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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/libgoby-java">Debian Med / libgoby-java</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/6146e554c346eece72624bcb1846f5defd0c39ff">6146e554</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-11-28T15:53:46+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Omitting a test that fails randomly, depending on some random variable
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<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/b5bfdff2dcdf96d260de5a8b51384590f876060b">b5bfdff2</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-11-29T20:21:28+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding jaxb-api.jar in the manifest of goby-distribution.jar and adding libjaxb-api-java as an explicit dependency of goby-java
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<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/0e83da0e18fab74290dfcdb87c13be53a4ffada0">0e83da0e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-11-29T21:36:18+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>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#0381ec0c3b0200674f7b457844cf110b4aa8d66b">
debian/goby-java.manifest
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<li class="file-stats">
<a href="#0757b2cc925b7236ab0a7b9793e90a7587a6237a">
<span class="new-file">
+
debian/patches/omit_test_failing_randomly.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/libgoby-java/-/compare/040ffd43d6c5d6a95b7c6744f9fb3195a8e4bc7f...0e83da0e18fab74290dfcdb87c13be53a4ffada0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libgoby-java (3.3.1+dfsg2-5) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Adding jaxb-api.jar in the manifest of goby-distribution.jar and putting</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> libjaxb-api-java as an explicit dependency of goby-java</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Omitting a test that fails depending on the output of a random number</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> generator.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> Mon, 29 Nov 2021 20:21:31 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">libgoby-java (3.3.1+dfsg2-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Adding missing dependency libjaxb-api-java, both in d/control and in</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/040ffd43d6c5d6a95b7c6744f9fb3195a8e4bc7f...0e83da0e18fab74290dfcdb87c13be53a4ffada0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" 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="diff-line-num unfold js-unfold new_line" data-linenumber="79" 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">@@ -79,6 +79,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> default-jre,</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> libgoby-io-java (= ${binary:Version}),</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> libdistlib-java,</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> libjaxb-api-java,</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> r-cran-rjava</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">Recommends: ${java:Recommends},</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> ${maven:OptionalDepends}</span>
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<li id="0381ec0c3b0200674f7b457844cf110b4aa8d66b">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/040ffd43d6c5d6a95b7c6744f9fb3195a8e4bc7f...0e83da0e18fab74290dfcdb87c13be53a4ffada0#0381ec0c3b0200674f7b457844cf110b4aa8d66b"><strong>debian/goby-java.manifest</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">usr/share/java/goby-distribution.jar:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/goby-io.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar /usr/share/java/distlib.jar</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/goby-io.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar <span class="idiff left right">/usr/share/java/jaxb-api.jar </span>/usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar /usr/share/java/distlib.jar</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Main-Class: org.campagnelab.goby.modes.GobyDriver</span></pre>
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<li id="0757b2cc925b7236ab0a7b9793e90a7587a6237a">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/040ffd43d6c5d6a95b7c6744f9fb3195a8e4bc7f...0e83da0e18fab74290dfcdb87c13be53a4ffada0#0757b2cc925b7236ab0a7b9793e90a7587a6237a"><strong>debian/patches/omit_test_failing_randomly.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: omit a test that fails randomly, as QualityTestFilter uses the</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> output of a random number generator</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: https://github.com/CampagneLaboratory/goby3/issues/11</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-11-28</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/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.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/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -322,6 +322,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </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"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore("Failing randomly as qualityScoreFilter uses a random variable")</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> public void testRemoveThresholdingEffectArtifact() {</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> QualityScoreFilter qualityScoreFilter = new QualityScoreFilter();</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/040ffd43d6c5d6a95b7c6744f9fb3195a8e4bc7f...0e83da0e18fab74290dfcdb87c13be53a4ffada0#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">@@ -13,3 +13,4 @@ goby_script.patch</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">path_of_goby_jar_for_Debian.patch</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">jaxb_dependency.patch</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">using_pcre2.patch</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">omit_test_failing_randomly.patch</span></pre>
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