[med-svn] r18670 - in trunk/packages/biojava4-live/trunk/debian: . patches

Sat Jan 31 14:14:15 UTC 2015

Author: osallou
Date: 2015-01-31 14:14:15 +0000 (Sat, 31 Jan 2015)
New Revision: 18670

Modified:
   trunk/packages/biojava4-live/trunk/debian/changelog
   trunk/packages/biojava4-live/trunk/debian/copyright
   trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
   trunk/packages/biojava4-live/trunk/debian/patches/series
Log:
fix some lintian warning, update copyright info, reapply unmappable character patch

Modified: trunk/packages/biojava4-live/trunk/debian/changelog
===================================================================

--- trunk/packages/biojava4-live/trunk/debian/changelog	2015-01-31 14:05:53 UTC (rev 18669)
+++ trunk/packages/biojava4-live/trunk/debian/changelog	2015-01-31 14:14:15 UTC (rev 18670)
@@ -1,7 +1,5 @@
 biojava4-live (4.0.0+dfsg-1) UNRELEASED; urgency=medium
 
-  * BioJava4 packaging 
-   [ TODO: test get-orig-source to recreate archive,
-     test generated packages, pbuilder ]
+  * BioJava4 packaging  (Closes: #776704).
 
  -- Olivier Sallou <osallou at debian.org>  Fri, 30 Jan 2015 17:24:21 +0100

Modified: trunk/packages/biojava4-live/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/copyright	2015-01-31 14:05:53 UTC (rev 18669)
+++ trunk/packages/biojava4-live/trunk/debian/copyright	2015-01-31 14:14:15 UTC (rev 18670)
@@ -1,8 +1,32 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: biojava3
+Upstream-Name: biojava4
 Source: http://www.biojava.org/
 
-Files: biojava4-forester
+Files: biojava4-jcolorbrewer
+Copyright: 2011 University of California San Diego
+           2011 J.L. Moreland
+           2011 A.Gramada
+           2011 O.V. Buzko
+           2011 Qing Zhang
+           2011 P.E. Bourne
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package 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 Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+Files: biojava-forester
 Copyright: 2008-2009 Christian M. Zmasek
            2008-2009 Burnham Institute for Medical Research
 License: LGPL-2.1+
@@ -33,7 +57,13 @@
     Jules Jacobsen <jacobsen at ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
     A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
     Spencer Bliven <sbliven at ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
-    Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin
+    Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin,
+    Jose Manuel Duarte, D. Myers, Andrew Yates, Ulysse Carion, M. L Heuer,
+    B. T. Boyle, emckee2006, paolopavan, J. Grzebyta, G. Waldon, D. Cameron,
+    A. Drager, kevinwu1, Siarhei, R. Thornton, C. Foti, sroughley, ferlan,
+    parit, M. Bizzari
+
+   
 License: LGPL-2.1+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU Lesser General Public License as published by
@@ -53,7 +83,7 @@
 
 
 Files: debian/*
-Copyright: 2012 Olivier Sallou <osallou at debian.org>
+Copyright: 2015 Olivier Sallou <osallou at debian.org>
 License: GPL-2+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by

Modified: trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping	2015-01-31 14:05:53 UTC (rev 18669)
+++ trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping	2015-01-31 14:14:15 UTC (rev 18670)
@@ -4,8 +4,8 @@
 Last-Updated: 2012-12-05
 Forwarded: yes
 Bug: http://code.google.com/p/forester/issues/detail?id=1
---- a/biojava3-forester/src/main/java/org/forester/test/Test.java
-+++ b/biojava3-forester/src/main/java/org/forester/test/Test.java
+--- a/biojava-forester/src/main/java/org/forester/test/Test.java
++++ b/biojava-forester/src/main/java/org/forester/test/Test.java
 @@ -1310,7 +1310,7 @@
                  return false;
              }
@@ -15,14 +15,3 @@
                  return false;
              }
              if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
---- a/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java
-+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java
-@@ -33,7 +33,7 @@
- 
- /**
-  * A chain, a start residue, and an end residue. May also store a length value. Because of insertion codes, this length
-- * is not necessarily {@code end − start}.
-+ * is not necessarily {@code end - start}.
-  * 
-  * @author dmyerstu
-  * @see ResidueNumber

Modified: trunk/packages/biojava4-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series	2015-01-31 14:05:53 UTC (rev 18669)
+++ trunk/packages/biojava4-live/trunk/debian/patches/series	2015-01-31 14:14:15 UTC (rev 18670)
@@ -2,3 +2,4 @@
 use_simple_json
 fix_import
 faketest
+fix_ascii_characters_mapping


