[Debian-med-packaging] [SCM] igv branch, master, updated. upstream/1.5.10-40-g12d8a6b

[Shaun Jackman]

The following commit has been merged in the master branch:
commit 12d8a6b10b37a2ac4265d0281d1fdf9ba4fc82c0
Author: Shaun Jackman <sjackman at debian.org>
Date:   Wed Jul 28 16:29:08 2010 -0700

    * New upstream release.
    * debian/control (Build-Depends, Depends): Remove libcolt-java.
    * debian/patches/01-build.xml: Refresh.

diff --git a/debian/changelog b/debian/changelog
index 558ef5b..25d3348 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+igv (1.5.14-1) unstable; urgency=low
+
+  * New upstream release.
+  * Remove libcolt-java from the dependencies.
+  * Bump Standards-Version to 3.9.1.
+
+ -- Shaun Jackman <sjackman at debian.org>  Wed, 28 Jul 2010 16:22:20 -0700
+
 igv (1.5.10-1) unstable; urgency=low
 
   * New upstream release.
diff --git a/debian/control b/debian/control
index 89f4da7..8c1e6d9 100644
--- a/debian/control
+++ b/debian/control
@@ -5,12 +5,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 DM-Upload-Allowed: yes
 Uploaders: Shaun Jackman <sjackman at debian.org>
 Build-Depends: ant, junit4, openjdk-6-jdk|java-compiler, debhelper (>= 7.0.50~),
- libbatik-java (>>1.7), libcolt-java,
+ libbatik-java (>>1.7),
  libcommons-math-java, libcommons-net-java, libconcurrent-java,
  libjlibeps-java, libjama-java, libjargs-java, libjaxp1.3-java, libjhdf5-java,
  liblog4j1.2-java, libsam-java, libswing-layout-java,
  libxml-commons-external-java
-Standards-Version: 3.9.0
+Standards-Version: 3.9.1
 Homepage: http://www.broadinstitute.org/igv/
 Vcs-Git: git://git.debian.org/git/debian-med/igv.git
 Vcs-Browser: http://git.debian.org/?p=debian-med/igv.git
@@ -18,7 +18,7 @@ Vcs-Browser: http://git.debian.org/?p=debian-med/igv.git
 Package: igv
 Architecture: all
 Depends: openjdk-6-jre|java-runtime, ${shlibs:Depends}, ${misc:Depends},
- libbatik-java (>>1.7), libcolt-java,
+ libbatik-java (>>1.7),
  libcommons-math-java, libcommons-net-java, libconcurrent-java,
  libjlibeps-java, libjama-java, libjargs-java, libjaxp1.3-java, libjhdf5-java,
  liblog4j1.2-java, libsam-java, libswing-layout-java,
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 16a45c4..62a034a 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -12,7 +12,7 @@ Forwarded: no
  
      <!-- Platform specific input files -->
      <property name="native.dir"        value="${basedir}/native/" />
-@@ -67,50 +67,43 @@
+@@ -67,49 +67,42 @@
                  <exclude name="**/manifest.mf"/>
              </fileset>
          </copy>
@@ -40,8 +40,7 @@ Forwarded: no
  			<pathelement path="${lib.dir}batik-svggen.jar" />
  			<pathelement path="${lib.dir}batik-transcoder.jar" />
 -            <pathelement path="${lib.dir}batik-util.jar" />
--            <pathelement path="${lib.dir}batik-xml.jar" />            
--            <pathelement path="${lib.dir}colt_nohep.jar" />
+-            <pathelement path="${lib.dir}batik-xml.jar" /> 
 -            <pathelement path="${lib.dir}commons-math-1.1.jar" />
 -			<pathelement path="${lib.dir}commons-net-2.0.jar" />
 -            <pathelement path="${lib.dir}concurrent.jar" />
@@ -64,7 +63,6 @@ Forwarded: no
 -            <pathelement path="${lib.dir}Jama-1.0.2.jar" />
 +			<pathelement path="${lib.dir}batik-util.jar" />
 +			<pathelement path="${lib.dir}batik-xml.jar" />
-+			<pathelement path="${lib.dir}colt.jar" />
 +			<pathelement path="${lib.dir}commons-math.jar" />
 +			<pathelement path="${lib.dir}commons-net.jar" />
 +			<pathelement path="${lib.dir}concurrent.jar" />
@@ -86,7 +84,7 @@ Forwarded: no
          </pathconvert>
  
          <tstamp>
-@@ -126,8 +119,8 @@
+@@ -125,8 +118,8 @@
      </target>
  
      <target name="build" depends="compile">
@@ -97,7 +95,7 @@ Forwarded: no
              <manifest>
              <attribute name="Class-Path" value="${class-path}" />
              <attribute name="Built-By" value="${user.name}" />
-@@ -139,6 +132,11 @@
+@@ -138,6 +131,11 @@
      <target name="compile" depends="init">
          <javac srcdir="${src.dir}"  debug="on" destdir="${tmp.dir}">
              <classpath refid="@jars" />

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