[Debian-med-packaging] [SCM] igv branch, master, updated. upstream/1.5.09-38-ge51be1b

[Shaun Jackman]

The following commit has been merged in the master branch:
commit e51be1b6cefff888e48b2077d3e7ec1181a32f02
Author: Shaun Jackman <sjackman at debian.org>
Date:   Fri Jul 23 15:47:20 2010 -0700

    * New upstream release.
    * debian/patches/01-build.xml: Refresh.
    * debian/copyright (ledatastream.jar): This file has been removed
    upstream.

diff --git a/debian/changelog b/debian/changelog
index 8c87035..558ef5b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+igv (1.5.10-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org>  Fri, 23 Jul 2010 14:19:24 -0700
+
 igv (1.5.09-1) unstable; urgency=low
 
   * New upstream release.
diff --git a/debian/copyright b/debian/copyright
index bce77c8..1a1a25e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -12,14 +12,6 @@ Copyright: 2001, 2002 Dipl. Ing. P. Szawlowski
 License: LGPL-2.1
  See `/usr/share/common-licenses/LGPL-2.1'.
 
-Files: src/org/broad/igv/tdf/LEDataInputStream.java
- lib/ledatastream.jar
-Copyright 1998-2009 Roedy Green, Canadian Mind Products
-License: other
- This software may be copied and used freely for any purpose but
- military. For explanatory text see
- `http://mindprod.com/contact/nonmil.html'.
-
 Files: lib/jlfgr-1_0.jar
 Copyright: 2000 by Sun Microsystems, Inc.
 License: other
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 8c1a6ee..16a45c4 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -12,15 +12,15 @@ Forwarded: no
  
      <!-- Platform specific input files -->
      <property name="native.dir"        value="${basedir}/native/" />
-@@ -67,51 +67,42 @@
+@@ -67,50 +67,43 @@
                  <exclude name="**/manifest.mf"/>
              </fileset>
          </copy>
--
 +        <unjar dest="${tmp.dir}">
 +            <fileset dir="lib" />
 +        </unjar>
  
+ 
          <!-- Create class path for manifest -->
          <path id="@jars">
 -            <pathelement path="${lib.dir}AbsoluteLayout.jar" />
@@ -41,7 +41,7 @@ Forwarded: no
  			<pathelement path="${lib.dir}batik-transcoder.jar" />
 -            <pathelement path="${lib.dir}batik-util.jar" />
 -            <pathelement path="${lib.dir}batik-xml.jar" />            
--            <pathelement path="${lib.dir}colt.jar" />
+-            <pathelement path="${lib.dir}colt_nohep.jar" />
 -            <pathelement path="${lib.dir}commons-math-1.1.jar" />
 -			<pathelement path="${lib.dir}commons-net-2.0.jar" />
 -            <pathelement path="${lib.dir}concurrent.jar" />
@@ -55,8 +55,7 @@ Forwarded: no
 -            <pathelement path="${lib.dir}jide-dock.jar" />
 -            <pathelement path="${lib.dir}jide-grids.jar" />
 -            <pathelement path="${lib.dir}jlfgr-1_0.jar" />
--            <pathelement path="${lib.dir}junit-4.5.jar" />            
--            <pathelement path="${lib.dir}ledatastream.jar" />
+-            <pathelement path="${lib.dir}junit-4.5.jar" />   
 -            <pathelement path="${lib.dir}log4j-1.2.15.jar" />
 -            <pathelement path="${lib.dir}sam-1.21.jar" />
 -            <pathelement path="${lib.dir}swing-layout-1.0.jar" />           
@@ -87,7 +86,7 @@ Forwarded: no
          </pathconvert>
  
          <tstamp>
-@@ -127,8 +118,8 @@
+@@ -126,8 +119,8 @@
      </target>
  
      <target name="build" depends="compile">
@@ -98,7 +97,7 @@ Forwarded: no
              <manifest>
              <attribute name="Class-Path" value="${class-path}" />
              <attribute name="Built-By" value="${user.name}" />
-@@ -140,6 +131,11 @@
+@@ -139,6 +132,11 @@
      <target name="compile" depends="init">
          <javac srcdir="${src.dir}"  debug="on" destdir="${tmp.dir}">
              <classpath refid="@jars" />

-- 
Integrative Genomics Viewer