[med-svn] r15942 - in trunk/packages/biojava3/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2014-02-01 08:37:58 +0000 (Sat, 01 Feb 2014)
New Revision: 15942

Added:
   trunk/packages/biojava3/trunk/debian/patches/fix_uselog4j1
Modified:
   trunk/packages/biojava3/trunk/debian/changelog
   trunk/packages/biojava3/trunk/debian/control
   trunk/packages/biojava3/trunk/debian/patches/series
Log:
upload new upstream release, apply specific patch on log4j to use Debian available version waiting for log4j2 availability

Modified: trunk/packages/biojava3/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog	2014-01-31 20:58:31 UTC (rev 15941)
+++ trunk/packages/biojava3/trunk/debian/changelog	2014-02-01 08:37:58 UTC (rev 15942)
@@ -1,7 +1,7 @@
-biojava3-live (3.0.6-1) UNRELEASED; urgency=low
+biojava3-live (3.0.7-1) UNRELEASED; urgency=low
 
   * New upstream release
-    TODO: needs Apache commons logging >= 2.0
+  * Use Standards 3.9.5
    
    [debian/watch]: use new upstream GitHub repository
 

Modified: trunk/packages/biojava3/trunk/debian/control
===================================================================
--- trunk/packages/biojava3/trunk/debian/control	2014-01-31 20:58:31 UTC (rev 15941)
+++ trunk/packages/biojava3/trunk/debian/control	2014-02-01 08:37:58 UTC (rev 15942)
@@ -11,7 +11,7 @@
  default-jdk (>= 1:1.6), junit4,javahelper (>=0.25),
  ant-optional, icedtea-netx, libhamcrest-java, libjson-simple-java
 Build-Depends: debhelper (>= 9), ant
-Standards-Version: 3.9.4
+Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava3/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava3/trunk/
 Homepage: http://www.biojava.org

Added: trunk/packages/biojava3/trunk/debian/patches/fix_uselog4j1
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/fix_uselog4j1	                        (rev 0)
+++ trunk/packages/biojava3/trunk/debian/patches/fix_uselog4j1	2014-02-01 08:37:58 UTC (rev 15942)
@@ -0,0 +1,74 @@
+Subject: use log4j v1.X
+Description: upstream use log4j v2.X which is not yet available in Debian.
+There is no specific v2 API usage, so applying a patch to use the log4j 
+version available in Debian waiting for new version availability.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2014-02-01
+Forwarded: no
+--- a/biojava3-structure/pom.xml
++++ b/biojava3-structure/pom.xml
+@@ -29,9 +29,9 @@
+ 		</dependency>
+ 
+ 		<dependency>
+-			<groupId>org.apache.logging.log4j</groupId>
+-			<artifactId>log4j-core</artifactId>
+-			<version>2.0-beta7</version>
++			<groupId>log4j</groupId>
++			<artifactId>log4j</artifactId>
++			<version>1.2.17</version>
+ 		</dependency>
+ 		
+ 		<!-- <dependency> <groupId>org.biojava</groupId> <artifactId>biojava3-core</artifactId> 
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java
+@@ -23,8 +23,8 @@
+ import java.io.InputStream;
+ import java.net.URL;
+ 
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+ import org.w3c.dom.Element;
+ import org.w3c.dom.NodeList;
+ 
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java
+@@ -25,8 +25,8 @@
+ import java.util.ArrayList;
+ import java.util.List;
+ 
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+ import org.w3c.dom.Element;
+ import org.w3c.dom.NodeList;
+ 
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java
+@@ -31,8 +31,8 @@
+ import javax.xml.parsers.DocumentBuilderFactory;
+ import javax.xml.parsers.ParserConfigurationException;
+ 
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+ import org.w3c.dom.Document;
+ import org.w3c.dom.Node;
+ import org.w3c.dom.NodeList;
+--- a/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
++++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java
+@@ -28,8 +28,8 @@
+ import java.util.Set;
+ import java.util.TreeSet;
+ 
+-import org.apache.logging.log4j.LogManager;
+-import org.apache.logging.log4j.Logger;
++import org.apache.log4j.LogManager;
++import org.apache.log4j.Logger;
+ 
+ /**
+  * Provides programmatic access to ASTRAL representative sets. See the paper by <a

Modified: trunk/packages/biojava3/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series	2014-01-31 20:58:31 UTC (rev 15941)
+++ trunk/packages/biojava3/trunk/debian/patches/series	2014-02-01 08:37:58 UTC (rev 15942)
@@ -3,3 +3,4 @@
 fix_ascii_characters_mapping
 skip_network_related_tests
 fix_itext_class_updates
+fix_uselog4j1