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