[med-svn] [trinityrnaseq] 01/01: libjung-java now relies on collections4

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 039b13ef2530a0606669e3995ada52f5a01e5cbb
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Sat Feb 21 16:02:27 2015 -0500

    libjung-java now relies on collections4
---
 debian/copyright                  |  1 +
 debian/patches/collections15-to-4 | 11 +++++++++++
 debian/patches/series             |  1 +
 debian/rules                      |  2 +-
 4 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/debian/copyright b/debian/copyright
index 4827b78..7bf4fd3 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,6 +4,7 @@ Source: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
 Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  util/support_scripts/*.jar
  Butterfly/Butterfly.jar
+ Butterfly/jar-in-jar-loader.zip
  Butterfly/src/lib/*.jar
  Butterfly/src/src/jaligner
  Butterfly/prev_vers
diff --git a/debian/patches/collections15-to-4 b/debian/patches/collections15-to-4
new file mode 100644
index 0000000..43a4ead
--- /dev/null
+++ b/debian/patches/collections15-to-4
@@ -0,0 +1,11 @@
+--- a/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
++++ b/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
+@@ -97,7 +97,7 @@
+ 				{
+ 					if (!w.equals(verToExclude) && !sd.distances.containsKey(w))
+ 					{
+-						double edge_weight = nev.transform(e).doubleValue();
++						double edge_weight = ((Number) nev.transform(e)).doubleValue();
+ 						if (edge_weight < 0)
+ 							throw new IllegalArgumentException("Edges weights must be non-negative");
+ 						double new_dist = v_dist + edge_weight;
diff --git a/debian/patches/series b/debian/patches/series
index c8d6b30..26aa8b3 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ chrysalis-make-tweak
 noExitTester
 jellyfish-path
 update-paths
+collections15-to-4
diff --git a/debian/rules b/debian/rules
index e7b6547..394c18d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,7 +3,7 @@
 DH_VERBOSE := 1
 
 JDIR=/usr/share/java
-export CLASSPATH=${JDIR}/collections15.jar:${JDIR}/gnu-getopt.jar:${JDIR}/jung-algorithms.jar:${JDIR}/jung-api.jar:${JDIR}/jung-graph-impl.jar:${JDIR}/jaligner.jar
+export CLASSPATH=${JDIR}/commons-collections4.jar:${JDIR}/gnu-getopt.jar:${JDIR}/jung-algorithms.jar:${JDIR}/jung-api.jar:${JDIR}/jung-graph-impl.jar:${JDIR}/jaligner.jar
 export JAVA_HOME=/usr/lib/jvm/default-java
 SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust
 BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq

-- 
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