[med-svn] [picard-tools] 01/03: Replaced the dependency on libsnappy1.0.3-java with libsnappy-java

[Emmanuel Bourg]

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

commit 75ff6ba6626f1ca49943bb8897c024c483dc1a1d
Author: Emmanuel Bourg <ebourg at apache.org>
Date:   Wed Sep 2 13:11:05 2015 +0200

    Replaced the dependency on libsnappy1.0.3-java with libsnappy-java
---
 debian/changelog                                  |  7 +++++++
 debian/control                                    |  2 +-
 debian/patches/01-build.xml                       |  2 +-
 debian/patches/02-snappy-java-compatibility.patch | 24 +++++++++++++++++++++++
 debian/patches/series                             |  1 +
 5 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index bf5e711..9ae495e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+picard-tools (1.113-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Replaced the dependency on libsnappy1.0.3-java with libsnappy-java.
+
+ -- Emmanuel Bourg <ebourg at apache.org>  Wed, 02 Sep 2015 13:10:32 +0200
+
 picard-tools (1.113-1) unstable; urgency=medium
 
   * New upstream release 1.113
diff --git a/debian/control b/debian/control
index fff4981..52aa451 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Priority: optional
 Build-Depends: ant,
                default-jdk,
                testng,
-               libsnappy1.0.3-java,
+               libsnappy-java,
                debhelper (>= 9),
                libjbzip2-java,
                libcofoja-java,
diff --git a/debian/patches/01-build.xml b/debian/patches/01-build.xml
index b663c6d..9031c63 100644
--- a/debian/patches/01-build.xml
+++ b/debian/patches/01-build.xml
@@ -30,7 +30,7 @@ Forwarded: no
                  <include name="**/*.jar"/>
              </fileset>
 +            <pathelement path="/usr/share/java/testng.jar"/>
-+            <pathelement path="/usr/share/java/snappy1.0.3-java.jar"/>
++            <pathelement path="/usr/share/java/snappy-java.jar"/>
 +            <pathelement path="/usr/share/java/jbzip2.jar"/>
 +            <pathelement path="/usr/share/java/cofoja.jar"/>
 +            <pathelement path="/usr/share/java/commons-jexl2.jar"/>
diff --git a/debian/patches/02-snappy-java-compatibility.patch b/debian/patches/02-snappy-java-compatibility.patch
new file mode 100644
index 0000000..ebe08ab
--- /dev/null
+++ b/debian/patches/02-snappy-java-compatibility.patch
@@ -0,0 +1,24 @@
+Description: Fix the compatibility with the latest version of snappy-java.
+ The fix is Debian specific and assumes the native library is always available
+ (which is true in Debian).
+Author: Emmanuel Bourg <ebourg at apache.org>
+Forwarded: not-needed
+--- a/src/java/net/sf/samtools/util/SnappyLoader.java
++++ b/src/java/net/sf/samtools/util/SnappyLoader.java
+@@ -24,7 +24,6 @@
+ package net.sf.samtools.util;
+ 
+ import net.sf.samtools.SAMException;
+-import org.xerial.snappy.LoadSnappy;
+ import org.xerial.snappy.SnappyInputStream;
+ 
+ import java.io.InputStream;
+@@ -83,7 +82,7 @@
+             // Don't try to call any Snappy code until classes have been found via reflection above.
+             boolean tmpSnappyAvailable;
+             try {
+-                if (!LoadSnappy.load()) {
++                if (false) {
+                     if (verbose) System.err.println("Snappy dll failed to load.");
+                     tmpSnappyAvailable = false;
+                 }
diff --git a/debian/patches/series b/debian/patches/series
index 24b6ad5..ec86589 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 use_libjbzip2-java
 01-build.xml
+02-snappy-java-compatibility.patch

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