[Debian-med-packaging] Bug#961700: picard-tools build depends on the removed libguava-java-doc
Andreas Tille
tille at debian.org
Fri May 29 07:55:48 BST 2020
Hi Adrian,
I think this question is for you ...
Kind regards
Andreas.
On Fri, May 29, 2020 at 08:12:02AM +0200, olivier sallou wrote:
> 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
> >
>
>
> --
>
> gpg key id: 4096R/326D8438 (keyring.debian.org)
>
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
--
http://fam-tille.de
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