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Re: Build time test failures for latest version of picard-tools

Hi Andreas,

Le 27/01/2021 à 21:46, Andreas Tille a écrit :

Hi,

I've tried to upgrade picard-tools in Git.  Unfortunately (and
admittedly not unexpected) the build time tests are failing:

...
Running Test: Test method testForVcf(picard.vcf.processor.WidthLimitingDecoratorTest)
Gradle Test Executor 1 finished executing tests.
Results: FAILURE (4972 tests, 4970 successes, 2 failures, 0 skipped)

4972 tests completed, 2 failed
Finished generating test XML results (0.188 secs) into: /build/picard-tools-2.24.1+dfsg/build/test-results/test
Generating HTML test report...
Finished generating test html results (0.191 secs) into: /build/picard-tools-2.24.1+dfsg/build/reports/tests/test
:test FAILED
:test (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 7 mins 33.86 secs.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':test'.

There were failing tests. See the report at: file:///build/picard-tools-2.24.1+dfsg/build/reports/tests/test/index.html


* Try:
Run with --debug option to get more log output. Run with --scan to get full insights.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':test'.
         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
         at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51)
         at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:62)
         at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
         at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60)
         at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97)
         at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87)
         at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
         at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
         at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
         at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
         at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
         at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
         at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
         at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
         at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123)
         at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79)
         at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104)
         at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98)
         at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626)
         at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581)
         at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98)
         at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
         at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
         at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: org.gradle.api.GradleException: There were failing tests. See the report at: file:///build/picard-tools-2.24.1+dfsg/build/reports/tests/test/index.html
         at org.gradle.api.tasks.testing.AbstractTestTask.handleTestFailures(AbstractTestTask.java:547)
         at org.gradle.api.tasks.testing.AbstractTestTask.executeTests(AbstractTestTask.java:464)
         at org.gradle.api.tasks.testing.Test.executeTests(Test.java:530)
         at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
         at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
         at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:46)
         at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39)
         at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26)
         at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:780)
         at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:747)
         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:121)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110)
         at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
         ... 29 more


* Get more help at https://help.gradle.org

BUILD FAILED in 7m 44s
5 actionable tasks: 3 executed, 2 up-to-date


Any hint / commit how to fix this is welcome.


Two tests are failing:

1. BuildBamIndexTest.testBuildBamIndexOK fails because of
java.io.FileNotFoundException: File 'testdata/picard/indices/index_test_b.bam.bai' does not exist
This file is indeed deleted during the build as shown by running "git status" afterwards, I don't know why. If you can save it from deletion then the test should run, else this test could be ignored by replacing its annotation 
	@Test
with
	@Test(enabled = false)
2. IntervalListToolsTest.testActionsWithDontMergeAbutting fails because its data provider does not provide it with the right types. For the second argument, long is expected but int is provided. I have committed a patch to Salsa, I tested it and it works. You will see in its header that I have already forwarded it as a Github issue. 



Kind regards

       Andreas.




Best regards,
Pierre
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