search

PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
Mozilla Public License 2.0
120 stars 39 forks source link

Build failure #24

Closed ianzavitz closed 5 years ago

ianzavitz commented 5 years ago

I'm trying to build pharmcat with gradle 5.6 and java 8.

It appears that i am getting a failure to execute ':compileJava' when building with the following command.

$ ./gradlew shadowJar --warning-mode all --stacktrace

> Configure project :
The osgi plugin has been deprecated. This is scheduled to be removed in Gradle 6.0. Consider using the biz.aQute.bnd plugin instead.
        at org.gradle.api.plugins.osgi.OsgiPlugin.apply(OsgiPlugin.java:42)
        at org.gradle.api.plugins.osgi.OsgiPlugin.apply(OsgiPlugin.java:37)
        at org.gradle.api.internal.plugins.ImperativeOnlyPluginTarget.applyImperative(ImperativeOnlyPluginTarget.java:42)
        at org.gradle.api.internal.plugins.RuleBasedPluginTarget.applyImperative(RuleBasedPluginTarget.java:50)
        at org.gradle.api.internal.plugins.DefaultPluginManager.addPlugin(DefaultPluginManager.java:177)
        at org.gradle.api.internal.plugins.DefaultPluginManager.access$300(DefaultPluginManager.java:51)
        at org.gradle.api.internal.plugins.DefaultPluginManager$AddPluginBuildOperation.run(DefaultPluginManager.java:267)
        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.plugins.DefaultPluginManager$2.execute(DefaultPluginManager.java:155)
        at org.gradle.api.internal.plugins.DefaultPluginManager$2.execute(DefaultPluginManager.java:152)
        at org.gradle.configuration.internal.DefaultUserCodeApplicationContext.apply(DefaultUserCodeApplicationContext.java:48)
        at org.gradle.api.internal.plugins.DefaultPluginManager.doApply(DefaultPluginManager.java:152)
        at org.gradle.api.internal.plugins.DefaultPluginManager.apply(DefaultPluginManager.java:125)
        at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator$4.run(DefaultPluginRequestApplicator.java:162)
        at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator.applyPlugin(DefaultPluginRequestApplicator.java:225)
        at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator.applyPlugins(DefaultPluginRequestApplicator.java:159)
        at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:201)
        at org.gradle.configuration.BuildOperationScriptPlugin$1$1.run(BuildOperationScriptPlugin.java:69)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$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.configuration.BuildOperationScriptPlugin$1.execute(BuildOperationScriptPlugin.java:66)
        at org.gradle.configuration.BuildOperationScriptPlugin$1.execute(BuildOperationScriptPlugin.java:63)
        at org.gradle.configuration.internal.DefaultUserCodeApplicationContext.apply(DefaultUserCodeApplicationContext.java:48)
        at org.gradle.configuration.BuildOperationScriptPlugin.apply(BuildOperationScriptPlugin.java:63)
        at org.gradle.configuration.project.BuildScriptProcessor$1.run(BuildScriptProcessor.java:44)
        at org.gradle.internal.Factories$1.create(Factories.java:25)
        at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.withMutableState(DefaultProjectStateRegistry.java:200)
        at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.withMutableState(DefaultProjectStateRegistry.java:186)
        at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:41)
        at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
        at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
        at org.gradle.configuration.project.LifecycleProjectEvaluator$EvaluateProject$1.run(LifecycleProjectEvaluator.java:106)
        at org.gradle.internal.Factories$1.create(Factories.java:25)
        at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:183)
        at org.gradle.internal.work.StopShieldingWorkerLeaseService.withLocks(StopShieldingWorkerLeaseService.java:40)
        at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.withProjectLock(DefaultProjectStateRegistry.java:226)
        at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.withMutableState(DefaultProjectStateRegistry.java:220)
        at org.gradle.api.internal.project.DefaultProjectStateRegistry$ProjectStateImpl.withMutableState(DefaultProjectStateRegistry.java:186)
        at org.gradle.configuration.project.LifecycleProjectEvaluator$EvaluateProject.run(LifecycleProjectEvaluator.java:95)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:402)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:394)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:92)
        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
        at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:67)
        at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:695)
        at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:143)
        at org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:35)
        at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:60)
        at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:41)
        at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuild.run(DefaultGradleLauncher.java:302)
        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.initialization.DefaultGradleLauncher.configureBuild(DefaultGradleLauncher.java:210)
        at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:151)
        at org.gradle.initialization.DefaultGradleLauncher.executeTasks(DefaultGradleLauncher.java:134)
        at org.gradle.internal.invocation.GradleBuildController$1.execute(GradleBuildController.java:58)
        at org.gradle.internal.invocation.GradleBuildController$1.execute(GradleBuildController.java:55)
        at org.gradle.internal.invocation.GradleBuildController$3.create(GradleBuildController.java:82)
        at org.gradle.internal.invocation.GradleBuildController$3.create(GradleBuildController.java:75)
        at org.gradle.internal.work.DefaultWorkerLeaseService.withLocks(DefaultWorkerLeaseService.java:183)
        at org.gradle.internal.work.StopShieldingWorkerLeaseService.withLocks(StopShieldingWorkerLeaseService.java:40)
        at org.gradle.internal.invocation.GradleBuildController.doBuild(GradleBuildController.java:75)
        at org.gradle.internal.invocation.GradleBuildController.run(GradleBuildController.java:55)
        at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:31)
        at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
        at org.gradle.launcher.exec.BuildOutcomeReportingBuildActionRunner.run(BuildOutcomeReportingBuildActionRunner.java:58)
        at org.gradle.tooling.internal.provider.ValidatingBuildActionRunner.run(ValidatingBuildActionRunner.java:32)
        at org.gradle.launcher.exec.BuildCompletionNotifyingBuildActionRunner.run(BuildCompletionNotifyingBuildActionRunner.java:39)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$3.call(RunAsBuildOperationBuildActionRunner.java:51)
        at org.gradle.launcher.exec.RunAsBuildOperationBuildActionRunner$3.call(RunAsBuildOperationBuildActionRunner.java:45)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$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.launcher.exec.RunAsBuildOperationBuildActionRunner.run(RunAsBuildOperationBuildActionRunner.java:45)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter$1.transform(InProcessBuildActionExecuter.java:49)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter$1.transform(InProcessBuildActionExecuter.java:46)
        at org.gradle.composite.internal.DefaultRootBuildState.run(DefaultRootBuildState.java:78)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:46)
        at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:31)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:42)
        at org.gradle.launcher.exec.BuildTreeScopeBuildActionExecuter.execute(BuildTreeScopeBuildActionExecuter.java:28)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:78)
        at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:52)
        at org.gradle.tooling.internal.provider.SubscribableBuildActionExecuter.execute(SubscribableBuildActionExecuter.java:59)
        at org.gradle.tooling.internal.provider.SubscribableBuildActionExecuter.execute(SubscribableBuildActionExecuter.java:36)
        at org.gradle.tooling.internal.provider.SessionScopeBuildActionExecuter.execute(SessionScopeBuildActionExecuter.java:68)
        at org.gradle.tooling.internal.provider.SessionScopeBuildActionExecuter.execute(SessionScopeBuildActionExecuter.java:38)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:37)
        at org.gradle.tooling.internal.provider.GradleThreadBuildActionExecuter.execute(GradleThreadBuildActionExecuter.java:26)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:43)
        at org.gradle.tooling.internal.provider.ParallelismConfigurationBuildActionExecuter.execute(ParallelismConfigurationBuildActionExecuter.java:29)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:60)
        at org.gradle.tooling.internal.provider.StartParamsValidatingActionExecuter.execute(StartParamsValidatingActionExecuter.java:32)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:55)
        at org.gradle.tooling.internal.provider.SessionFailureReportingActionExecuter.execute(SessionFailureReportingActionExecuter.java:41)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:48)
        at org.gradle.tooling.internal.provider.SetupLoggingActionExecuter.execute(SetupLoggingActionExecuter.java:32)
        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:104)
        at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:37)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
        at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
        at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
        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:104)
        at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:55)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
        at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:62)
        at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
        at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:81)
        at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
        at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:104)
        at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
        at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:295)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
        at java.base/java.lang.Thread.run(Thread.java:835)

> Task :compileJava FAILED
/Users/ian.zavitz/Documents/GitHub/PharmCAT/src/main/java/org/pharmgkb/pharmcat/reporter/model/OntologyTerm.java:4: error: cannot find symbol
import javax.annotation.Generated;
                       ^
  symbol:   class Generated
  location: package javax.annotation
/Users/ian.zavitz/Documents/GitHub/PharmCAT/src/main/java/org/pharmgkb/pharmcat/reporter/model/OntologyTerm.java:8: error: cannot find symbol
@Generated("org.jsonschema2pojo")
 ^
  symbol: class Generated
/Users/ian.zavitz/Documents/GitHub/PharmCAT/src/main/java/org/pharmgkb/pharmcat/reporter/model/Type.java:4: error: cannot find symbol
import javax.annotation.Generated;
                       ^
  symbol:   class Generated
  location: package javax.annotation
/Users/ian.zavitz/Documents/GitHub/PharmCAT/src/main/java/org/pharmgkb/pharmcat/reporter/model/Type.java:8: error: cannot find symbol
@Generated("org.jsonschema2pojo")
 ^
  symbol: class Generated
Note: /Users/ian.zavitz/Documents/GitHub/PharmCAT/src/main/java/org/pharmgkb/pharmcat/haplotype/CombinationUtil.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 errors

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':compileJava'.
> Compilation failed; see the compiler error output for details.

* 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 ':compileJava'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$3.accept(ExecuteActionsTaskExecuter.java:151)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$3.accept(ExecuteActionsTaskExecuter.java:148)
        at org.gradle.internal.Try$Failure.ifSuccessfulOrElse(Try.java:191)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:141)
        at org.gradle.api.internal.tasks.execution.ResolveBeforeExecutionStateTaskExecuter.execute(ResolveBeforeExecutionStateTaskExecuter.java:75)
        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:73)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:52)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:49)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:416)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:406)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:102)
        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.call(DelegatingBuildOperationExecutor.java:36)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:49)
        at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:43)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$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: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:52)
        at org.gradle.api.internal.tasks.compile.JdkJavaCompiler.execute(JdkJavaCompiler.java:36)
        at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.delegateAndHandleErrors(NormalizingJavaCompiler.java:100)
        at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:52)
        at org.gradle.api.internal.tasks.compile.NormalizingJavaCompiler.execute(NormalizingJavaCompiler.java:38)
        at org.gradle.api.internal.tasks.compile.AnnotationProcessorDiscoveringCompiler.execute(AnnotationProcessorDiscoveringCompiler.java:51)
        at org.gradle.api.internal.tasks.compile.AnnotationProcessorDiscoveringCompiler.execute(AnnotationProcessorDiscoveringCompiler.java:37)
        at org.gradle.api.internal.tasks.compile.CleaningJavaCompilerSupport.execute(CleaningJavaCompilerSupport.java:39)
        at org.gradle.api.internal.tasks.compile.incremental.IncrementalCompilerFactory$2.execute(IncrementalCompilerFactory.java:110)
        at org.gradle.api.internal.tasks.compile.incremental.IncrementalCompilerFactory$2.execute(IncrementalCompilerFactory.java:106)
        at org.gradle.api.internal.tasks.compile.incremental.IncrementalResultStoringCompiler.execute(IncrementalResultStoringCompiler.java:60)
        at org.gradle.api.internal.tasks.compile.incremental.IncrementalResultStoringCompiler.execute(IncrementalResultStoringCompiler.java:44)
        at org.gradle.api.internal.tasks.compile.CompileJavaBuildOperationReportingCompiler$2.call(CompileJavaBuildOperationReportingCompiler.java:59)
        at org.gradle.api.internal.tasks.compile.CompileJavaBuildOperationReportingCompiler$2.call(CompileJavaBuildOperationReportingCompiler.java:51)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$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.compile.CompileJavaBuildOperationReportingCompiler.execute(CompileJavaBuildOperationReportingCompiler.java:51)
        at org.gradle.api.tasks.compile.JavaCompile.performCompilation(JavaCompile.java:154)
        at org.gradle.api.tasks.compile.JavaCompile.compile(JavaCompile.java:122)
        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.IncrementalTaskInputsTaskAction.doExecute(IncrementalTaskInputsTaskAction.java:46)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:41)
        at org.gradle.api.internal.project.taskfactory.AbstractIncrementalTaskAction.execute(AbstractIncrementalTaskAction.java:25)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:28)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$5.run(ExecuteActionsTaskExecuter.java:404)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$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:393)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:376)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.access$200(ExecuteActionsTaskExecuter.java:80)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$TaskExecution.execute(ExecuteActionsTaskExecuter.java:213)
        at org.gradle.internal.execution.steps.ExecuteStep.lambda$execute$0(ExecuteStep.java:32)
        at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:32)
        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:201)
        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:77)
        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.impl.DefaultWorkExecutor.execute(DefaultWorkExecutor.java:33)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:120)
        ... 35 more

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

BUILD FAILED in 1s
1 actionable task: 1 executed`

  - PharmCAT Version: Current
  - JDK Version: [ JDK8 ]
  - Environment: [macOS]
whaleyr commented 5 years ago

Use the bundled gradle version (5.4.1) and it compiles successfully. From the project root:

./gradlew compileJava
ianzavitz commented 5 years ago

Oh wow okay, so apparently I just had another version of java installed on this machine and wasn't aware. Switching to the correct version fixed the issue.