[med-svn] r1618 - in trunk/packages/haploview/trunk/debian: . patches

smoe-guest at alioth.debian.org smoe-guest at alioth.debian.org
Mon Mar 17 23:41:24 UTC 2008 

Author: smoe-guest
Date: 2008-03-17 23:41:24 +0000 (Mon, 17 Mar 2008)
New Revision: 1618

Modified:
   trunk/packages/haploview/trunk/debian/README.Debian
   trunk/packages/haploview/trunk/debian/changelog
   trunk/packages/haploview/trunk/debian/control
   trunk/packages/haploview/trunk/debian/patches/build.xml
   trunk/packages/haploview/trunk/debian/rules
Log:
Smaller changes to help the build process.


Modified: trunk/packages/haploview/trunk/debian/README.Debian
===================================================================
--- trunk/packages/haploview/trunk/debian/README.Debian	2008-03-17 22:35:30 UTC (rev 1617)
+++ trunk/packages/haploview/trunk/debian/README.Debian	2008-03-17 23:41:24 UTC (rev 1618)
@@ -1,8 +1,14 @@
 haploview for Debian
 --------------------
 
-javahelp2 has just appeared on Debian and thus
-the packaging of Haploview can continue. Many
-thanks for that!
+javahelp2 has just appeared on Debian and thus the packaging of Haploview
+can continue. Many thanks for that!
 
+I found the Jimi classes to be problematic, though. These seem to be
+available as binaries only http://java.sun.com/products/jimi/. All other
+tar files could be removed from the source they these were already
+available in Debian.
+
+Many thanks also to the Debian-Med community for their ongoing support.
+
  -- Steffen Moeller <moeller at debian.org>  Sun, 14 Jan 2007 15:28:10 +0100

Modified: trunk/packages/haploview/trunk/debian/changelog
===================================================================
--- trunk/packages/haploview/trunk/debian/changelog	2008-03-17 22:35:30 UTC (rev 1617)
+++ trunk/packages/haploview/trunk/debian/changelog	2008-03-17 23:41:24 UTC (rev 1618)
@@ -1,11 +1,5 @@
-haploview (4.0-2) UNRELEASED; urgency=low
+haploview (4.0-1) UNRELEASED; urgency=low
 
-  * Updated to Standards-Version 3.7.3 (no changes needed)
-
- -- David Paleino <d.paleino at gmail.com>  Wed, 06 Feb 2008 13:11:53 +0100
-
-haploview (4.0-1) unstable; urgency=low
-
   * Initial release (Closes: #311421)
 
  -- Steffen Moeller <moeller at debian.org>  Sun, 14 Jan 2007 15:28:10 +0100

Modified: trunk/packages/haploview/trunk/debian/control
===================================================================
--- trunk/packages/haploview/trunk/debian/control	2008-03-17 22:35:30 UTC (rev 1617)
+++ trunk/packages/haploview/trunk/debian/control	2008-03-17 23:41:24 UTC (rev 1618)
@@ -2,7 +2,7 @@
 Section: contrib/science
 Priority: extra
 Maintainer: Steffen Moeller <steffen_moeller at gmx.de>
-Build-Depends-Indep: cdbs, ant, debhelper (>= 5), kaffe|java-compiler, libjfreechart-java, libjgrapht-java, liblog4j1.2-java, javahelp2
+Build-Depends-Indep: cdbs, ant, debhelper (>= 5), kaffe|java-compiler, libjfreechart-java, libjgrapht-java, liblog4j1.2-java, javahelp2, quilt
 Standards-Version: 3.7.3
 Homepage: http://www.broad.mit.edu/mpg/haploview/
 
@@ -14,5 +14,3 @@
  variation in a population. Such investigations are performed
  to determine genes and genetic pathways that are associated
  with diseases. This is an early stage in the quest for new drugs.
- .
-  

Modified: trunk/packages/haploview/trunk/debian/patches/build.xml
===================================================================
--- trunk/packages/haploview/trunk/debian/patches/build.xml	2008-03-17 22:35:30 UTC (rev 1617)
+++ trunk/packages/haploview/trunk/debian/patches/build.xml	2008-03-17 23:41:24 UTC (rev 1618)
@@ -1,8 +1,6 @@
-Index: haploview-4.0/build.xml
-===================================================================
---- haploview-4.0.orig/build.xml	2007-10-05 00:37:11.044728970 +0200
-+++ haploview-4.0/build.xml	2007-10-05 01:18:27.383231681 +0200
-@@ -14,6 +14,14 @@
+--- haploview-4.0.orig/build.xml
++++ haploview-4.0/build.xml
+@@ -14,10 +14,18 @@
  <!-- Classpath -->
  
   <path id="library.classpath">
@@ -17,6 +15,11 @@
     <fileset dir="resources/">
         <include name="*.jar"/>
         <include name="*.zip"/>
+-       <include name="jfreechart/*.jar"/>
++<!--       <include name="jfreechart/*.jar"/> -->
+      </fileset>
+    <fileset dir="docs/">
+        <include name="HaploHelp.jar"/>
 @@ -51,7 +59,9 @@
  
  <target name="compile-haploview" depends="prepare-compile">
@@ -28,7 +31,7 @@
     <classpath refid="library.classpath"/>
     </javac>
  
-@@ -72,12 +82,16 @@
+@@ -72,12 +82,17 @@
         <attribute name="Main-Class" value="edu.mit.wi.haploview.HVWrap"/>
       </manifest>
       <zipfileset src="resources/JimiProClasses.zip"/>
@@ -42,12 +45,24 @@
       <zipfileset src="resources/jfreechart/jfreechart-1.0.5.jar"/>
       <zipfileset src="resources/jfreechart/jcommon-1.0.9.jar"/>
 +-->
++<!--
       <zipfileset src="resources/jfreechart/batik-xml.jar"/>
       <zipfileset src="resources/jfreechart/xml-apis.jar"/>
       <zipfileset src="resources/jfreechart/batik-awt-util.jar"/>
-@@ -102,10 +116,12 @@
+@@ -85,6 +100,7 @@
+      <zipfileset src="resources/jfreechart/batik-svggen.jar"/>
+      <zipfileset src="resources/jfreechart/batik-util.jar"/>
+      <zipfileset src="resources/jfreechart/batik-ext.jar"/>
++-->
+    </jar>
+ </target>
+ 
+@@ -100,12 +116,15 @@
+        <attribute name="Main-Class" value="edu.mit.wi.haploview.HaploView"/>
+      </manifest>
       <zipfileset src="resources/JimiProClasses.zip"/>
-      <zipfileset src="resources/jh.jar"/>
+-     <zipfileset src="resources/jh.jar"/>
++     <!-- <zipfileset src="resources/jh.jar"/> -->
       <zipfileset src="docs/HaploHelp.jar"/>
 +<!--
       <zipfileset src="resources/jgrapht-0.5.3.jar"/>
@@ -55,6 +70,15 @@
       <zipfileset src="resources/jfreechart/jfreechart-1.0.5.jar"/>
       <zipfileset src="resources/jfreechart/jcommon-1.0.9.jar"/>
 +-->
++<!--
       <zipfileset src="resources/jfreechart/batik-xml.jar"/>
       <zipfileset src="resources/jfreechart/xml-apis.jar"/>
       <zipfileset src="resources/jfreechart/batik-awt-util.jar"/>
+@@ -113,6 +132,7 @@
+      <zipfileset src="resources/jfreechart/batik-svggen.jar"/>
+      <zipfileset src="resources/jfreechart/batik-util.jar"/>
+      <zipfileset src="resources/jfreechart/batik-ext.jar"/>
++-->
+    </jar>
+ </target>
+ 

Modified: trunk/packages/haploview/trunk/debian/rules
===================================================================
--- trunk/packages/haploview/trunk/debian/rules	2008-03-17 22:35:30 UTC (rev 1617)
+++ trunk/packages/haploview/trunk/debian/rules	2008-03-17 23:41:24 UTC (rev 1618)
@@ -5,11 +5,10 @@
 include /usr/share/cdbs/1/rules/debhelper.mk
 #include /usr/share/cdbs/1/class/makefile.mk
 include /usr/share/cdbs/1/class/ant.mk
-#include /usr/share/quilt/quilt.make
 include /usr/share/cdbs/1/rules/patchsys-quilt.mk
 
-JAVA_HOME=/usr/lib/kaffe
-JAVACMD=/usr/bin/java
+export JAVA_HOME=/usr/lib/jvm/java-6-sun/
+export JAVACMD=/usr/bin/java
 DEB_ANT_INSTALL_TARGET=haploview
 
 # Add here any variable or target overrides you need.

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