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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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BUILD FAILED: Javadoc generation failed #4155

Open avapirev opened 6 years ago

avapirev commented 6 years ago

System specs - (RedHat, Java 1.8.0_144) Clean git clone.

gradlew --stacktrace
Creating GATK Python package archive...
:createPythonPackageArchive UP-TO-DATE
:compileJava UP-TO-DATE
:processResources UP-TO-DATE
:classes UP-TO-DATE
:gatkTabComplete
error: error reading /vsc-hard-mounts/leuven-user/304/vsc30484/.gradle/caches/modules-2/files-2.1/org.spire-math/spire_2.11/0.11.0/998b1c1d841baf4fc5d1b119ea55f165f6684ef5/spire_2.11-0.11.0.jar; error in opening zip file
1 error
:gatkTabComplete FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':gatkTabComplete'.
> Javadoc generation failed. Generated Javadoc options file (useful for troubleshooting): '/vsc-hard-mounts/leuven-data/304/vsc30484/git/gatk/build/tmp/gatkTabComplete/javadoc.options'

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':gatkTabComplete'.
        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.execution.taskgraph.DefaultTaskPlanExecutor.process(DefaultTaskPlanExecutor.java:32)
        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter.execute(DefaultTaskGraphExecuter.java:113)
        at org.gradle.execution.SelectedTaskExecutionAction.execute(SelectedTaskExecutionAction.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.access$000(DefaultBuildExecuter.java:23)
        at org.gradle.execution.DefaultBuildExecuter$1.proceed(DefaultBuildExecuter.java:43)
        at org.gradle.execution.DryRunBuildExecutionAction.execute(DryRunBuildExecutionAction.java:32)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:37)
        at org.gradle.execution.DefaultBuildExecuter.execute(DefaultBuildExecuter.java:30)
        at org.gradle.initialization.DefaultGradleLauncher$4.run(DefaultGradleLauncher.java:186)
        at org.gradle.internal.Factories$1.create(Factories.java:22)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:53)
        at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:183)
        at org.gradle.initialization.DefaultGradleLauncher.access$200(DefaultGradleLauncher.java:33)
        at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:112)
        at org.gradle.initialization.DefaultGradleLauncher$1.create(DefaultGradleLauncher.java:106)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:91)
        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:63)
        at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:106)
        at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:92)
        at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:66)
        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:79)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:51)
        at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:59)
        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:55)
        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.HintGCAfterBuild.execute(HintGCAfterBuild.java:44)
        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$1.run(DaemonStateCoordinator.java:293)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:54)
        at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:40)
Caused by: org.gradle.api.GradleException: Javadoc generation failed. Generated Javadoc options file (useful for troubleshooting): '/vsc-hard-mounts/leuven-data/304/vsc30484/git/gatk/build/tmp/gatkTabComplete/javadoc.options'
        at org.gradle.api.tasks.javadoc.internal.JavadocGenerator.execute(JavadocGenerator.java:58)
        at org.gradle.api.tasks.javadoc.internal.JavadocGenerator.execute(JavadocGenerator.java:31)
        at org.gradle.api.tasks.javadoc.Javadoc.executeExternalJavadoc(Javadoc.java:152)
        at org.gradle.api.tasks.javadoc.Javadoc.generate(Javadoc.java:140)
        at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:75)
        at org.gradle.api.internal.project.taskfactory.DefaultTaskClassInfoStore$StandardTaskAction.doExecute(DefaultTaskClassInfoStore.java:136)
        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.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:623)
        at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:606)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:80)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:61)
        ... 68 more
Caused by: org.gradle.process.internal.ExecException: Process 'command '/vsc-hard-mounts/leuven-apps/thinking/2015a/software/Java/1.8.0_144/bin/javadoc'' finished with non-zero exit value 1
        at org.gradle.process.internal.DefaultExecHandle$ExecResultImpl.assertNormalExitValue(DefaultExecHandle.java:369)
        at org.gradle.process.internal.DefaultExecAction.execute(DefaultExecAction.java:31)
        at org.gradle.api.tasks.javadoc.internal.JavadocGenerator.execute(JavadocGenerator.java:53)
        ... 79 more

BUILD FAILED
jberghout commented 4 years ago

I'm encountering the same bug. Linux OS. Brand new GATK install from github (17 Dec 2019). Did you manage to figure anything out?

cmnbroad commented 4 years ago

@jberghout If you post your actual output we might be able to track down your variant of the problem (the error message in the original post looks to me somewhat like a corrupt gradle cache: error reading /vsc-hard-mounts/leuven-user/304/vsc30484/.gradle/caches/modules-2/files-2.1/org.spire-math/spire_2.11/0.11.0/998b1c1d841baf4fc5d1b119ea55f165f6684ef5/spire_2.11-0.11.0.jar; error in opening zip file). Is it the gatkTabComplete task that is failing for you as well ?

jberghout commented 4 years ago

The concise message is:

cb2@cb2-VirtualBox:~/gatk$ ./gradlew bundle
> Configure project :
Executing: git lfs pull --include src/main/resources/large

> Task :condaStandardEnvironmentDefinition
Created standard Conda environment yml file: gatkcondaenv.yml

> Task :pythonPackageArchive
Created GATK Python package archive in /home/cb2/gatk/build/gatkPythonPackageArchive.zip

> Task :gatkDoc FAILED
Unable to find the 'javadoc' executable. Tried the java home: /usr/lib/jvm/java-11-openjdk-amd64 and the PATH. We will assume the executable can be ran in the current working folder.

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':gatkDoc'.
> Javadoc generation failed. Generated Javadoc options file (useful for troubleshooting): '/home/cb2/gatk/build/tmp/gatkDoc/javadoc.options'

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

And stacktrace flag output looks like:

`cb2@cb2-VirtualBox:~/gatk$ ./gradlew bundle --stacktrace
> Task :gatkDoc FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':gatkDoc'.
> Javadoc generation failed. Generated Javadoc options file (useful for troubleshooting): '/home/cb2/gatk/build/tmp/gatkDoc/javadoc.options'

* Try:
Run with --info or --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 ':gatkDoc'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$3.accept(ExecuteActionsTaskExecuter.java:166)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$3.accept(ExecuteActionsTaskExecuter.java:163)
        at org.gradle.internal.Try$Failure.ifSuccessfulOrElse(Try.java:191)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:156)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:62)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:108)
        at org.gradle.api.internal.tasks.execution.ResolveBeforeExecutionOutputsTaskExecuter.execute(ResolveBeforeExecutionOutputsTaskExecuter.java:67)
        at org.gradle.api.internal.tasks.execution.ResolveAfterPreviousExecutionStateTaskExecuter.execute(ResolveAfterPreviousExecutionStateTaskExecuter.java:46)
        at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:94)
        at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)
        at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:95)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:56)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:36)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.executeTask(EventFiringTaskExecuter.java:77)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:55)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:52)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:416)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:406)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:102)
        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.call(DelegatingBuildOperationExecutor.java:36)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)
        at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:43)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:355)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:343)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:336)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:322)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker$1.execute(DefaultPlanExecutor.java:134)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker$1.execute(DefaultPlanExecutor.java:129)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:202)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.executeNextNode(DefaultPlanExecutor.java:193)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:129)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
Caused by: org.gradle.api.GradleException: Javadoc generation failed. Generated Javadoc options file (useful for troubleshooting): '/home/cb2/gatk/build/tmp/gatkDoc/javadoc.options'
        at org.gradle.api.tasks.javadoc.internal.JavadocGenerator.execute(JavadocGenerator.java:58)
        at org.gradle.api.tasks.javadoc.internal.JavadocGenerator.execute(JavadocGenerator.java:31)
        at org.gradle.api.tasks.javadoc.Javadoc.executeExternalJavadoc(Javadoc.java:158)
        at org.gradle.api.tasks.javadoc.Javadoc.generate(Javadoc.java:146)
        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:103)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:49)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:42)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:28)
        at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:717)
        at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:684)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$5.run(ExecuteActionsTaskExecuter.java:476)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:402)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:394)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:92)
        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:461)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:444)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.access$200(ExecuteActionsTaskExecuter.java:93)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$TaskExecution.execute(ExecuteActionsTaskExecuter.java:237)
        at org.gradle.internal.execution.steps.ExecuteStep.lambda$execute$1(ExecuteStep.java:33)
        at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:33)
        at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:26)
        at org.gradle.internal.execution.steps.CleanupOutputsStep.execute(CleanupOutputsStep.java:58)
        at org.gradle.internal.execution.steps.CleanupOutputsStep.execute(CleanupOutputsStep.java:35)
        at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:48)
        at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:33)
        at org.gradle.internal.execution.steps.CancelExecutionStep.execute(CancelExecutionStep.java:39)
        at org.gradle.internal.execution.steps.TimeoutStep.executeWithoutTimeout(TimeoutStep.java:73)
        at org.gradle.internal.execution.steps.TimeoutStep.execute(TimeoutStep.java:54)
        at org.gradle.internal.execution.steps.CatchExceptionStep.execute(CatchExceptionStep.java:35)
        at org.gradle.internal.execution.steps.CreateOutputsStep.execute(CreateOutputsStep.java:51)
        at org.gradle.internal.execution.steps.SnapshotOutputsStep.execute(SnapshotOutputsStep.java:45)
        at org.gradle.internal.execution.steps.SnapshotOutputsStep.execute(SnapshotOutputsStep.java:31)
        at org.gradle.internal.execution.steps.CacheStep.executeWithoutCache(CacheStep.java:208)
        at org.gradle.internal.execution.steps.CacheStep.execute(CacheStep.java:70)
        at org.gradle.internal.execution.steps.CacheStep.execute(CacheStep.java:45)
        at org.gradle.internal.execution.steps.BroadcastChangingOutputsStep.execute(BroadcastChangingOutputsStep.java:49)
        at org.gradle.internal.execution.steps.StoreSnapshotsStep.execute(StoreSnapshotsStep.java:43)
        at org.gradle.internal.execution.steps.StoreSnapshotsStep.execute(StoreSnapshotsStep.java:32)
        at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:38)
        at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:24)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.executeBecause(SkipUpToDateStep.java:96)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.lambda$execute$0(SkipUpToDateStep.java:89)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:54)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:38)
        at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:76)
        at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:37)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:36)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:26)
        at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:90)
        at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:48)
        at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:69)
        at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:47)
        at org.gradle.internal.execution.impl.DefaultWorkExecutor.execute(DefaultWorkExecutor.java:33)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:140)
        ... 34 more
Caused by: org.gradle.process.internal.ExecException: A problem occurred starting process 'command 'javadoc''
        at org.gradle.process.internal.DefaultExecHandle.execExceptionFor(DefaultExecHandle.java:237)
        at org.gradle.process.internal.DefaultExecHandle.setEndStateInfo(DefaultExecHandle.java:214)
        at org.gradle.process.internal.DefaultExecHandle.failed(DefaultExecHandle.java:364)
        at org.gradle.process.internal.ExecHandleRunner.run(ExecHandleRunner.java:87)
        at org.gradle.internal.operations.CurrentBuildOperationPreservingRunnable.run(CurrentBuildOperationPreservingRunnable.java:42)
        ... 3 more
Caused by: net.rubygrapefruit.platform.NativeException: Could not start 'javadoc'
        at net.rubygrapefruit.platform.internal.DefaultProcessLauncher.start(DefaultProcessLauncher.java:27)
        at net.rubygrapefruit.platform.internal.WrapperProcessLauncher.start(WrapperProcessLauncher.java:36)
        at org.gradle.process.internal.ExecHandleRunner.startProcess(ExecHandleRunner.java:98)
        at org.gradle.process.internal.ExecHandleRunner.run(ExecHandleRunner.java:71)
        ... 4 more
Caused by: java.io.IOException: Cannot run program "javadoc" (in directory "/home/cb2/gatk"): error=2, No such file or directory
        at net.rubygrapefruit.platform.internal.DefaultProcessLauncher.start(DefaultProcessLauncher.java:25)
        ... 7 more
Caused by: java.io.IOException: error=2, No such file or directory
        ... 8 more

* Get more help at https://help.gradle.org

BUILD FAILED in 1s
5 actionable tasks: 1 executed, 4 up-to-date
`

I'm open to it being a lot of things. For context, I'm just setting up GATK on a new Linux virtual machine, so some dependencies may not exist.

cmnbroad commented 4 years ago

Oh, looks like you're using Java 11. Officially we still require Java 8 to build (building with 11 is beta status), and I don't believe any of the javadoc tasks (javadoc, gatkDoc, and gatkTabComplete) will work on Java 11.

lbergelson commented 4 years ago

@cmnbroad They are supposed to work on 11. They do on my machine.

cmnbroad commented 4 years ago

@lbergelson Oh ok, good to know. @jberghout It looks like gradle can't find the javadoc app to run. Do you have a full JDK installed ?

shafeeJan commented 4 years ago

I am also facing the same issue while running ./gradlew build

lbergelson commented 4 years ago

@shafeeJan Are you also building with java 11?

shafeeJan commented 4 years ago

I am trying to build it with java 8

lbergelson commented 4 years ago

Could you share the result of java -version on your system?

shafeeJan commented 4 years ago

openjdk version "1.8.0_252" OpenJDK Runtime Environment (build 1.8.0_252-8u252-b09-1~18.04-b09) OpenJDK 64-Bit Server VM (build 25.252-b09, mixed mode)

shafeeJan commented 4 years ago

I have shared my results about

lbergelson commented 4 years ago

Strange. That looks fine. Sorry to keep asking question, but a) what operating system are you using? b) how did you install java? Every java 8 jdk should come with javadoc.

lbergelson commented 4 years ago

What does which javadoc say?

98rahul commented 1 year ago

getting same error Execution failed for task ':react-native-reanimated:androidJavadoc'.

Javadoc generation failed.

RN-0.71.1 any solution?

cmnbroad commented 1 year ago

@98rahul Without more context, it's very hard to say what the problem is. Usually this is caused by using the wrong Java version, or using a JRE instead of a JDK. But in order to help, we'd need to know the platform you're running on, the Java version, the command you're using, and the gradle output.