[Debian-med-packaging] Bug#961700: picard-tools build depends on the removed libguava-java-doc

[olivier sallou]

Le jeu. 28 mai 2020 à 13:00, Andreas Tille <tille at debian.org> a écrit :

> Hi Olivier and Vincent
>
> On Thu, May 28, 2020 at 09:47:37AM +0300, Adrian Bunk wrote:
> >
> > picard-tools build depends on libguava-java-doc,
> > which is no longer built by src:guava-libraries.
>

Hi andreas,
looking at issue, where did you find that libguava-java-doc is no longer
built ?
I looked at https://packages.debian.org/source/sid/guava-libraries and
still see -doc package

Olivier



>
> I've tried to simply leave out libguava-java-doc but either this breaks
> a test or the package is failing its build time test for some other
> reason:
>
>
> * Exception is:
> org.gradle.api.tasks.TaskExecutionException: Execution failed for task
> ':barclayTest'.
>         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-2.18.25+dfsg/build/reports/tests/barclayTest/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
>
>
> The actual test that fails is
> src/test/java/picard/sam/PipedDataTest.java (for whatever reason).
>
> We are lagging behind upstream anyway and I wonder whether you might
> find some time to update the package to the recent upstream version.  I
> would do so but from the past I've learned that this package always
> creates hassle I can't solve when trying to upgrade.  So any help would
> be really welcome here - specifically since I'm currently hunting behind
> so many other stuff that I'd love to avoid things where I've proven to
> be incompetent for.
>
> Kind regards
>
>       Andreas.
>
> --
> http://fam-tille.de
>


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