[ImageJ-bugs] [Bug 1008] New: Fiji.app double clicking not starting up Fiji in OSX / Java8

bugzilla at fiji.sc bugzilla at fiji.sc
Fri Feb 20 07:27:29 CST 2015 

http://fiji.sc/bugzilla/show_bug.cgi?id=1008

            Bug ID: 1008
           Summary: Fiji.app double clicking not starting up Fiji in OSX /
                    Java8
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: miura at embl.de
                CC: miura at embl.de

In JRE 1.8 environment, double clicking Fiji.app does not launch Fiji. 

>From command line it's possible to start up Fiji by 

   <fiji no-jre root>/Contents/MacOS/ImageJ-OSX

but then there will be error messages printed in console. I pasete them below. 

---

miura$ ./ImageJ-macosx
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m;
support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated
and will likely be removed in a future release
java.lang.IllegalArgumentException: Cannot handle replace call to list in
ij.Menus's public static synchronized java.lang.String[] getPlugins()
    at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:725)
    at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:650)
    at
net.imagej.patcher.LegacyExtensions.addExtraPlugins(LegacyExtensions.java:477)
    at
net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:175)
    at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
    at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
    at
net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
    at
net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
    at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
    at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
    at
net.imagej.legacy.DefaultLegacyService.<clinit>(DefaultLegacyService.java:124)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
    at java.lang.Class.newInstance(Class.java:438)
    at
org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:302)
    at
org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
    at org.scijava.Context.<init>(Context.java:265)
    at org.scijava.Context.<init>(Context.java:222)
    at org.scijava.Context.<init>(Context.java:161)
    at org.scijava.Context.<init>(Context.java:117)
    at org.scijava.Context.<init>(Context.java:105)
    at net.imagej.ImageJ.<init>(ImageJ.java:82)
    at net.imagej.Main.launch(Main.java:61)
    at net.imagej.Main.main(Main.java:73)
    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:483)
    at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
    at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
    at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant
type: 18 at 168
    at javassist.CtClassType.getClassFile2(CtClassType.java:204)
    at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:98)
    at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:84)
    at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:711)
    at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:688)
    at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:157)
    at javassist.compiler.ast.CallExpr.accept(CallExpr.java:46)
    at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:242)
    at javassist.compiler.CodeGen.atStmnt(CodeGen.java:330)
    at javassist.compiler.ast.Stmnt.accept(Stmnt.java:50)
    at javassist.compiler.CodeGen.atIfStmnt(CodeGen.java:391)
    at javassist.compiler.CodeGen.atStmnt(CodeGen.java:355)
    at javassist.compiler.ast.Stmnt.accept(Stmnt.java:50)
    at javassist.compiler.Javac.compileStmnt(Javac.java:569)
    at javassist.expr.MethodCall.replace(MethodCall.java:235)
    at net.imagej.patcher.CodeHacker$7.edit(CodeHacker.java:686)
    at javassist.expr.ExprEditor.loopBody(ExprEditor.java:192)
    at javassist.expr.ExprEditor.doit(ExprEditor.java:91)
    at javassist.CtBehavior.instrument(CtBehavior.java:679)
    at
net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.java:1279)
    at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:670)
    ... 35 more
Caused by: java.io.IOException: invalid constant type: 18 at 168
    at javassist.bytecode.ConstPool.readOne(ConstPool.java:1044)
    at javassist.bytecode.ConstPool.read(ConstPool.java:984)
    at javassist.bytecode.ConstPool.<init>(ConstPool.java:125)
    at javassist.bytecode.ClassFile.read(ClassFile.java:770)
    at javassist.bytecode.ClassFile.<init>(ClassFile.java:114)
    at javassist.CtClassType.getClassFile2(CtClassType.java:191)
    ... 55 more
java.lang.IllegalArgumentException: Cannot handle app name in ij.ImageJ's
public <init>(java.applet.Applet applet, int mode)
    at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:446)
    at
net.imagej.patcher.LegacyExtensions.insertAppNameHooks(LegacyExtensions.java:406)
    at
net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:292)
    at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
    at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
    at
net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
    at
net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
    at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
    at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
    at
net.imagej.legacy.DefaultLegacyService.<clinit>(DefaultLegacyService.java:124)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
    at java.lang.Class.newInstance(Class.java:438)
    at
org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:302)
    at
org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
    at org.scijava.Context.<init>(Context.java:265)
    at org.scijava.Context.<init>(Context.java:222)
    at org.scijava.Context.<init>(Context.java:161)
    at org.scijava.Context.<init>(Context.java:117)
    at org.scijava.Context.<init>(Context.java:105)
    at net.imagej.ImageJ.<init>(ImageJ.java:82)
    at net.imagej.Main.launch(Main.java:61)
    at net.imagej.Main.main(Main.java:73)
    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:483)
    at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
    at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
    at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant
type: 18 at 1
    at javassist.CtClassType.getClassFile2(CtClassType.java:204)
    at javassist.CtClassType.subtypeOf(CtClassType.java:304)
    at javassist.CtClassType.subtypeOf(CtClassType.java:319)
    at
javassist.compiler.MemberResolver.compareSignature(MemberResolver.java:235)
    at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:107)
    at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:84)
    at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:711)
    at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:688)
    at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:157)
    at javassist.compiler.ast.CallExpr.accept(CallExpr.java:46)
    at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:242)
    at javassist.compiler.CodeGen.atStmnt(CodeGen.java:330)
    at javassist.compiler.ast.Stmnt.accept(Stmnt.java:50)
    at javassist.compiler.Javac.compileStmnt(Javac.java:569)
    at javassist.expr.MethodCall.replace(MethodCall.java:235)
    at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:427)
    at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:441)
    at javassist.expr.ExprEditor.loopBody(ExprEditor.java:220)
    at javassist.expr.ExprEditor.doit(ExprEditor.java:91)
    at javassist.CtBehavior.instrument(CtBehavior.java:679)
    at
net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.java:1279)
    at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:402)
    ... 34 more
Caused by: java.io.IOException: invalid constant type: 18 at 1
    at javassist.bytecode.ConstPool.readOne(ConstPool.java:1044)
    at javassist.bytecode.ConstPool.read(ConstPool.java:984)
    at javassist.bytecode.ConstPool.<init>(ConstPool.java:125)
    at javassist.bytecode.ClassFile.read(ClassFile.java:770)
    at javassist.bytecode.ClassFile.<init>(ClassFile.java:114)
    at javassist.CtClassType.getClassFile2(CtClassType.java:191)
    ... 55 more
[ERROR] Cannot create plugin:
class='org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage',
name='JavaScript', priority=0.0, enabled=true, pluginType=ScriptLanguage
java.lang.NullPointerException
    at
org.scijava.script.AdaptedScriptLanguage.<init>(AdaptedScriptLanguage.java:63)
    at
org.scijava.script.AdaptedScriptLanguage.<init>(AdaptedScriptLanguage.java:73)
    at
org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage.<init>(JavaScriptScriptLanguage.java:59)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
    at java.lang.Class.newInstance(Class.java:438)
    at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:302)
    at
org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:236)
    at
org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:225)
    at
org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:216)
    at
org.scijava.plugin.AbstractSingletonService.initInstances(AbstractSingletonService.java:114)
    at
org.scijava.plugin.AbstractSingletonService.getInstances(AbstractSingletonService.java:72)
    at
org.scijava.script.DefaultScriptService.initScriptLanguageIndex(DefaultScriptService.java:342)
    at
org.scijava.script.DefaultScriptService.scriptLanguageIndex(DefaultScriptService.java:307)
    at
org.scijava.script.DefaultScriptService.getIndex(DefaultScriptService.java:117)
    at
org.scijava.script.DefaultScriptService.canHandleFile(DefaultScriptService.java:233)
    at org.scijava.script.ScriptFinder.discoverScripts(ScriptFinder.java:131)
    at org.scijava.script.ScriptFinder.discoverScripts(ScriptFinder.java:125)
    at org.scijava.script.ScriptFinder.findScripts(ScriptFinder.java:93)
    at
org.scijava.script.DefaultScriptService.initScripts(DefaultScriptService.java:391)
    at
org.scijava.script.DefaultScriptService.scripts(DefaultScriptService.java:325)
    at
org.scijava.script.DefaultScriptService.getScripts(DefaultScriptService.java:167)
    at
net.imagej.legacy.DefaultLegacyService.getScriptsAndNonLegacyCommands(DefaultLegacyService.java:643)
    at net.imagej.legacy.IJ1Helper.addMenuItems(IJ1Helper.java:560)
    at
net.imagej.legacy.DefaultLegacyService.initialize(DefaultLegacyService.java:454)
    at
org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:353)
    at
org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
    at org.scijava.Context.<init>(Context.java:265)
    at org.scijava.Context.<init>(Context.java:222)
    at org.scijava.Context.<init>(Context.java:161)
    at org.scijava.Context.<init>(Context.java:117)
    at org.scijava.Context.<init>(Context.java:105)
    at net.imagej.ImageJ.<init>(ImageJ.java:82)
    at net.imagej.Main.launch(Main.java:61)
    at net.imagej.Main.main(Main.java:73)
    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:483)
    at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
    at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
    at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
[INFO] Overriding Upload Sample Image; identifier:
command:net.imagej.plugins.commands.upload.SampleImageUploader; jar:
file:/Users/miura/Desktop/fiji-nojre/Fiji.app/jars/imagej-plugins-commands-0.4.1.jar

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.5
  java.version => 1.8.0_31
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_31-b13
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.31-b07
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to:
/Library/Java/JavaVirtualMachines/jdk1.8.0_31.jdk/Contents/Home/jre
  imagej.dir => /Users/miura/Desktop/fiji-nojre/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150122044514)
Fiji: http://fiji.sc/update/ (last check:20150127132630)

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