[Debian-med-packaging] Bug#847736: src:htsjdk: New upstream version available

[olivier sallou]

I will gave a look, but looks gradle related (build system),  and i am not
familiar with this system.

Olivier

Le dim. 11 déc. 2016 09:03, Andreas Tille <tille at debian.org> a écrit :

> Package: src:htsjdk
> Severity: normal
>
> Hi,
>
> I have injected version 2.8.1+dfsg and tried to build in pbuilder but
> there are remaining errors where I have no idea how to deal with:
>
> * Exception is:
> org.gradle.api.tasks.TaskExecutionException: Execution failed for task
> ':compileTestJava'.
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:69)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:46)
>         at
> org.gradle.api.internal.tasks.execution.PostExecutionAnalysisTaskExecuter.execute(PostExecutionAnalysisTaskExecuter.java:35)
>         at
> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:64)
>         at
> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>         at
> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.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:53)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:233)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:215)
>         at
> org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.processTask(AbstractTaskPlanExecutor.java:74)
>         at
> org.gradle.execution.taskgraph.AbstractTaskPlanExecutor$TaskExecutorWorker.run(AbstractTaskPlanExecutor.java:55)
>         at
> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
>         at
> org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
> Caused by:
> org.gradle.api.internal.tasks.compile.CompilationFailedException:
> Compilation failed; see the compiler error output for details.
>         at
> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:48)
>         at
> org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:33)
>         at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:104)
>         at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:53)
>         at
> org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:38)
>         at
> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:35)
>         at
> org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:25)
>         at
> org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:189)
>         at
> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:170)
>         at
> org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:113)
>         at
> org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:75)
>         at
> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$IncrementalTaskAction.doExecute(DefaultTaskClassInfoStore.java:158)
>         at
> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:129)
>         at
> org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.execute(DefaultTaskClassInfoStore.java:118)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:80)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:61)
>         ... 14 more
>
>
> BUILD FAILED
>
> It would be great if somebody would care.  I have also upgraded
> picard-tools in Git which should be uploaded as well.
>
> Kind regards
>
>         Andreas.
>
> -- System Information:
> Debian Release: 8.6
>   APT prefers stable-updates
>   APT policy: (500, 'stable-updates'), (500, 'stable')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
> Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
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