Re: Again help needed to upgrade picard-tools

[Sascha Steinbiss <satta@debian.org>]

Hi all,

> seems I always have trouble with picard-tools.  I have injected new
> upstream version in Git but it fails to build.  The upgrade of
> libhtsjdk-java went fine but it would be great if somebody could have a
> look at picard-tools.

Something in the build system changed; I patched it slightly to work again.
Builds now with libhtsjdk-java 2.6, but one test fails at the moment:

Gradle Test Executor 1 finished executing tests.
Results: FAILURE (1833 tests, 1832 successes, 1 failures, 0 skipped)

Here’s the output from the test’s HTML report:

org.testng.internal.reflect.MethodMatcherException: 
Data provider mismatch
Method: runCollectTargetedMetricsTest([Parameter{index=0, type=java.lang.String, declaredAnnotations=[]}, Parameter{index=1, type=java.lang.String, declaredAnnotations=[]}, Parameter{index=2, type=java.lang.String, declaredAnnotations=[]}, Parameter{index=3, type=java.lang.String, declaredAnnotations=[]}, Parameter{index=4, type=int, declaredAnnotations=[]}, Parameter{index=5, type=int, declaredAnnotations=[]}, Parameter{index=6, type=boolean, declaredAnnotations=[]}, Parameter{index=7, type=int, declaredAnnotations=[]}, Parameter{index=8, type=int, declaredAnnotations=[]}, Parameter{index=9, type=double, declaredAnnotations=[]}, Parameter{index=10, type=double, declaredAnnotations=[]}, Parameter{index=11, type=double, declaredAnnotations=[]}, Parameter{index=12, type=double, declaredAnnotations=[]}, Parameter{index=13, type=int, declaredAnnotations=[]}])
Arguments: [(java.lang.String)testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam,(java.lang.String)testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta,(java.lang.String)testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list,(java.lang.String)NONE,(java.lang.Integer)2,(java.lang.Integer)0,(java.lang.Boolean)true,(java.lang.Integer)2,(java.lang.Integer)202,(java.lang.Integer)0,(java.lang.Double)0.0,(java.lang.Double)0.505,(java.lang.Double)0.0,(java.lang.Integer)1000]
	at org.testng.internal.reflect.DataProviderMethodMatcher.getConformingArguments(DataProviderMethodMatcher.java:52)
	at org.testng.internal.Invoker.injectParameters(Invoker.java:1225)
	at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1123)
	at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129)
	at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
	at org.testng.TestRunner.privateRun(TestRunner.java:746)
	at org.testng.TestRunner.run(TestRunner.java:600)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:366)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319)
	at org.testng.SuiteRunner.run(SuiteRunner.java:268)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1189)
	at org.testng.TestNG.runSuites(TestNG.java:1104)
	at org.testng.TestNG.run(TestNG.java:1076)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:133)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:83)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
	at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.messaging.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
	at org.gradle.messaging.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
	at com.sun.proxy.$Proxy2.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:120)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
	at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.messaging.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:364)
	at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
	at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Any ideas from someone with more detailed insight?

Cheers
Sascha