[Debian-med-packaging] [SCM] picard-tools branch, master, updated. upstream/1.25-17-gae7cb59

[Shaun Jackman]

The following commit has been merged in the master branch:
commit ae7cb59b4f86991dd41f5da2804cab11816fe157
Author: Shaun Jackman <sjackman at debian.org>
Date:   Tue Jul 6 16:29:06 2010 -0700

    * debian/changelog: New upstream release.
    * debian/control (Uploaders): Add Charles Plessy.
    (Standards-Version): Bump to 3.9.0.0.
    (picard-tools::Depends): Require libsam-java (>= ${source:Version}).
    * debian/copyright: The files that were licensed `All rights reserved'
    are now licensed MIT.
    * debian/patches/01-build.xml: Refresh.

diff --git a/debian/changelog b/debian/changelog
index 7464363..dfe3ee7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+picard-tools (1.25-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org>  Tue, 06 Jul 2010 16:06:18 -0700
+
 picard-tools (1.24-1) UNRELEASED; urgency=low
 
   * Initial release. Closes: #586015.
diff --git a/debian/control b/debian/control
index 183fdda..9e34115 100644
--- a/debian/control
+++ b/debian/control
@@ -3,10 +3,11 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
-Uploaders: Shaun Jackman <sjackman at debian.org>
-Build-Depends: ant, openjdk-6-jdk|java-compiler, debhelper (>= 7.0.50~),
- testng
-Standards-Version: 3.8.4
+Uploaders: Shaun Jackman <sjackman at debian.org>,
+ Charles Plessy <plessy at debian.org>
+Build-Depends: ant, openjdk-6-jdk|java-compiler, testng,
+ debhelper (>= 7.0.50~)
+Standards-Version: 3.9.0.0
 Homepage: http://picard.sourceforge.net/
 Vcs-Git: git://git.debian.org/git/debian-med/picard-tools.git
 Vcs-Browser: http://git.debian.org/?p=debian-med/picard-tools.git
@@ -23,7 +24,7 @@ Description: Java library to manipulate SAM and BAM files
 Package: picard-tools
 Architecture: any
 Depends: openjdk-6-jre|java-runtime, ${misc:Depends},
- libsam-java
+ libsam-java (>= ${source:Version})
 Suggests: python, r-base-core
 Description: Command line tools to manipulate SAM and BAM files
  SAM (Sequence Alignment/Map) format is a generic format for storing
diff --git a/debian/copyright b/debian/copyright
index 6b70009..f3b9967 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -92,21 +92,6 @@ License: GPL-2
 Comment: On Debian systems, the complete text of the GNU General Public License
  version 2 is available in the file ‘/usr/share/common-licenses/GPL-2’.
 
-Files: src/scripts/release_picard.sh, src/scripts/explain_sam_flags.py, src/java/net/sf/samtools/apps/TimeRandomAccessFile.java, src/java/net/sf/samtools/apps/TimeChannel.java, src/java/net/sf/samtools/FixBAMFile.java
-Copyright: The Broad Institute/Massachusetts Institute of Technology
-License: all rights reserved
- The Broad Institute
- SOFTWARE COPYRIGHT NOTICE AGREEMENT
- This software and its documentation are copyright 2006 by the
- Broad Institute/Massachusetts Institute of Technology. All rights are
- reserved.
- .
- This software is supplied without any warranty or guaranteed support
- whatsoever. Neither the Broad Institute nor MIT can be responsible for its
- use, misuse, or functionality.
-Comment: I thin that it is obvious that the authors forgot to add a MIT license
- header on these files. -- Charles Plessy
-
 Files: debian/*
 Copyright: 2010 Shaun Jackman <sjackman at debian.org>
 License: ISC
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index 4c59e1b..7d0603b 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -5,8 +5,8 @@ Description: Modifies the upstream build system.
  from src/scripts/net/sf/picard/analysis/.
 Origin: vendor
 Forwarded: no
---- picard-tools-1.24.orig/build.xml
-+++ picard-tools-1.24/build.xml
+--- picard-tools-1.25.orig/build.xml
++++ picard-tools-1.25/build.xml
 @@ -23,7 +23,7 @@
    ~ THE SOFTWARE.
    -->
@@ -22,9 +22,9 @@ Forwarded: no
              </fileset>
 +            <pathelement path="/usr/share/java/testng.jar"/>
          </path>
-     </target>
- 
-@@ -93,7 +94,7 @@
+         <path  id="metrics.classpath">
+             <pathelement path="${classpath}"/>
+@@ -97,7 +98,7 @@
                 sourcepath="" srcdir="${src}"
                 includes ="net/sf/samtools/**/*.*"
                 excludes = "net/sf/picard/**/*.*"
@@ -33,7 +33,7 @@ Forwarded: no
                 compiler="javac1.5" fork="true">
              <!--<compilerarg value="-Xlint:all"/>-->
              <!--<compilerarg value="-Xlint:unchecked"/>-->
-@@ -122,7 +123,7 @@
+@@ -126,7 +127,7 @@
                 optimize="${javac.opt}"
                 debug="${javac.debug}"
                 includes ="net/sf/samtools/**/*.*"
@@ -42,7 +42,7 @@ Forwarded: no
                 compiler="javac1.5" fork="true"> <!-- Force SAM-JDK to be built with 1.5 -->
              <!--<compilerarg value="-Xlint:unchecked"/>-->
              <src path="${src.test}"/>
-@@ -199,9 +200,12 @@
+@@ -203,9 +204,12 @@
          <mkdir dir="${dist}"/>
          <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
              <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
@@ -54,4 +54,4 @@ Forwarded: no
 +
      <target name="javadoc" depends="init" description="Generates the project javadoc.">
          <javadoc
-            sourcepath="${src}"
+                 sourcepath="${src}"

-- 
manipulate SAM and BAM files