[Debian-med-packaging] Bug#905706: Bug#905706: libpicard-java-doc: ships /usr/share/javascript/jquery/jquery.min.js

Tue Sep 18 12:48:47 BST 2018


On 09/18/2018 12:12 PM, Andreas Tille wrote:
> Hi Olivier,
>
> the build failure changed after your changes but it does not build here
> in a clean and up to date pbuilder chroot (with htsjdk from unstable,
> not your new version):
strange, unless linked to htsjdk version... I gonna have a look.
Everything built nicely on my computer
>
>
> * 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 ':compileJava'.
>         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.internal.tasks.compile.CompilationFailedException: Compilation failed; see the compiler error output for details.
>         at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:50)
>         at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:35)
>         at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:98)
>         at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:51)
>         at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:37)
>         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:207)
>         at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:192)
>         at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:124)
>         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.IncrementalTaskAction.doExecute(IncrementalTaskAction.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.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 14s
> 1 actionable task: 1 executed
>
>
> I remain clueless here as well.
>
> Thanks for your work anyway
>
>        Andreas.
>
>
> On Tue, Sep 18, 2018 at 10:38:31AM +0200, Olivier Sallou wrote:
>>
>> On 09/18/2018 10:02 AM, Olivier Sallou wrote:
>>> On 09/17/2018 04:36 PM, Andreas Tille wrote:
>>>> Control: tags -1 pending
>>>>
>>>> This issue should be fixed in
>>>>    https://salsa.debian.org/med-team/picard-tools/commit/4da851972983cee93a3cce27bfbb40f9648dcc3d
>>>>
>>>>
>>>> While fixing the bug I also tried to upgrade the package to the latest upstream
>>>> version.  Unfortunately this failed with:
>>>>
>>>>
>>>> Compiling build file '/build/picard-tools-2.18.14+dfsg/build.gradle' using BuildScriptTransformer.
>>>>         Adding Maven pom generation to project 'picard'
>>>>         Linking the generated javadoc to the system JDK API documentation
>>>>
>>>> FAILURE: Build failed with an exception.
>>>>
>>>> * Where:
>>>> Build file '/build/picard-tools-2.18.14+dfsg/build.gradle' line: 53
>> I have fixed the build issue, and pushed updates in git.
>> build was tested against latest htsjdk 2.16.1 (not yet pushed to sid)
>>>> * What went wrong:
>>>> A problem occurred evaluating root project 'picard'.
>>>>> The ClassLoader obtained from the Java ToolProvider is null. A Java 8 JDK must be installed. See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard
>>> I fixed the issue and could compile, however there is one test failing
>>> for the moment.
>>> I gonna investiguate and push my updates afterwards.
>>>
>>> Olivier
>>>> * Try:
>>>> Run with --debug option to get more log output.
>>>>
>>>> * Exception is:
>>>> org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'picard'.
>>>>         at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92)
>>>>         at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)
>>>>         at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)
>>>>         at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)
>>>>         at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:39)
>>>>         at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
>>>>         at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
>>>>         at org.gradle.configuration.project.LifecycleProjectEvaluator.doConfigure(LifecycleProjectEvaluator.java:70)
>>>>         at org.gradle.configuration.project.LifecycleProjectEvaluator.access$000(LifecycleProjectEvaluator.java:33)
>>>>         at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:53)
>>>>         at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:50)
>>>>         at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
>>>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
>>>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:61)
>>>>         at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:50)
>>>>         at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:599)
>>>>         at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:125)
>>>>         at org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:35)
>>>>         at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:60)
>>>>         at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38)
>>>>         at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:233)
>>>>         at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:230)
>>>>         at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
>>>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
>>>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:56)
>>>>         at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:160)
>>>>         at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:119)
>>>>         at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:102)
>>>>         at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:71)
>>>>         at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
>>>>         at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
>>>>         at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:41)
>>>>         at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:26)
>>>>         at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:75)
>>>>         at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:49)
>>>>         at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:49)
>>>>         at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:31)
>>>>         at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67)
>>>>         at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:47)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
>>>>         at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
>>>>         at org.gradle.util.Swapper.swap(Swapper.java:38)
>>>>         at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:60)
>>>>         at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:72)
>>>>         at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
>>>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>>>         at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
>>>>         at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:297)
>>>>         at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>>>>         at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:46)
>>>> Caused by: org.gradle.api.GradleException: The ClassLoader obtained from the Java ToolProvider is null. A Java 8 JDK must be installed. See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard
>>>>         at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>>>         at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>>>         at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>>>         at build_e2g2wljk0xfne1q452c0qhi2d.ensureBuildPrerequisites(/build/picard-tools-2.18.14+dfsg/build.gradle:53)
>>>>         at build_e2g2wljk0xfne1q452c0qhi2d$ensureBuildPrerequisites.callCurrent(Unknown Source)
>>>>         at build_e2g2wljk0xfne1q452c0qhi2d.run(/build/picard-tools-2.18.14+dfsg/build.gradle:61)
>>>>         at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)
>>>>         ... 62 more
>>>>
>>>>
>>>> BUILD FAILED
>>>>
>>>> Total time: 6.725 secs
>>>>
>>>>
>>>>
>>>> Could any of the more skilled Java developers of the team please have a look?
>>>>
>>>> Kind regards
>>>>
>>>>      Andreas.
>>>>
>> -- 
>> Olivier Sallou
>> Univ Rennes, Inria, CNRS, IRISA
>> Irisa, Campus de Beaulieu
>> F-35042 RENNES - FRANCE
>> Tel: 02.99.84.71.95
>>
>> gpg key id: 4096R/326D8438  (keyring.debian.org)
>> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
>>
>>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438