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

[Andreas Tille]

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)