[med-svn] r18254 - in trunk/packages/biosquid/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-10-09 14:47:05 +0000 (Thu, 09 Oct 2014)
New Revision: 18254

Added:
   trunk/packages/biosquid/trunk/debian/README.test
   trunk/packages/biosquid/trunk/debian/biosquid.docs
Modified:
   trunk/packages/biosquid/trunk/debian/changelog
   trunk/packages/biosquid/trunk/debian/copyright
   trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch
   trunk/packages/biosquid/trunk/debian/rules
Log:
Fix some remaining lintian issues and upload to unstable


Added: trunk/packages/biosquid/trunk/debian/README.test
===================================================================
--- trunk/packages/biosquid/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/biosquid/trunk/debian/README.test	2014-10-09 14:47:05 UTC (rev 18254)
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package you can do
+
+   sh  run-unit-test
+
+in this directory.

Added: trunk/packages/biosquid/trunk/debian/biosquid.docs
===================================================================
--- trunk/packages/biosquid/trunk/debian/biosquid.docs	                        (rev 0)
+++ trunk/packages/biosquid/trunk/debian/biosquid.docs	2014-10-09 14:47:05 UTC (rev 18254)
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test

Modified: trunk/packages/biosquid/trunk/debian/changelog
===================================================================
--- trunk/packages/biosquid/trunk/debian/changelog	2014-10-09 14:36:41 UTC (rev 18253)
+++ trunk/packages/biosquid/trunk/debian/changelog	2014-10-09 14:47:05 UTC (rev 18254)
@@ -1,4 +1,4 @@
-biosquid (1.9g+cvs20050121-4) UNRELEASED; urgency=medium
+biosquid (1.9g+cvs20050121-4) unstable; urgency=medium
 
   * Fix segmentation fault with ambiguous arguments (thanks for the patch
     to artin Steghöfer <martin at steghoefer.eu>)
@@ -7,6 +7,7 @@
   * Add autopkgtest
   * Very basic DEP3 headers
   * Documentation how the package can be tested
+  * Fix DEP5 name of license
 
  -- Andreas Tille <tille at debian.org>  Thu, 09 Oct 2014 15:35:25 +0200
 

Modified: trunk/packages/biosquid/trunk/debian/copyright
===================================================================
--- trunk/packages/biosquid/trunk/debian/copyright	2014-10-09 14:36:41 UTC (rev 18253)
+++ trunk/packages/biosquid/trunk/debian/copyright	2014-10-09 14:47:05 UTC (rev 18254)
@@ -9,9 +9,9 @@
 Files: *
 Copyright: 1992-2006 Sean Eddy <eddy at genetics.wustl.edu>
                      Washington University School of Medicine
-License: GPLv2
+License: GPL-2
 
-License: GPLv2
+License: GPL-2
  This suite of programs 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
@@ -48,6 +48,6 @@
 
 Files: debian/*
 Copyright: © 2005-2008 Nelson A. de Oliveira <naoliv at gmail.com>
-             2008-2013 Andreas Tille <tille at debian.org>
-License: GPLv2
+             2008-2014 Andreas Tille <tille at debian.org>
+License: GPL-2
 

Modified: trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch
===================================================================
--- trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch	2014-10-09 14:36:41 UTC (rev 18253)
+++ trunk/packages/biosquid/trunk/debian/patches/sindex.man.patch	2014-10-09 14:47:05 UTC (rev 18254)
@@ -8,6 +8,15 @@
  
  .SH NAME
  .TP 
+@@ -67,7 +67,7 @@ Specify that the sequence file is defini
+ .I <s>;
+ blocks sequence file format autodetection. This is useful in automated
+ pipelines, because it improves robustness (autodetection can
+-occasionally go wrong on a perversely misformed file). Common examples
++occasionally go wrong on a perversely malformed file). Common examples
+ include genbank, embl, gcg, pir, stockholm, clustal, msf, or phylip;
+ see the printed documentation for a complete list of accepted format
+ names.
 @@ -83,12 +83,24 @@ and accession (as a secondary key).
  .SH SEE ALSO
  

Modified: trunk/packages/biosquid/trunk/debian/rules
===================================================================
--- trunk/packages/biosquid/trunk/debian/rules	2014-10-09 14:36:41 UTC (rev 18253)
+++ trunk/packages/biosquid/trunk/debian/rules	2014-10-09 14:47:05 UTC (rev 18254)
@@ -25,6 +25,7 @@
 override_dh_installexamples:
 	dh_installexamples
 	cd $(CURDIR)/debian/biosquid-dev/usr/share/doc/biosquid-dev/examples/Testsuite; make clean
+	sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(CURDIR)/debian/biosquid-dev/usr/share/doc/biosquid-dev/examples/Formats/*.pl
 
 override_dh_auto_test:
 	chmod u+x Testsuite/x-base-* Testsuite/bug-1-sfetch*