[med-svn] [Git][med-team/trinityrnaseq][master] 2 commits: using apply() instead of transform() for various fields inside classes of libjung-free-java

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / trinityrnaseq


Commits:
16264edb by Pierre Gruet at 2021-11-15T20:56:50+01:00
using apply() instead of transform() for various fields inside classes of libjung-free-java

- - - - -
bba1be80 by Pierre Gruet at 2021-11-15T23:11:10+01:00
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/extending_Function_in_jung.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+trinityrnaseq (2.13.2+dfsg-3) unstable; urgency=medium
+
+  * Team upload
+  * Applying a new patch to build against newest libjung-free-java, adding a
+    versioned dependency
+
+ -- Pierre Gruet <pgt at debian.org>  Mon, 15 Nov 2021 21:52:59 +0100
+
 trinityrnaseq (2.13.2+dfsg-2) unstable; urgency=medium
 
   * debian/javabuild: updated to correct path to the Butterfly source


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                jellyfish,
-               libjung-free-java,
+               libjung-free-java (>= 2.1.1-1),
                javahelper,
                libgetopt-java,
                default-jdk,


=====================================
debian/patches/extending_Function_in_jung.patch
=====================================
@@ -0,0 +1,37 @@
+Description: various fields in libjung-free-java have a type that now extends
+ Function, so that they use apply() instead of transform().
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2021-11-15
+
+--- a/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
++++ b/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java
+@@ -9211,7 +9211,7 @@
+ 		HashMap<List<Integer>, Integer> gene_grouping = new HashMap<List<Integer>, Integer>();
+ 		
+ 		WeakComponentClusterer<List<Integer>, String> compClus = new WeakComponentClusterer<List<Integer>,String>();
+-		Set<Set<List<Integer>>> comps = compClus.transform(sparseGraph);
++		Set<Set<List<Integer>>> comps = compClus.apply(sparseGraph);
+ 		
+ 		debugMes("IsoformClustering, number of clusters = " + comps.size(), 10);
+ 		
+@@ -13378,7 +13378,7 @@
+ 	{
+ 
+ 		WeakComponentClusterer<SeqVertex, SimpleEdge> compClus = new WeakComponentClusterer<SeqVertex, SimpleEdge>();
+-		Set<Set<SeqVertex>> comps = compClus.transform(graph);
++		Set<Set<SeqVertex>> comps = compClus.apply(graph);
+ 		
+ 		int comp_counter = 0;
+ 		for (Set<SeqVertex> s : comps) {
+--- a/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java
++++ b/Butterfly/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 = ((Number) nev.transform(e)).doubleValue();
++						double edge_weight = ((Number) nev.apply(e)).doubleValue();
+ 						if (edge_weight < 0)
+ 							throw new IllegalArgumentException("Edges weights must be non-negative");
+ 						double new_dist = v_dist + edge_weight;


=====================================
debian/patches/series
=====================================
@@ -17,3 +17,4 @@ skip_blat
 fix-gcc-10.patch
 bamsifter_build
 strip_m64
+extending_Function_in_jung.patch



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/45515ca9019bb7722044c6f808c73deb642686e2...bba1be801a474037e1e4a05b1681b60f317c7506

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/45515ca9019bb7722044c6f808c73deb642686e2...bba1be801a474037e1e4a05b1681b60f317c7506
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