[med-svn] [picard-tools] 01/02: Avoid warnings when running PicardCommandLine

[Vincent Danjean]

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vdanjean pushed a commit to branch master
in repository picard-tools.

commit 55ab58cf6495e1a66703051dce8a747f6b69446b
Author: Vincent Danjean <vdanjean at debian.org>
Date:   Thu Jul 7 22:39:28 2016 +0200

    Avoid warnings when running PicardCommandLine
    
    * MaxPermSize does not exist anymore with java 8
    
    * add tools.jar in libpicard-java classpath
      Note that, as tools.jar is provided by the jre
      and we do not want to depend on the current (build time) default jre,
      we manually set dependencies in libpicard-java
---
 debian/bin/PicardCommandLine    | 2 +-
 debian/changelog                | 6 ++++++
 debian/control                  | 4 +++-
 debian/libpicard-java.classpath | 2 +-
 4 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/debian/bin/PicardCommandLine b/debian/bin/PicardCommandLine
index 72769ba..cd3c0ca 100755
--- a/debian/bin/PicardCommandLine
+++ b/debian/bin/PicardCommandLine
@@ -12,4 +12,4 @@ PicardCommandLine)
 	;;
 esac
 
-exec java ${JAVA_OPTIONS-} -XX:MaxPermSize=256m -jar /usr/share/java/picard.jar "$@"
+exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
diff --git a/debian/changelog b/debian/changelog
index da1f528..83f21a7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+picard-tools (2.5.0-gradle+dfsg-2) UNRELEASED; urgency=medium
+
+  * Avoid warnings when running PicardCommandLine
+
+ -- Vincent Danjean <vdanjean at debian.org>  Thu, 07 Jul 2016 15:45:40 +0200
+
 picard-tools (2.5.0-gradle+dfsg-1) unstable; urgency=medium
 
   * New upstream release
diff --git a/debian/control b/debian/control
index 57a5899..b781e87 100644
--- a/debian/control
+++ b/debian/control
@@ -81,8 +81,10 @@ Package: libpicard-java
 Architecture: all
 Section: java
 Depends: ${misc:Depends},
-         ${java:Depends},
+         libguava-java (>= 15.0),
          libhtsjdk-java (>= 2.5.0)
+# avoid ${java:Depends} that contains openjdk-8-jdk-headless
+# due to tools.jar in classpath
 Recommends: ${java:Recommends},
             r-base-core
 Suggests: picard-tools
diff --git a/debian/libpicard-java.classpath b/debian/libpicard-java.classpath
index 5de4c77..0607a86 100644
--- a/debian/libpicard-java.classpath
+++ b/debian/libpicard-java.classpath
@@ -1 +1 @@
-usr/share/java/picard.jar /usr/share/java/htsjdk.jar /usr/share/java/guava.jar
+usr/share/java/picard.jar /usr/share/java/htsjdk.jar /usr/share/java/guava.jar /usr/lib/jvm/default-java/lib/tools.jar

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