[med-svn] r12732 - in trunk/packages/biojava3/tags: . 3.0.5-2/debian 3.0.5-2/debian/patches

[Olivier Sallou]

Author: osallou
Date: 2013-01-03 10:23:31 +0000 (Thu, 03 Jan 2013)
New Revision: 12732

Added:
   trunk/packages/biojava3/tags/3.0.5-2/
   trunk/packages/biojava3/tags/3.0.5-2/debian/changelog
   trunk/packages/biojava3/tags/3.0.5-2/debian/patches/series
   trunk/packages/biojava3/tags/3.0.5-2/debian/patches/skip_network_related_tests
Removed:
   trunk/packages/biojava3/tags/3.0.5-2/debian/changelog
   trunk/packages/biojava3/tags/3.0.5-2/debian/patches/series
Log:
[svn-buildpackage] Tagging biojava3-live 3.0.5-2

Deleted: trunk/packages/biojava3/tags/3.0.5-2/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog	2013-01-01 21:26:01 UTC (rev 12730)
+++ trunk/packages/biojava3/tags/3.0.5-2/debian/changelog	2013-01-03 10:23:31 UTC (rev 12732)
@@ -1,22 +0,0 @@
-biojava3-live (3.0.5-1) unstable; urgency=low
-
-  * New upstream release
-  * Use forester 1.005
-
- -- Olivier Sallou <osallou at debian.org>  Sun, 02 Dec 2012 22:35:09 +0100
-
-biojava3-live (3.0.4-2) unstable; urgency=low
-
-  [ Olivier Sallou ]
-  Patch from James Page <james.page at ubuntu.com> (Closes: #683513).
-  * Transition to use default java implementation:
-    - d/control: Use default-jdk (>= 1:1.6) instead of openjdk-6-jdk
-      for package build. 
-
- -- Olivier Sallou <osallou at debian.org>  Wed, 01 Aug 2012 15:45:32 +0200
-
-biojava3-live (3.0.4-1) unstable; urgency=low
-
-  * Initial release (Closes: #674265)
-
- -- Olivier Sallou <osallou at debian.org>  Wed, 23 May 2012 18:13:46 +0200

Copied: trunk/packages/biojava3/tags/3.0.5-2/debian/changelog (from rev 12731, trunk/packages/biojava3/trunk/debian/changelog)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-2/debian/changelog	                        (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-2/debian/changelog	2013-01-03 10:23:31 UTC (rev 12732)
@@ -0,0 +1,28 @@
+biojava3-live (3.0.5-2) unstable; urgency=low
+
+  * Remove tests needing network access (Closes: #696947)
+
+ -- Olivier Sallou <osallou at debian.org>  Thu, 03 Jan 2013 11:08:51 +0100
+
+biojava3-live (3.0.5-1) unstable; urgency=low
+
+  * New upstream release
+  * Use forester 1.005
+
+ -- Olivier Sallou <osallou at debian.org>  Sun, 02 Dec 2012 22:35:09 +0100
+
+biojava3-live (3.0.4-2) unstable; urgency=low
+
+  [ Olivier Sallou ]
+  Patch from James Page <james.page at ubuntu.com> (Closes: #683513).
+  * Transition to use default java implementation:
+    - d/control: Use default-jdk (>= 1:1.6) instead of openjdk-6-jdk
+      for package build. 
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 01 Aug 2012 15:45:32 +0200
+
+biojava3-live (3.0.4-1) unstable; urgency=low
+
+  * Initial release (Closes: #674265)
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 23 May 2012 18:13:46 +0200

Deleted: trunk/packages/biojava3/tags/3.0.5-2/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series	2013-01-01 21:26:01 UTC (rev 12730)
+++ trunk/packages/biojava3/tags/3.0.5-2/debian/patches/series	2013-01-03 10:23:31 UTC (rev 12732)
@@ -1,3 +0,0 @@
-use_simple_json
-fix_code_to_support_latest_jmol
-fix_ascii_characters_mapping

Copied: trunk/packages/biojava3/tags/3.0.5-2/debian/patches/series (from rev 12731, trunk/packages/biojava3/trunk/debian/patches/series)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-2/debian/patches/series	                        (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-2/debian/patches/series	2013-01-03 10:23:31 UTC (rev 12732)
@@ -0,0 +1,4 @@
+use_simple_json
+fix_code_to_support_latest_jmol
+fix_ascii_characters_mapping
+skip_network_related_tests

Copied: trunk/packages/biojava3/tags/3.0.5-2/debian/patches/skip_network_related_tests (from rev 12731, trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests)
===================================================================
--- trunk/packages/biojava3/tags/3.0.5-2/debian/patches/skip_network_related_tests	                        (rev 0)
+++ trunk/packages/biojava3/tags/3.0.5-2/debian/patches/skip_network_related_tests	2013-01-03 10:23:31 UTC (rev 12732)
@@ -0,0 +1,31 @@
+Author: Olivier Sallou <osallou at debian/org>
+Last-Updated: 2013-01-03
+Subject: Some tests use network access
+Description: Remove tests requiring external
+ network access
+Forwarded: yes
+Bug: https://redmine.open-bio.org/issues/3402
+--- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
++++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
+@@ -40,20 +40,7 @@
+ 	
+ 	public void testUniprot(String uniprotID) throws Exception{
+ 		
+-		ProteinSequence seq = getUniprot(uniprotID);
+-		
+-		AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+-		
+-/*		for (AminoAcidCompound compound : seq) {
+-			System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
+-		} 
+-		*/
+-		compoundSet.verifySequence(seq);
+-		
+-		
+-		
+-		float[] values = Jronn.getDisorderScores(seq);
+-		
++	// Skip network related tests
+ 		
+ 	}
+