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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/trinityrnaseq">Debian Med / trinityrnaseq</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/16264edb61d6733fe009f5cda9f6f2ee08d3e2cf">16264edb</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-15T20:56:50+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">using apply() instead of transform() for various fields inside classes of libjung-free-java
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<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/bba1be801a474037e1e4a05b1681b60f317c7506">bba1be80</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-15T23:11:10+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#d56039476f9a7b5429adf8679be097e5c3658cbd">
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+
debian/patches/extending_Function_in_jung.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/45515ca9019bb7722044c6f808c73deb642686e2...bba1be801a474037e1e4a05b1681b60f317c7506#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.13.2+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Applying a new patch to build against newest libjung-free-java, adding a</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> versioned dependency</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> Mon, 15 Nov 2021 21:52:59 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">trinityrnaseq (2.13.2+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * debian/javabuild: updated to correct path to the Butterfly source</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/45515ca9019bb7722044c6f808c73deb642686e2...bba1be801a474037e1e4a05b1681b60f317c7506#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> jellyfish,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> libjung-free-java,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> libjung-free-java<span class="idiff left right"> (>= 2.1.1-1)</span>,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> javahelper,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libgetopt-java,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> default-jdk,</span>
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<li id="d56039476f9a7b5429adf8679be097e5c3658cbd">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/45515ca9019bb7722044c6f808c73deb642686e2...bba1be801a474037e1e4a05b1681b60f317c7506#d56039476f9a7b5429adf8679be097e5c3658cbd"><strong>debian/patches/extending_Function_in_jung.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: various fields in libjung-free-java have a type that now extends</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Function, so that they use apply() instead of transform().</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-11-15</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Butterfly/Butterfly/src/src/TransAssembly_allProbPaths.java</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -9211,7 +9211,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> HashMap<List<Integer>, Integer> gene_grouping = new HashMap<List<Integer>, Integer>();</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> WeakComponentClusterer<List<Integer>, String> compClus = new WeakComponentClusterer<List<Integer>,String>();</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Set<Set<List<Integer>>> comps = compClus.transform(sparseGraph);</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Set<Set<List<Integer>>> comps = compClus.apply(sparseGraph);</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> debugMes("IsoformClustering, number of clusters = " + comps.size(), 10);</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -13378,7 +13378,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> WeakComponentClusterer<SeqVertex, SimpleEdge> compClus = new WeakComponentClusterer<SeqVertex, SimpleEdge>();</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Set<Set<SeqVertex>> comps = compClus.transform(graph);</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Set<Set<SeqVertex>> comps = compClus.apply(graph);</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> int comp_counter = 0;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> for (Set<SeqVertex> s : comps) {</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Butterfly/Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -97,7 +97,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> if (!w.equals(verToExclude) && !sd.distances.containsKey(w))</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- double edge_weight = ((Number) nev.transform(e)).doubleValue();</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double edge_weight = ((Number) nev.apply(e)).doubleValue();</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> if (edge_weight < 0)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> throw new IllegalArgumentException("Edges weights must be non-negative");</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> double new_dist = v_dist + edge_weight;</span></pre>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/45515ca9019bb7722044c6f808c73deb642686e2...bba1be801a474037e1e4a05b1681b60f317c7506#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,3 +17,4 @@ skip_blat</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">fix-gcc-10.patch</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">bamsifter_build</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">strip_m64</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">extending_Function_in_jung.patch</span></pre>
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