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

Tue Sep 18 09:02:09 BST 2018


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
>
> * 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