Olivier Sallou pushed to branch master at Debian Med / htsjdk
Commits: 53597888 by Olivier Sallou at 2019-01-25T08:00:14Z use scala-library 2.11 (2.12 not in debian) - - - - - f8b2102c by Olivier Sallou at 2019-01-25T08:09:20Z remove test failing due to testng version with reflection data provider issues - - - - - fc6971e5 by Olivier Sallou at 2019-01-25T08:14:36Z fix lint warn - - - - - 4 changed files: - debian/changelog - + debian/patches/110-debian-lib-version.patch - debian/patches/70-removesometests-testng.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,11 +1,15 @@ htsjdk (2.18.2+dfsg-1) UNRELEASED; urgency=medium - TODO: Fix or drop failing tests * New upstream version * debhelper 12 * Standards-Version: 4.3.0 * Remove trailing whitespace in debian/changelog + [ Olivier Sallou ] + * d/p/110-debian-lib-version.patch: use scala-library 2.11, + v2.12 not yet in Debian + * fix some reflection tests issues with testng + -- Andreas Tille <[email protected]> Thu, 24 Jan 2019 17:31:54 +0100 htsjdk (2.16.1+dfsg-3) unstable; urgency=medium ===================================== debian/patches/110-debian-lib-version.patch ===================================== @@ -0,0 +1,16 @@ +Subject: use debian available library version +Description: scala-library 2.12 not yet in debian, use 2.11 +Author: Olivier Sallou <[email protected]> +Forwarded: no +Last-Updated: 2019-01-25 +--- a/build.gradle ++++ b/build.gradle +@@ -24,7 +24,7 @@ + compile "gov.nih.nlm.ncbi:ngs-java:2.9.0" + compile "javax.xml.bind:jaxb-api:debian" + +- testCompile "org.scala-lang:scala-library:2.12.x" ++ testCompile "org.scala-lang:scala-library:2.11.x" + //testCompile "org.scalatest:scalatest_2.12:3.0.5" + //testRuntime 'org.pegdown:pegdown:1.6.0' // Necessary for generating HTML reports with ScalaTest + testCompile "org.testng:testng:debian" ===================================== debian/patches/70-removesometests-testng.patch ===================================== @@ -27,7 +27,7 @@ Last-Updated: 2018-02-19 params.add(new Object[]{-1L, format, stringency}); --- a/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java +++ b/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java -@@ -115,10 +115,10 @@ +@@ -132,10 +132,10 @@ intervalList_unmapped.add(interval); return new Object[][]{ @@ -92,3 +92,27 @@ Last-Updated: 2018-02-19 -} \ No newline at end of file +} +--- a/src/test/java/htsjdk/samtools/cram/io/LTF8Test.java ++++ b/src/test/java/htsjdk/samtools/cram/io/LTF8Test.java +@@ -52,21 +52,6 @@ + }; + } + +- @Test(dataProvider = "predefined") +- public void testPredefined (long value, byte[] ltf8) throws IOException { +- try (ByteArrayOutputStream ltf8TestBAOS = new ByteArrayOutputStream()) { +- final int len = LTF8.writeUnsignedLTF8(value, ltf8TestBAOS); +- Assert.assertTrue(len <= LTF8.MAX_BITS); +- +- byte[] actualArray = ltf8TestBAOS.toByteArray(); +- Assert.assertEquals(ltf8, actualArray); +- +- try (ByteArrayInputStream ltf8TestBAIS = new ByteArrayInputStream(actualArray)) { +- final long actual = LTF8.readUnsignedLTF8(ltf8TestBAIS); +- Assert.assertEquals(actual, value); +- } +- } +- } + + @Test(expectedExceptions = RuntimeEOFException.class) + public void emptyStreamTest() throws IOException { ===================================== debian/patches/series ===================================== @@ -10,3 +10,4 @@ 90-disable-testftp.patch 92-disable-testhttp.patch 100-fix-java11 +110-debian-lib-version.patch View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/3b36bbcfc8c0e131f5292530a2da483803aa9b88...fc6971e58f3c0844ad23093039fee81b1eb0af64 -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/compare/3b36bbcfc8c0e131f5292530a2da483803aa9b88...fc6971e58f3c0844ad23093039fee81b1eb0af64 You're receiving this email because of your account on salsa.debian.org.
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