philipp Benner <mail at philipp-benner.de>  Thu, 21 Sep 2006 14:22:39 +0200
-
-wise (2.2.0-2) unstable; urgency=low
-
-  * removed \ref tags from package description
-  * moved examples to package wise-doc
-  * fixed typo in README.Debian
-  * minor changes in debian/control
-  * fixed typo in package description (Closes: #380451)
-  * new html documentation
-
- -- Philipp Benner <mail at philipp-benner.de>  Sun, 30 Jul 2006 14:08:20 +0200
-
-wise (2.2.0-1) unstable; urgency=low
-
-  * Initial release (Closes: #379604)
-
- -- Philipp Benner <mail at philipp-benner.de>  Sun, 23 Jul 2006 17:29:49 +0200

Copied: trunk/packages/wise/tags/2.4.1-9/debian/changelog (from rev 7785, trunk/packages/wise/trunk/debian/changelog)
===================================================================
--- trunk/packages/wise/tags/2.4.1-9/debian/changelog	                        (rev 0)
+++ trunk/packages/wise/tags/2.4.1-9/debian/changelog	2011-09-14 09:35:54 UTC (rev 7786)
@@ -0,0 +1,146 @@
+wise (2.4.1-9) unstable; urgency=low
+
+  * Correct src/models/makefile to link --as-needed (Closes: #641333).
+  * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
+  * Corrected VCS URLs (debian/control).
+  * Use Debhelper 8 (debian/compat, debian/control).
+  * Added build-arch and build-indep targets to debian/rules.
+  * Machine-readable debian/copryight file conforms to DEP 5.
+  * Compress binary package with xz (debian/rules).
+
+ -- Charles Plessy <plessy at debian.org>  Wed, 14 Sep 2011 17:52:32 +0900
+
+wise (2.4.1-8) unstable; urgency=low
+
+  * Fixed conflicting definitions of getline(). (Closes: #552821)
+  * Added README.source.
+  * Standards version 3.8.3.
+  * Fixed spelling error in package description.
+
+ -- Philipp Benner <philipp at debian.org>  Sat, 31 Oct 2009 21:25:52 +0000
+
+wise (2.4.1-7) unstable; urgency=low
+
+  [ 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.
+
+  [ 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).
+  * wise now suggests wise-doc (downgraded from 'recommends').
+  [ Steffen Moeller ]
+  * Using quilt instead of dpatch.
+  [ Philipp Benner ]
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de>  Sun, 25 Jan 2009 22:57:27 +0000
+
+wise (2.4.1-5) unstable; urgency=low
+
+  * Removed a bashism in debian/rules (Closes: #478639).
+
+ -- Charles Plessy <plessy at debian.org>  Sun, 04 May 2008 15:19:01 +0900
+
+wise (2.4.1-4) unstable; urgency=low
+
+  * Changed the doc-base section according to the new policy
+    [Charles Plessy].
+    
+ -- Philipp Benner <pbenner at uni-osnabrueck.de>  Mon, 31 Mar 2008 10:07:35 +0200
+
+wise (2.4.1-3) unstable; urgency=low
+
+  * New maintainer e-mail address.
+  * debian/control: Added DM-Upload-Allowed: yes.
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de>  Mon, 14 Jan 2008 18:33:27 +0100
+
+wise (2.4.1-2) unstable; urgency=low
+
+  * Using official Vcs-Browser and Vcs-Svn fields (debian/control).
+  * Moved the Homepage: field out from the package's description
+  + (Charles Plessy).
+  * Converted copyright file to machine interpretable format.
+  * Changed maintainer to Debian-Med Packaging Team.
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun, 02 Dec 2007 16:15:50 +0100
+
+wise (2.4.1-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sat, 15 Sep 2007 17:18:49 +0200
+
+wise (2.4.0-3) unstable; urgency=low
+
+  * Removed debtags from debian/control.
+  * Updated package description (Closes: #435904).
+  * Excluded genewise21.eps and genewise6.eps from documentation
+  + (workaround for a bug in gs-esp).
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun, 05 Aug 2007 20:21:35 +0200
+
+wise (2.4.0-2) unstable; urgency=low
+
+  * Converted wise2.tex to a pdflatex compatible latex file
+  + (workaround for a bug in dvips)
+
+ -- Philipp Benner <mail at philipp-benner.de>  Fri, 27 Jul 2007 18:46:33 +0200
+
+wise (2.4.0-1) unstable; urgency=low
+
+  * New upstream release (Closes: #431392)
+  * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
+  * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
+
+ -- Philipp Benner <mail at philipp-benner.de>  Tue, 24 Jul 2007 11:58:36 +0200
+
+wise (2.2.0-5) unstable; urgency=low
+
+  * Removed obsolete dependencies (Closes: #422123)
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun,  6 May 2007 22:42:27 +0200
+
+wise (2.2.0-4) unstable; urgency=low
+
+  * Adapted debian-med tags
+  * Uscan support
+  * Migrating to texlive
+  * use /bin/sh instead of /bin/csh in src/welcome.csh
+
+ -- Philipp Benner <mail at philipp-benner.de>  Tue, 27 Mar 2007 19:29:08 +0200
+
+wise (2.2.0-3) unstable; urgency=low
+
+  * package tags
+  * fixed typos in package description
+
+ -- Philipp Benner <mail at philipp-benner.de>  Thu, 21 Sep 2006 14:22:39 +0200
+
+wise (2.2.0-2) unstable; urgency=low
+
+  * removed \ref tags from package description
+  * moved examples to package wise-doc
+  * fixed typo in README.Debian
+  * minor changes in debian/control
+  * fixed typo in package description (Closes: #380451)
+  * new html documentation
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun, 30 Jul 2006 14:08:20 +0200
+
+wise (2.2.0-1) unstable; urgency=low
+
+  * Initial release (Closes: #379604)
+
+ -- Philipp Benner <mail at philipp-benner.de>  Sun, 23 Jul 2006 17:29:49 +0200

Deleted: trunk/packages/wise/tags/2.4.1-9/debian/compat
===================================================================
--- trunk/packages/wise/trunk/debian/compat	2011-09-14 00:43:42 UTC (rev 7780)
+++ trunk/packages/wise/tags/2.4.1-9/debian/compat	2011-09-14 09:35:54 UTC (rev 7786)
@@ -1 +0,0 @@
-7

Copied: trunk/packages/wise/tags/2.4.1-9/debian/compat (from rev 7785, trunk/packages/wise/trunk/debian/compat)
===================================================================
--- trunk/packages/wise/tags/2.4.1-9/debian/compat	                        (rev 0)
+++ trunk/packages/wise/tags/2.4.1-9/debian/compat	2011-09-14 09:35:54 UTC (rev 7786)
@@ -0,0 +1 @@
+8

Deleted: trunk/packages/wise/tags/2.4.1-9/debian/control
===================================================================
--- trunk/packages/wise/trunk/debian/control	2011-09-14 00:43:42 UTC (rev 7780)
+++ trunk/packages/wise/tags/2.4.1-9/debian/control	2011-09-14 09:35:54 UTC (rev 7786)
@@ -1,48 +0,0 @@
-Source: wise
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Philipp Benner <philipp at debian.org>, Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7), quilt, texlive-latex-base,
- texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
-Standards-Version: 3.8.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/wise/trunk/
-Homepage: http://www.ebi.ac.uk/~birney/wise2/
-
-Package: wise
-Architecture: any
-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
- 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 environment 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.
-
-Package: wise-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer
-Description: documentation for the wise package
- This package contains the documentation for Wise2, a package focused on
- comparisons of biopolymers, commonly DNA and protein sequences.

Copied: trunk/packages/wise/tags/2.4.1-9/debian/control (from rev 7785, trunk/packages/wise/trunk/debian/control)
===================================================================
--- trunk/packages/wise/tags/2.4.1-9/debian/control	                        (rev 0)
+++ trunk/packages/wise/tags/2.4.1-9/debian/control	2011-09-14 09:35:54 UTC (rev 7786)
@@ -0,0 +1,48 @@
+Source: wise
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Philipp Benner <philipp at debian.org>, Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 8), quilt, texlive-latex-base,
+ texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wise/trunk/
+Homepage: http://www.ebi.ac.uk/~birney/wise2/
+
+Package: wise
+Architecture: any
+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
+ 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 environment 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.
+
+Package: wise-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer
+Description: documentation for the wise package
+ This package contains the documentation for Wise2, a package focused on
+ comparisons of biopolymers, commonly DNA and protein sequences.

Deleted: trunk/packages/wise/tags/2.4.1-9/debian/copyright
===================================================================
--- trunk/packages/wise/trunk/debian/copyright	2011-09-14 00:43:42 UTC (rev 7780)
+++ trunk/packages/wise/tags/2.4.1-9/debian/copyright	2011-09-14 09:35:54 UTC (rev 7786)
@@ -1,70 +0,0 @@
-Name: Wise2
-Source: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz
-
-Copyright: © 1996-2001 Genome Research Limited (GRL) and
- Ewan Birney <birney at sanger.ac.uk> and Sean Eddy
-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
- after the 'BSD' style license and is appropriate for use by both
- academic and commercial sites, without placing any restriction on the
- distribution of source code from other sources with this software.
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are
- met:
- .
-  1.Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
- .
-  2.Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in
-    the documentation and/or other materials provided with the
-    distribution.
- .
-  3.Neither the name GRL nor the names of its contributors may be used
-    to endorse or promote products derived from this software without
-    specific prior written permission.
- .
- It is considered polite to indicate where appropriate that software which
- is developed using this source code includes a statement that it was developed
- using the Wise2 soure code. This is not a requirement however.
- .
- THIS SOFTWARE IS PROVIDED BY THE GRL AND CONTRIBUTORS ``AS IS'' AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
- PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE GRL OR CONTRIBUTORS BE
- LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
- BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
- OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
- IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Files: src/HMMer2/*
-Copyright: © 1992-1996 Sean R. Eddy
-License: GPL-2
- This source code is distributed under the terms of the
- GNU General Public License. See the files COPYING and
- GNULICENSE for details.
-
-Files:
- 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 <philipp at debian.org>
-           © 2009 Steffen Moeller <moeller at debian.org>
-           © 2009 Charles Plessy <plessy at debian.org>
-           © 2009 Barry deFreese <bdefreese at debian.org>
-License: GPL-2+
-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 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-3'.

Copied: trunk/packages/wise/tags/2.4.1-9/debian/copyright (from rev 7784, trunk/packages/wise/trunk/debian/copyright)
===================================================================
--- trunk/packages/wise/tags/2.4.1-9/debian/copyright	                        (rev 0)
+++ trunk/packages/wise/tags/2.4.1-9/debian/copyright	2011-09-14 09:35:54 UTC (rev 7786)
@@ -0,0 +1,86 @@
+Format: http://dep.debian.net/deps/dep5/
+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: GRL
+ 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
+ after the 'BSD' style license and is appropriate for use by both
+ academic and commercial sites, without placing any restriction on the
+ distribution of source code from other sources with this software.
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+  1.Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ .
+  2.Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+ .
+  3.Neither the name GRL nor the names of its contributors may be used
+    to endorse or promote products derived from this software without
+    specific prior written permission.
+ .
+ It is considered polite to indicate where appropriate that software which
+ is developed using this source code includes a statement that it was developed
+ using the Wise2 soure code. This is not a requirement however.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE GRL AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE GRL OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+ IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: src/HMMer2/*
+Copyright: © 1992-1996 Sean R. Eddy
+License: GPL-2
+ This source code is distributed under the terms of the
+ GNU General Public License. See the files COPYING and
+ GNULICENSE for details.
+
+Files:
+ 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
+ Converted by Ewan Birney to Dynamite source June 98.
+ Copyright is LGPL. For more info read READMEs
+Comment: On Debian GNU/Linux systems, the complete text of the GNU Lesser
+ General Public License version 3 can be found in `/usr/share/common-licenses/LGPL-3'.
+
+Files: debian/*
+Copyright: © 2006-2007 Philipp Benner <philipp at debian.org>
+           © 2009 Steffen Moeller <moeller at debian.org>
+           © 2009 Charles Plessy <plessy at debian.org>
+           © 2009 Barry deFreese <bdefreese at debian.org>
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+Comment: 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-3'.

Deleted: trunk/packages/wise/tags/2.4.1-9/debian/patches/series
===================================================================
--- trunk/packages/wise/trunk/debian/patches/series	2011-09-14 00:43:42 UTC (rev 7780)
+++ trunk/packages/wise/tags/2.4.1-9/debian/patches/series	2011-09-14 09:35:54 UTC (rev 7786)
@@ -1 +0,0 @@
-07_ld--as-needed.patch

Copied: trunk/packages/wise/tags/2.4.1-9/debian/patches/series (from rev 7781, trunk/packages/wise/trunk/debian/patches/series)
===================================================================
--- trunk/packages/wise/tags/2.4.1-9/debian/patches/series	                        (rev 0)
+++ trunk/packages/wise/tags/2.4.1-9/debian/patches/series	2011-09-14 09:35:54 UTC (rev 7786)
@@ -0,0 +1,7 @@
+01_welcome-csh.patch
+02_isnumber.patch
+03_doc-nodycache.patch
+04_wise2-pdflatex-update.patch
+05_glib2.patch
+06_getline.patch
+07_ld--as-needed.patch

Deleted: trunk/packages/wise/tags/2.4.1-9/debian/rules
===================================================================
--- trunk/packages/wise/trunk/debian/rules	2011-09-14 00:43:42 UTC (rev 7780)
+++ trunk/packages/wise/tags/2.4.1-9/debian/rules	2011-09-14 09:35:54 UTC (rev 7786)
@@ -1,149 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-CFLAGS = -Wall -g
-
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
-	CFLAGS += -O0
-else
-	CFLAGS += -O2
-endif
-
-include /usr/share/quilt/quilt.make
-
-configure: configure-stamp
-configure-stamp:
-	dh_testdir
-
-	touch configure-stamp
-
-build: patch build-stamp
-build-stamp: $(QUILT_STAMPFN) configure-stamp
-	dh_testdir
-
-	$(MAKE) -C src all
-	$(MAKE) -C debian/manpages.d
-
-#	build documentation manually (docs/makefile is not useable)
-	cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex
-	cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex
-#	<bugfix>
-	sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex
-	sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex
-	sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex
-#	</bugfix>
-	cd docs && pdflatex api.tex
-	cd docs && pdflatex api.tex
-	cd docs && pdflatex dynamite.tex
-	cd docs && pdflatex dynamite.tex
-#	cd docs && ps2pdf genewise6.eps  # segfaults on s390
-#	cd docs && ps2pdf genewise21.eps
-	cd docs && pdflatex wise2.tex
-	cd docs && pdflatex wise2.tex
-
-	cd docs && hevea api.tex
-	cd docs && hevea api.tex
-	cd docs && hevea dynamite.tex
-	cd docs && hevea dynamite.tex
-	cd docs && hevea wise2.tex
-	cd docs && hevea wise2.tex
-
-	mkdir -p docs/api
-	mkdir -p docs/dynamite
-	mkdir -p docs/wise2
-
-	mv docs/api.html docs/api
-	mv docs/dynamite.html docs/dynamite
-	mv docs/wise2.html docs/wise2
-
-	touch $@
-
-clean: unpatch
-	dh_testdir
-	dh_testroot
-	rm -f build-stamp configure-stamp
-
-	$(MAKE) -C src clean
-	$(MAKE) -C debian/manpages.d clean
-
-#	bugfix
-	$(RM) -r src/oldbin
-	for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do $(RM) src/modules/$$i; done
-	$(RM) src/network/scanwise_server
-
-#	clean documentation
-	$(RM) docs/temp.tex
-	$(RM) docs/api.*
-	$(RM) docs/wise2.image.tex
-	$(RM) docs/*.pdf
-	$(RM) docs/*.aux
-	$(RM) docs/*.log
-	$(RM) docs/*.toc
-	$(RM) docs/*.pdf
-	$(RM) docs/*.dvi
-	$(RM) docs/*.ps
-	$(RM) docs/*.4ct
-	$(RM) docs/*.4tc
-	$(RM) docs/*.css
-	$(RM) docs/*.idv
-	$(RM) docs/*.lg
-	$(RM) docs/*.tmp
-	$(RM) docs/*.xref
-	$(RM) docs/*.haux
-	$(RM) docs/*.htoc
-	$(RM) docs/*.html
-
-	$(RM) -r docs/api
-	$(RM) -r docs/dynamite
-	$(RM) -r docs/wise2
-
-	dh_clean
-
-install: build
-	dh_testdir
-	dh_testroot
-	dh_prep 
-	dh_installdirs
-
-#	$(MAKE) install DESTDIR=$(CURDIR)/debian/wise
-	install -m 755 src/bin/* debian/wise/usr/bin
-	install -m 755 src/models/genomewise debian/wise/usr/bin
-
-binary-indep: build install
-	dh_testdir -i
-	dh_testroot -i
-	dh_installchangelogs -i
-	dh_installdocs -i
-	dh_installexamples -i
-	dh_installman -i
-	dh_link -i
-	dh_strip -i
-	dh_compress -i
-	dh_fixperms -i
-	dh_installdeb -i
-	dh_gencontrol -i
-	dh_md5sums -i
-	dh_builddeb -i
-
-binary-arch: build install
-	dh_testdir -a
-	dh_testroot -a
-	dh_installchangelogs -a
-	dh_installdocs -a
-	dh_installexamples -a
-	dh_installman -a
-	dh_link -a
-	dh_strip -a
-	dh_compress -a
-	dh_fixperms -a
-	dh_installdeb -a
-	dh_shlibdeps -a
-	dh_gencontrol -a
-	dh_md5sums -a
-	dh_builddeb -a
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure

Copied: trunk/packages/wise/tags/2.4.1-9/debian/rules (from rev 7785, trunk/packages/wise/trunk/debian/rules)
===================================================================
--- trunk/packages/wise/tags/2.4.1-9/debian/rules	                        (rev 0)
+++ trunk/packages/wise/tags/2.4.1-9/debian/rules	2011-09-14 09:35:54 UTC (rev 7786)
@@ -0,0 +1,158 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+include /usr/share/quilt/quilt.make
+
+configure: configure-stamp
+configure-stamp:
+	dh_testdir
+
+	touch configure-stamp
+
+build: patch build-stamp
+build-stamp: $(QUILT_STAMPFN) configure-stamp build-arch-stamp build-indep-stamp
+	dh_testdir
+	touch $@
+
+build-arch: build-arch-stamp
+build-arch-stamp:
+	dh_testdir
+	$(MAKE) -C src all
+	$(MAKE) -C debian/manpages.d
+	touch $@
+
+build-indep: build-indep-stamp
+build-indep-stamp:
+	dh_testdir
+
+#	build documentation manually (docs/makefile is not useable)
+	cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex
+	cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex
+#	<bugfix>
+	sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex
+	sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex
+	sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex
+#	</bugfix>
+	cd docs && pdflatex api.tex
+	cd docs && pdflatex api.tex
+	cd docs && pdflatex dynamite.tex
+	cd docs && pdflatex dynamite.tex
+#	cd docs && ps2pdf genewise6.eps  # segfaults on s390
+#	cd docs && ps2pdf genewise21.eps
+	cd docs && pdflatex wise2.tex
+	cd docs && pdflatex wise2.tex
+
+	cd docs && hevea api.tex
+	cd docs && hevea api.tex
+	cd docs && hevea dynamite.tex
+	cd docs && hevea dynamite.tex
+	cd docs && hevea wise2.tex
+	cd docs && hevea wise2.tex
+
+	mkdir -p docs/api
+	mkdir -p docs/dynamite
+	mkdir -p docs/wise2
+
+	mv docs/api.html docs/api
+	mv docs/dynamite.html docs/dynamite
+	mv docs/wise2.html docs/wise2
+
+	touch $@
+
+clean: unpatch
+	dh_testdir
+	dh_testroot
+	rm -f build-stamp configure-stamp
+
+	$(MAKE) -C src clean
+	$(MAKE) -C debian/manpages.d clean
+
+#	bugfix
+	$(RM) -r src/oldbin
+	for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do $(RM) src/modules/$$i; done
+	$(RM) src/network/scanwise_server
+
+#	clean documentation
+	$(RM) docs/temp.tex
+	$(RM) docs/api.*
+	$(RM) docs/wise2.image.tex
+	$(RM) docs/*.pdf
+	$(RM) docs/*.aux
+	$(RM) docs/*.log
+	$(RM) docs/*.toc
+	$(RM) docs/*.pdf
+	$(RM) docs/*.dvi
+	$(RM) docs/*.ps
+	$(RM) docs/*.4ct
+	$(RM) docs/*.4tc
+	$(RM) docs/*.css
+	$(RM) docs/*.idv
+	$(RM) docs/*.lg
+	$(RM) docs/*.tmp
+	$(RM) docs/*.xref
+	$(RM) docs/*.haux
+	$(RM) docs/*.htoc
+	$(RM) docs/*.html
+
+	$(RM) -r docs/api
+	$(RM) -r docs/dynamite
+	$(RM) -r docs/wise2
+
+	dh_clean
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_prep 
+	dh_installdirs
+
+#	$(MAKE) install DESTDIR=$(CURDIR)/debian/wise
+	install -m 755 src/bin/* debian/wise/usr/bin
+	install -m 755 src/models/genomewise debian/wise/usr/bin
+
+binary-indep: build install
+	dh_testdir -i
+	dh_testroot -i
+	dh_installchangelogs -i
+	dh_installdocs -i
+	dh_installexamples -i
+	dh_installman -i
+	dh_link -i
+	dh_strip -i
+	dh_compress -i
+	dh_fixperms -i
+	dh_installdeb -i
+	dh_gencontrol -i
+	dh_md5sums -i
+	dh_builddeb -i -- -Z xz
+
+binary-arch: build install
+	dh_testdir -a
+	dh_testroot -a
+	dh_installchangelogs -a
+	dh_installdocs -a
+	dh_installexamples -a
+	dh_installman -a
+	dh_link -a
+	dh_strip -a
+	dh_compress -a
+	dh_fixperms -a
+	dh_installdeb -a
+	dh_shlibdeps -a
+	dh_gencontrol -a
+	dh_md5sums -a
+	dh_builddeb -a -- -Z xz
+
+binary: binary-indep binary-arch
+.PHONY: build build-arch build-indep clean binary-indep binary-arch binary install configure




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