[med-svn] [Git][med-team/htsjdk][master] 3 commits: use scala-library 2.11 (2.12 not in debian)
Olivier Sallou
gitlab at salsa.debian.org
Fri Jan 25 08:14:43 GMT 2019
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 <tille at debian.org> 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 <osallou at debian.org>
+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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190125/8d027dab/attachment-0001.html>
More information about the debian-med-commit
mailing list