synthetichealth/synthea

Error: "Deprecated Gradle features were used in this build, making it incompatible with Gradle 9.0."

Closed this issue · 2 comments

martinhinze commented

What happened?

Hello! When I run

git clone https://github.com/synthetichealth/synthea.git
cd synthea
./gradlew build check test

I get the following error:

> Task :javadoc FAILED

FAILURE: Build failed with an exception.
[...]
Deprecated Gradle features were used in this build, making it incompatible with Gradle 9.0.

For more log output, I ran ./gradlew --stacktrace javadoc and posted the output below.

Has someone an idea to make this run? Any help will be greatly appreciated. :-)

Output of `java --version':

openjdk 17.0.9 2023-10-17
OpenJDK Runtime Environment (Red_Hat-17.0.9.0.9-4) (build 17.0.9+9)
OpenJDK 64-Bit Server VM (Red_Hat-17.0.9.0.9-4) (build 17.0.9+9, mixed mode, sharing)

Environment

- OS: Fedora Linux 39 (Container Image based on registry.fedoraproject.org/fedora)
- Architecture: X64
- Java: OpenJDK 17.0.9 2023-10-17

Relevant log output

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':javadoc'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.lambda$executeIfValid$1(ExecuteActionsTaskExecuter.java:149)
        at org.gradle.internal.Try$Failure.ifSuccessfulOrElse(Try.java:282)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:147)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:135)
        at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)
        at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:51)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:74)
        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$1.call(EventFiringTaskExecuter.java:52)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)
        at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:42)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:337)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:324)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:317)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:303)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:463)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:380)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
        at org.gradle.internal.concurrent.AbstractManagedExecutor$1.run(AbstractManagedExecutor.java:47)
Caused by: org.gradle.api.GradleException: Javadoc generation failed. Generated Javadoc options file (useful for troubleshooting): '/data/idim/git-repos/synthea/build/tmp/javadoc/javadoc.options'
        at org.gradle.api.tasks.javadoc.internal.JavadocGenerator.execute(JavadocGenerator.java:56)
        at org.gradle.api.tasks.javadoc.internal.JavadocToolAdapter.execute(JavadocToolAdapter.java:37)
        at org.gradle.api.tasks.javadoc.Javadoc.generate(Javadoc.java:175)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:125)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:58)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:51)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:29)
        at org.gradle.api.internal.tasks.execution.TaskExecution$3.run(TaskExecution.java:248)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:29)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:26)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.run(DefaultBuildOperationRunner.java:47)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:68)
        at org.gradle.api.internal.tasks.execution.TaskExecution.executeAction(TaskExecution.java:233)
        at org.gradle.api.internal.tasks.execution.TaskExecution.executeActions(TaskExecution.java:216)
        at org.gradle.api.internal.tasks.execution.TaskExecution.executeWithPreviousOutputFiles(TaskExecution.java:199)
        at org.gradle.api.internal.tasks.execution.TaskExecution.execute(TaskExecution.java:166)
        at org.gradle.internal.execution.steps.ExecuteStep.executeInternal(ExecuteStep.java:105)
        at org.gradle.internal.execution.steps.ExecuteStep.access$000(ExecuteStep.java:44)
        at org.gradle.internal.execution.steps.ExecuteStep$1.call(ExecuteStep.java:59)
        at org.gradle.internal.execution.steps.ExecuteStep$1.call(ExecuteStep.java:56)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)
        at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:56)
        at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:44)
        at org.gradle.internal.execution.steps.RemovePreviousOutputsStep.execute(RemovePreviousOutputsStep.java:67)
        at org.gradle.internal.execution.steps.RemovePreviousOutputsStep.execute(RemovePreviousOutputsStep.java:37)
        at org.gradle.internal.execution.steps.CancelExecutionStep.execute(CancelExecutionStep.java:41)
        at org.gradle.internal.execution.steps.TimeoutStep.executeWithoutTimeout(TimeoutStep.java:74)
        at org.gradle.internal.execution.steps.TimeoutStep.execute(TimeoutStep.java:55)
        at org.gradle.internal.execution.steps.CreateOutputsStep.execute(CreateOutputsStep.java:50)
        at org.gradle.internal.execution.steps.CreateOutputsStep.execute(CreateOutputsStep.java:28)
        at org.gradle.internal.execution.steps.CaptureStateAfterExecutionStep.executeDelegateBroadcastingChanges(CaptureStateAfterExecutionStep.java:100)
        at org.gradle.internal.execution.steps.CaptureStateAfterExecutionStep.execute(CaptureStateAfterExecutionStep.java:72)
        at org.gradle.internal.execution.steps.CaptureStateAfterExecutionStep.execute(CaptureStateAfterExecutionStep.java:50)
        at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:40)
        at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:29)
        at org.gradle.internal.execution.steps.BuildCacheStep.executeWithoutCache(BuildCacheStep.java:179)
        at org.gradle.internal.execution.steps.BuildCacheStep.lambda$execute$1(BuildCacheStep.java:70)
        at org.gradle.internal.Either$Right.fold(Either.java:175)
        at org.gradle.internal.execution.caching.CachingState.fold(CachingState.java:59)
        at org.gradle.internal.execution.steps.BuildCacheStep.execute(BuildCacheStep.java:68)
        at org.gradle.internal.execution.steps.BuildCacheStep.execute(BuildCacheStep.java:46)
        at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:36)
        at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:25)
        at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:36)
        at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:22)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.executeBecause(SkipUpToDateStep.java:91)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.lambda$execute$2(SkipUpToDateStep.java:55)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:55)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:37)
        at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:65)
        at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:36)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:37)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:27)
        at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:77)
        at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:38)
        at org.gradle.internal.execution.steps.ValidateStep.execute(ValidateStep.java:94)
        at org.gradle.internal.execution.steps.ValidateStep.execute(ValidateStep.java:49)
        at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:71)
        at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:45)
        at org.gradle.internal.execution.steps.SkipEmptyWorkStep.executeWithNonEmptySources(SkipEmptyWorkStep.java:177)
        at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:86)
        at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:53)
        at org.gradle.internal.execution.steps.RemoveUntrackedExecutionStateStep.execute(RemoveUntrackedExecutionStateStep.java:32)
        at org.gradle.internal.execution.steps.RemoveUntrackedExecutionStateStep.execute(RemoveUntrackedExecutionStateStep.java:21)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsStartedStep.execute(MarkSnapshottingInputsStartedStep.java:38)
        at org.gradle.internal.execution.steps.LoadPreviousExecutionStateStep.execute(LoadPreviousExecutionStateStep.java:36)
        at org.gradle.internal.execution.steps.LoadPreviousExecutionStateStep.execute(LoadPreviousExecutionStateStep.java:23)
        at org.gradle.internal.execution.steps.CleanupStaleOutputsStep.execute(CleanupStaleOutputsStep.java:75)
        at org.gradle.internal.execution.steps.CleanupStaleOutputsStep.execute(CleanupStaleOutputsStep.java:41)
        at org.gradle.internal.execution.steps.AssignWorkspaceStep.lambda$execute$0(AssignWorkspaceStep.java:32)
        at org.gradle.api.internal.tasks.execution.TaskExecution$4.withWorkspace(TaskExecution.java:293)
        at org.gradle.internal.execution.steps.AssignWorkspaceStep.execute(AssignWorkspaceStep.java:30)
        at org.gradle.internal.execution.steps.AssignWorkspaceStep.execute(AssignWorkspaceStep.java:21)
        at org.gradle.internal.execution.steps.IdentityCacheStep.execute(IdentityCacheStep.java:37)
        at org.gradle.internal.execution.steps.IdentityCacheStep.execute(IdentityCacheStep.java:27)
        at org.gradle.internal.execution.steps.IdentifyStep.execute(IdentifyStep.java:47)
        at org.gradle.internal.execution.steps.IdentifyStep.execute(IdentifyStep.java:34)
        at org.gradle.internal.execution.impl.DefaultExecutionEngine$1.execute(DefaultExecutionEngine.java:64)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:146)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:135)
        at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)
        at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:51)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:74)
        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$1.call(EventFiringTaskExecuter.java:52)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:204)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:199)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:66)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$2.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:157)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:59)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:53)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:73)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)
        at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:42)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:337)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:324)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:317)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:303)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:463)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:380)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
        at org.gradle.internal.concurrent.AbstractManagedExecutor$1.run(AbstractManagedExecutor.java:47)
Caused by: org.gradle.process.internal.ExecException: A problem occurred starting process 'command '/usr/lib/jvm/java-17-openjdk-17.0.9.0.9-3.fc39.x86_64/bin/javadoc''
        at org.gradle.process.internal.DefaultExecHandle.execExceptionFor(DefaultExecHandle.java:241)
        at org.gradle.process.internal.DefaultExecHandle.setEndStateInfo(DefaultExecHandle.java:218)
        at org.gradle.process.internal.DefaultExecHandle.failed(DefaultExecHandle.java:370)
        at org.gradle.process.internal.ExecHandleRunner.run(ExecHandleRunner.java:87)
        at org.gradle.internal.operations.CurrentBuildOperationPreservingRunnable.run(CurrentBuildOperationPreservingRunnable.java:42)
        ... 2 more
Caused by: net.rubygrapefruit.platform.NativeException: Could not start '/usr/lib/jvm/java-17-openjdk-17.0.9.0.9-3.fc39.x86_64/bin/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)
        ... 3 more
Caused by: java.io.IOException: Cannot run program "/usr/lib/jvm/java-17-openjdk-17.0.9.0.9-3.fc39.x86_64/bin/javadoc" (in directory "/data/idim/git-repos/synthea"): error=2, No such file or directory
        at net.rubygrapefruit.platform.internal.DefaultProcessLauncher.start(DefaultProcessLauncher.java:25)
        ... 6 more
Caused by: java.io.IOException: error=2, No such file or directory
        ... 7 more
dehall commented

The javadoc task isn't strictly required so let's see if the more important parts actually run. Can you try running ./run_synthea -p 0 and see if you get any errors? If no errors then you're good to go with running it for real.

The root cause seems to be this error: Cannot run program "/usr/lib/jvm/java-17-openjdk-17.0.9.0.9-3.fc39.x86_64/bin/javadoc" (in directory "/data/idim/git-repos/synthea"): error=2, No such file or directory. I'm wondering if somehow just the javadoc program is missing. Or alternatively if run_synthea fails then the JVM might be configured incorrectly.

martinhinze commented

Thank you so much for the kind, fast and helpful replay, I was stuck on this, but it works indeed.