[med-svn] r12584 - in trunk/packages/biojava3/trunk/debian: . patches

[olivier sallou]

Author: osallou-guest
Date: 2012-12-04 12:56:48 +0000 (Tue, 04 Dec 2012)
New Revision: 12584

Removed:
   trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue
Modified:
   trunk/packages/biojava3/trunk/debian/build.xml
   trunk/packages/biojava3/trunk/debian/control
   trunk/packages/biojava3/trunk/debian/get-orig-source
   trunk/packages/biojava3/trunk/debian/patches/series
Log:
update forester source location and dependencies

Modified: trunk/packages/biojava3/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava3/trunk/debian/build.xml	2012-12-03 21:09:36 UTC (rev 12583)
+++ trunk/packages/biojava3/trunk/debian/build.xml	2012-12-04 12:56:48 UTC (rev 12584)
@@ -21,7 +21,7 @@
 	<property environment="env"/>
 	<property name="project.jarfile.name" value="BJLIB.jar"/>	
 	
-	<property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar"/>
+	<property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar"/>
 								
 	<path id="compile.classpath">
                         <fileset dir="${lib.dir}">
@@ -29,10 +29,13 @@
 				<include name="commons-collections.jar"/>
 				<include name="commons-dbcp.jar"/>
 				<include name="commons-pool.jar"/>
+				<include name="commons-codec.jar"/>
+				<include name="itext5.jar"/>
+				<include name="Jmol.jar"/>
 				<include name="junit4.jar"/>
 				<include name="guava.jar"/>
 				<include name="jgrapht0.8.jar"/>
-				<include name="Jmol.jar"/>
+				<include name="JmolApplet.jar"/>
 				<include name="hamcrest.jar"/>
 				<include name="json_simple.jar"/>
 			</fileset>

Modified: trunk/packages/biojava3/trunk/debian/control
===================================================================
--- trunk/packages/biojava3/trunk/debian/control	2012-12-03 21:09:36 UTC (rev 12583)
+++ trunk/packages/biojava3/trunk/debian/control	2012-12-04 12:56:48 UTC (rev 12584)
@@ -7,8 +7,9 @@
 Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
  libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
  libcommons-cli-java, libguava-java (>= 11.0.1),
+ libcommons-codec-java, libitext5-java, libjmol-java, jmol-applet,
  default-jdk (>= 1:1.6), junit4,javahelper (>=0.25), libjgrapht-java,
- ant-optional, jmol-applet, icedtea-netx, libhamcrest-java, libjson-simple-java
+ ant-optional, icedtea-netx, libhamcrest-java, libjson-simple-java
 Build-Depends: debhelper (>= 9), ant
 Standards-Version: 3.9.3
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
@@ -24,7 +25,10 @@
  libhsqldb-java,
  libbytecode-java,
  jmol-applet, icedtea-netx,
- libjson-simple-java
+ libjson-simple-java,
+ libcommons-codec-java,
+ libitext5-java,
+ libjmol-java
 Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
 Description: Java API to biological data and applications (version 3)
  This package presents the Open Source Java API to biological databases

Modified: trunk/packages/biojava3/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/trunk/debian/get-orig-source	2012-12-03 21:09:36 UTC (rev 12583)
+++ trunk/packages/biojava3/trunk/debian/get-orig-source	2012-12-04 12:56:48 UTC (rev 12584)
@@ -24,8 +24,8 @@
 
 mkdir -p biojava3-forester/src/main/java
 cd biojava3-forester/src/main/java
- wget http://www.biojava.org/download/maven/org/forester/1.005/forester-1.005-sources.jar
- jar xf forester-1.005-sources.jar
+ wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar
+ jar xf forester-1.005-sources-1.005.jar
  find . -name *.class | xargs rm -f
 cd ../../../..
 cd ..

Deleted: trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue	2012-12-03 21:09:36 UTC (rev 12583)
+++ trunk/packages/biojava3/trunk/debian/patches/fix_ascii_character_issue	2012-12-04 12:56:48 UTC (rev 12584)
@@ -1,16 +0,0 @@
-Subject: ASCII error in pbuilder
-Description: unmappable character for encoding ASCII
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2012-05-31
-
---- a/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
-+++ b/biojava3-forester/src/main/java/org/forester/archaeopteryx/Blast.java
-@@ -44,7 +44,7 @@
-     /**
-      * Method for access REST
-      * @param query
--     * service name¡¢method name and parameter for exection rest
-+     * service name method name and parameter for exection rest
-      * @return
-      * execution result
-      * @throws IOException

Modified: trunk/packages/biojava3/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series	2012-12-03 21:09:36 UTC (rev 12583)
+++ trunk/packages/biojava3/trunk/debian/patches/series	2012-12-04 12:56:48 UTC (rev 12584)
@@ -1,3 +1,2 @@
 use_simple_json
 fix_code_to_support_latest_jmol
-fix_ascii_character_issue