[JAL-4276] Exception when groovy console is opened in 2.11.3.0 - Jalview

Details

Type: Bug
Status: Ready for testing
Priority: Major
Resolution: Unresolved
Affects Version/s: 2.11.3.0
Fix Version/s: None
Component/s: Scriptable API
Labels:
None
Environment:

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Verified on

Java version: 11.0.16.1
Java home: /usr/local/Cellar/openjdk@11/11.0.16.1_1/libexec/openjdk.jdk/Contents/Home
Java arch: x86_64 Mac OS X 12.6.8
Jalview non-release version: TEST (Source git-commit:3feb95a4ca [reviews/jims_review_ofbigbensmerge])

and

Java version: 1.8.0_382
Java home: /usr/local/Cellar/openjdk@8/1.8.0+382/libexec/openjdk.jdk/Contents/Home/jre
Java arch: x86_64 Mac OS X 12.6.8

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Verified on Java version: 11.0.16.1 Java home: /usr/local/Cellar/openjdk@11/11.0.16.1_1/libexec/openjdk.jdk/Contents/Home Java arch: x86_64 Mac OS X 12.6.8 Jalview non-release version: TEST (Source git-commit:3feb95a4ca [reviews/jims_review_ofbigbensmerge]) and Java version: 1.8.0_382 Java home: /usr/local/Cellar/openjdk@8/1.8.0+382/libexec/openjdk.jdk/Contents/Home/jre Java arch: x86_64 Mac OS X 12.6.8

Description

Open the groovy console on OSX.

A bunch of exceptions appear - these don't seem to affect running Groovy, but may be an indicator of other issues (see Shutdown hook hang issue).

Java 11 error output:
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass (file:/Users/jprocter/git/jalview/build/libs/jalview-all-TEST-j11.jar) to method java.lang.Object.finalize()
WARNING: Please consider reporting this to the maintainers of org.codehaus.groovy.reflection.CachedClass
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
script16940833021531558877614.groovy: 6: unable to resolve class MRJQuitHandler
@ line 6, column 1.
   class ConsoleMacOsSupport implements MRJQuitHandler, MRJAboutHandler {
   ^

script16940833021531558877614.groovy: 6: unable to resolve class MRJAboutHandler
@ line 6, column 1.
   class ConsoleMacOsSupport implements MRJQuitHandler, MRJAboutHandler {
   ^

2 errors

at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:309)
at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:981)
at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:626)
at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:575)
at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:323)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:293)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:279)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:236)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:246)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1192)
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 java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1225)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:947)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:930)
at groovy.util.FactoryInterceptorMetaClass.invokeMethod(FactoryBuilderSupport.java:1349)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.view.MacOSXMenuBar.run(MacOSXMenuBar.groovy:49)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1181)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1164)
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 java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:352)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.Console$__clinit__closure25.doCall(Console.groovy:267)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.ConsoleView$_run_closure1.doCall(ConsoleView.groovy:62)
at groovy.ui.ConsoleView$_run_closure1.doCall(ConsoleView.groovy)
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 java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at groovy.lang.Closure.call(Closure.java:420)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.util.FactoryBuilderSupport.dispatchNodeCall(FactoryBuilderSupport.java:899)
at groovy.util.FactoryBuilderSupport.doInvokeMethod(FactoryBuilderSupport.java:791)
at groovy.util.FactoryBuilderSupport.invokeMethod(FactoryBuilderSupport.java:511)
at groovy.util.FactoryInterceptorMetaClass.invokeMethod(FactoryBuilderSupport.java:1347)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.ConsoleView.run(ConsoleView.groovy:59)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1181)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1164)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.Console.run(Console.groovy:308)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.Console.run(Console.groovy:271)
at jalview.gui.Desktop.openGroovyConsole(Desktop.java:2618)

Java 8 output
2023-09-07 11:45:04.382 java[47557:2139940] JavaNativeFoundation: GetGlobalVM: Failed to locate @rpath/libjvm.dylib for JNI_GetCreatedJavaVMs(). A JVM must be loaded before calling this function.
org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
script16940835139921558877614.groovy: 6: unable to resolve class MRJQuitHandler
@ line 6, column 1.
   class ConsoleMacOsSupport implements MRJQuitHandler, MRJAboutHandler {
   ^

script16940835139921558877614.groovy: 6: unable to resolve class MRJAboutHandler
@ line 6, column 1.
   class ConsoleMacOsSupport implements MRJQuitHandler, MRJAboutHandler {
   ^

2 errors

at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:309)
at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:981)
at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:626)
at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:575)
at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:323)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:293)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:279)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:236)
at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:246)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1192)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1225)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:947)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:930)
at groovy.util.FactoryInterceptorMetaClass.invokeMethod(FactoryBuilderSupport.java:1349)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.view.MacOSXMenuBar.run(MacOSXMenuBar.groovy:49)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1181)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1164)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:352)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.Console$__clinit__closure25.doCall(Console.groovy:267)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.ConsoleView$_run_closure1.doCall(ConsoleView.groovy:62)
at groovy.ui.ConsoleView$_run_closure1.doCall(ConsoleView.groovy)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:98)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:264)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1034)
at groovy.lang.Closure.call(Closure.java:420)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.util.FactoryBuilderSupport.dispatchNodeCall(FactoryBuilderSupport.java:899)
at groovy.util.FactoryBuilderSupport.doInvokeMethod(FactoryBuilderSupport.java:791)
at groovy.util.FactoryBuilderSupport.invokeMethod(FactoryBuilderSupport.java:511)
at groovy.util.FactoryInterceptorMetaClass.invokeMethod(FactoryBuilderSupport.java:1347)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.ConsoleView.run(ConsoleView.groovy:59)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1181)
at groovy.util.FactoryBuilderSupport.build(FactoryBuilderSupport.java:1164)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.Console.run(Console.groovy:308)
at org.codehaus.groovy.vmplugin.v7.IndyInterface.selectMethod(IndyInterface.java:236)
at groovy.ui.Console.run(Console.groovy:271)
at jalview.gui.Desktop.openGroovyConsole(Desktop.java:2618)

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JAL-3783 Groovy console does not open when Jalview launched from shadowJar in Java 11 for recent versions of groovy

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Exception when groovy console is opened in 2.11.3.0

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