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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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