[med-svn] [Git][med-team/libgoby-java][master] 3 commits: Omitting a test that fails randomly, depending on some random variable

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / libgoby-java


Commits:
6146e554 by Pierre Gruet at 2021-11-28T15:53:46+01:00
Omitting a test that fails randomly, depending on some random variable

- - - - -
b5bfdff2 by Pierre Gruet at 2021-11-29T20:21:28+01:00
Adding jaxb-api.jar in the manifest of goby-distribution.jar and adding libjaxb-api-java as an explicit dependency of goby-java

- - - - -
0e83da0e by Pierre Gruet at 2021-11-29T21:36:18+01:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/goby-java.manifest
- + debian/patches/omit_test_failing_randomly.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libgoby-java (3.3.1+dfsg2-5) unstable; urgency=medium
+
+  * Adding jaxb-api.jar in the manifest of goby-distribution.jar and putting
+    libjaxb-api-java as an explicit dependency of goby-java
+  * Omitting a test that fails depending on the output of a random number
+    generator.
+
+ -- Pierre Gruet <pgt at debian.org>  Mon, 29 Nov 2021 20:21:31 +0100
+
 libgoby-java (3.3.1+dfsg2-4) unstable; urgency=medium
 
   * Adding missing dependency libjaxb-api-java, both in d/control and in


=====================================
debian/control
=====================================
@@ -79,6 +79,7 @@ Depends: ${shlibs:Depends},
          default-jre,
          libgoby-io-java (= ${binary:Version}),
          libdistlib-java,
+         libjaxb-api-java,
          r-cran-rjava
 Recommends: ${java:Recommends},
             ${maven:OptionalDepends}


=====================================
debian/goby-java.manifest
=====================================
@@ -1,3 +1,3 @@
 usr/share/java/goby-distribution.jar:
- 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
+ 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/jaxb-api.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
  Main-Class: org.campagnelab.goby.modes.GobyDriver


=====================================
debian/patches/omit_test_failing_randomly.patch
=====================================
@@ -0,0 +1,16 @@
+Description: omit a test that fails randomly, as QualityTestFilter uses the
+ output of a random number generator
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: https://github.com/CampagneLaboratory/goby3/issues/11
+Last-Update: 2021-11-28
+
+--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java
++++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java
+@@ -322,6 +322,7 @@
+ 
+     }
+ 
++    @Ignore("Failing randomly as qualityScoreFilter uses a random variable")
+     @Test
+     public void testRemoveThresholdingEffectArtifact() {
+         QualityScoreFilter qualityScoreFilter = new QualityScoreFilter();


=====================================
debian/patches/series
=====================================
@@ -13,3 +13,4 @@ goby_script.patch
 path_of_goby_jar_for_Debian.patch
 jaxb_dependency.patch
 using_pcre2.patch
+omit_test_failing_randomly.patch



View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/040ffd43d6c5d6a95b7c6744f9fb3195a8e4bc7f...0e83da0e18fab74290dfcdb87c13be53a4ffada0

-- 
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/040ffd43d6c5d6a95b7c6744f9fb3195a8e4bc7f...0e83da0e18fab74290dfcdb87c13be53a4ffada0
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