[med-svn] [Git][med-team/picard-tools][master] Update patches

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / picard-tools


Commits:
c29ce28b by Andreas Tille at 2018-12-01T09:15:51Z
Update patches

- - - - -


1 changed file:

- debian/patches/40-tests-fix-testng.patch


Changes:

=====================================
debian/patches/40-tests-fix-testng.patch
=====================================
@@ -7,7 +7,7 @@ Description: Fix testng version and disable some tests.
  This patch disable some tests around this
 --- a/build.gradle
 +++ b/build.gradle
-@@ -74,9 +74,6 @@
+@@ -74,9 +74,6 @@ final googleNio = 'org.broadinstitute:go
  configurations {
      cloudConfiguration {
          extendsFrom runtime
@@ -17,7 +17,7 @@ Description: Fix testng version and disable some tests.
      }
  }
  
-@@ -88,14 +85,13 @@
+@@ -88,14 +85,13 @@ dependencies {
      compile 'org.apache.commons:commons-math3:3.5'
      compile 'com.github.samtools:htsjdk:' + htsjdkVersion
      compile 'org.broadinstitute:barclay:2.0.0'
@@ -34,7 +34,7 @@ Description: Fix testng version and disable some tests.
  }
  
  configurations.all {
-@@ -234,6 +230,7 @@
+@@ -233,6 +229,7 @@ shadowJar {
  }
  */
  
@@ -42,7 +42,7 @@ Description: Fix testng version and disable some tests.
  task cloudJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar)  {
      configurations = [project.configurations.cloudConfiguration]
      from project.sourceSets.main.output
-@@ -258,6 +255,7 @@
+@@ -257,6 +254,7 @@ task barclayShadowJar(type: com.github.j
      }
      archiveName 'picardBarclay.jar'
  }
@@ -50,7 +50,7 @@ Description: Fix testng version and disable some tests.
  
  // Run the tests using the legacy parser only. Assumes that test code is written using
  // legacy command line parser syntax.
-@@ -268,6 +266,8 @@
+@@ -267,6 +265,8 @@ task legacyTest(type: Test)
  task barclayTest(type: Test) {
      systemProperty 'picard.convertCommandLine', 'true'
      systemProperty 'picard.useLegacyParser', 'false'
@@ -59,7 +59,7 @@ Description: Fix testng version and disable some tests.
  }
  
  // Run tests using both the legacy and barclay command line parsers.
-@@ -279,6 +279,9 @@
+@@ -278,6 +278,9 @@ tasks.withType(Test) {
      outputs.upToDateWhen { false } // tests will always rerun
      description = "Runs the unit tests"
  
@@ -71,7 +71,7 @@ Description: Fix testng version and disable some tests.
              excludeGroups "slow", "broken"
 --- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
 +++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
-@@ -41,51 +41,6 @@
+@@ -41,51 +41,6 @@ public class CollectHsMetricsTest extend
          };
      }
  
@@ -123,7 +123,7 @@ Description: Fix testng version and disable some tests.
  
      @Test
      public void testCoverageHistogram() throws IOException {
-@@ -106,7 +61,7 @@
+@@ -106,7 +61,7 @@ public class CollectHsMetricsTest extend
          final boolean clipOverlappingReads = true;
          final int sampleSize = 10;
  
@@ -134,7 +134,7 @@ Description: Fix testng version and disable some tests.
          final String[] args = new String[] {
 --- a/src/test/java/picard/analysis/artifacts/TransitionTest.java
 +++ b/src/test/java/picard/analysis/artifacts/TransitionTest.java
-@@ -34,13 +34,4 @@
+@@ -34,13 +34,4 @@ public class TransitionTest {
          return new Object[][] {{Character.MIN_VALUE}, {Transition.Base.A.base - 1}, {'Z'}, {Character.MAX_VALUE}};
      }
  
@@ -150,7 +150,7 @@ Description: Fix testng version and disable some tests.
  }
 --- a/src/test/java/picard/util/IntervalListToolsTest.java
 +++ b/src/test/java/picard/util/IntervalListToolsTest.java
-@@ -80,12 +80,6 @@
+@@ -105,12 +105,6 @@ public class IntervalListToolsTest exten
          };
      }
  
@@ -165,7 +165,7 @@ Description: Fix testng version and disable some tests.
      public Object[][] actionAndTotalBasesWithInvertData() {
 --- a/src/test/java/picard/analysis/TheoreticalSensitivityTest.java
 +++ b/src/test/java/picard/analysis/TheoreticalSensitivityTest.java
-@@ -351,10 +351,11 @@
+@@ -351,10 +351,11 @@ public class TheoreticalSensitivityTest
          };
      }
  



View it on GitLab: https://salsa.debian.org/med-team/picard-tools/commit/c29ce28b0c83184c89a587967558f5f642761724

-- 
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/commit/c29ce28b0c83184c89a587967558f5f642761724
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