Commit c29ce28b authored by Andreas Tille's avatar Andreas Tille
Browse files

Update patches

parent 84f8db61

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

+11 −11
Original line number Diff line number Diff line
@@ -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

         };

     }