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  1. Jalview
  2. JAL-4276

Exception when groovy console is opened in 2.11.3.0

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.11.3.0
    • Fix Version/s: 2.11.3.0
    • Component/s: Scriptable API
    • Labels:
      None
    • Environment:

      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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              Assignee:
              soares Ben Soares
              Reporter:
              jprocter James Procter
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                Created:
                Updated:
                Resolved: