Can't run FIJI updater

I recently loaded CLearVolume and imagej-matlab update sites, and now would like to remove ClearVolume since it makes all dialog boxes use a transparent background that makes text hard to see.
If I launch help/updateFiji, the console spews red ink and updater does not complete. I wish there were uninstallers for plugins! I manually moved 3 “clear” files but fiji still has a menu item and updater fails to launch. I hate to reinstall barebone and try o migrate scores of plugins. Any suggestions? Err text:

java.lang.Error: The markup in the document preceding the root element must be well-formed.

Public ID: None, System ID: None,
Line number: 2, Column number: 2
	at net.imagej.updater.XMLFileErrorHandler.throwError(XMLFileErrorHandler.java:65)
	at net.imagej.updater.XMLFileErrorHandler.fatalError(XMLFileErrorHandler.java:52)
	at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	at net.imagej.updater.XMLFileReader.read(XMLFileReader.java:135)
	at net.imagej.updater.XMLFileReader.read(XMLFileReader.java:111)
	at net.imagej.updater.FilesCollection.read(FilesCollection.java:424)
	at net.imagej.updater.FilesCollection.read(FilesCollection.java:418)
	at net.imagej.updater.FilesCollection.read(FilesCollection.java:412)
	at net.imagej.updater.FilesCollection.downloadIndexAndChecksum(FilesCollection.java:1128)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:140)
	at fiji.updater.IJ2Updater.run(IJ2Updater.java:78)
	at fiji.updater.Updater.run(Updater.java:30)
	at ij.IJ.runUserPlugIn(IJ.java:216)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
java.lang.ClassNotFoundException: imagej.updater.gui.ImageJUpdater
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at fiji.updater.Updater.run(Updater.java:35)
	at ij.IJ.runUserPlugIn(IJ.java:216)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
Falling back to remote updater at http://update.imagej.net/bootstrap.js
javax.script.ScriptException: ReferenceError: "importPackage" is not defined in <eval> at line number 1
	at jdk.nashorn.api.scripting.NashornScriptEngine.throwAsScriptException(NashornScriptEngine.java:467)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:451)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:403)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:399)
	at jdk.nashorn.api.scripting.NashornScriptEngine.eval(NashornScriptEngine.java:155)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
	at fiji.updater.Updater.runRemote(Updater.java:82)
	at fiji.updater.Updater.run(Updater.java:41)
	at ij.IJ.runUserPlugIn(IJ.java:216)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
Caused by: <eval>:1 ReferenceError: "importPackage" is not defined
	at jdk.nashorn.internal.runtime.ECMAErrors.error(ECMAErrors.java:57)
	at jdk.nashorn.internal.runtime.ECMAErrors.referenceError(ECMAErrors.java:319)
	at jdk.nashorn.internal.runtime.ECMAErrors.referenceError(ECMAErrors.java:291)
	at jdk.nashorn.internal.objects.Global.__noSuchProperty__(Global.java:1432)
	at jdk.nashorn.internal.scripts.Script$\^eval\_.:program(<eval>:1)
	at jdk.nashorn.internal.runtime.ScriptFunctionData.invoke(ScriptFunctionData.java:640)
	at jdk.nashorn.internal.runtime.ScriptFunction.invoke(ScriptFunction.java:228)
	at jdk.nashorn.internal.runtime.ScriptRuntime.apply(ScriptRuntime.java:393)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:446)
	... 11 more
java.lang.IllegalArgumentException: argument type mismatch
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at java.lang.invoke.MethodHandleImpl$BindCaller$T/1506396460.invoke_V(MethodHandleImpl.java:1258)
	at jdk.nashorn.internal.scripts.Script$15$Untitled_ijm.:program(Untitled.ijm.js:329)
	at jdk.nashorn.internal.runtime.ScriptFunctionData.invoke(ScriptFunctionData.java:640)
	at jdk.nashorn.internal.runtime.ScriptFunction.invoke(ScriptFunction.java:228)
	at jdk.nashorn.internal.runtime.ScriptRuntime.apply(ScriptRuntime.java:393)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:446)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:403)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:399)
	at jdk.nashorn.api.scripting.NashornScriptEngine.eval(NashornScriptEngine.java:150)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:249)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
java.lang.IllegalArgumentException: argument type mismatch
	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:497)
	at java.lang.invoke.MethodHandleImpl$BindCaller$T/1284169337.invoke_V(MethodHandleImpl.java:1258)
	at jdk.nashorn.internal.scripts.Script$24$Untitled_ijm.:program(Untitled.ijm.js:329)
	at jdk.nashorn.internal.runtime.ScriptFunctionData.invoke(ScriptFunctionData.java:640)
	at jdk.nashorn.internal.runtime.ScriptFunction.invoke(ScriptFunction.java:228)
	at jdk.nashorn.internal.runtime.ScriptRuntime.apply(ScriptRuntime.java:393)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:446)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:403)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:399)
	at jdk.nashorn.api.scripting.NashornScriptEngine.eval(NashornScriptEngine.java:150)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:249)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
java.lang.IllegalArgumentException: argument type mismatch
	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:497)
	at java.lang.invoke.MethodHandleImpl$BindCaller$T/914645768.invoke_V(MethodHandleImpl.java:1258)
	at jdk.nashorn.internal.scripts.Script$33$Untitled_ijm.:program(Untitled.ijm.js:329)
	at jdk.nashorn.internal.runtime.ScriptFunctionData.invoke(ScriptFunctionData.java:640)
	at jdk.nashorn.internal.runtime.ScriptFunction.invoke(ScriptFunction.java:228)
	at jdk.nashorn.internal.runtime.ScriptRuntime.apply(ScriptRuntime.java:393)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:446)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:403)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:399)
	at jdk.nashorn.api.scripting.NashornScriptEngine.eval(NashornScriptEngine.java:150)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:249)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
java.lang.Error: The markup in the document preceding the root element must be well-formed.

Public ID: None, System ID: None,
Line number: 2, Column number: 2
	at net.imagej.updater.XMLFileErrorHandler.throwError(XMLFileErrorHandler.java:65)
	at net.imagej.updater.XMLFileErrorHandler.fatalError(XMLFileErrorHandler.java:52)
	at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	at net.imagej.updater.XMLFileReader.read(XMLFileReader.java:135)
	at net.imagej.updater.XMLFileReader.read(XMLFileReader.java:111)
	at net.imagej.updater.FilesCollection.read(FilesCollection.java:424)
	at net.imagej.updater.FilesCollection.read(FilesCollection.java:418)
	at net.imagej.updater.FilesCollection.read(FilesCollection.java:412)
	at net.imagej.updater.FilesCollection.downloadIndexAndChecksum(FilesCollection.java:1128)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:140)
	at fiji.updater.IJ2Updater.run(IJ2Updater.java:78)
	at fiji.updater.Updater.run(Updater.java:30)
	at ij.IJ.runUserPlugIn(IJ.java:216)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
java.lang.ClassNotFoundException: imagej.updater.gui.ImageJUpdater
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at fiji.updater.Updater.run(Updater.java:35)
	at ij.IJ.runUserPlugIn(IJ.java:216)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
Falling back to remote updater at http://update.imagej.net/bootstrap.js
javax.script.ScriptException: ReferenceError: "importPackage" is not defined in <eval> at line number 1
	at jdk.nashorn.api.scripting.NashornScriptEngine.throwAsScriptException(NashornScriptEngine.java:467)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:451)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:403)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:399)
	at jdk.nashorn.api.scripting.NashornScriptEngine.eval(NashornScriptEngine.java:155)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:264)
	at fiji.updater.Updater.runRemote(Updater.java:82)
	at fiji.updater.Updater.run(Updater.java:41)
	at ij.IJ.runUserPlugIn(IJ.java:216)
	at ij.IJ.runPlugIn(IJ.java:180)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
Caused by: <eval>:1 ReferenceError: "importPackage" is not defined
	at jdk.nashorn.internal.runtime.ECMAErrors.error(ECMAErrors.java:57)
	at jdk.nashorn.internal.runtime.ECMAErrors.referenceError(ECMAErrors.java:319)
	at jdk.nashorn.internal.runtime.ECMAErrors.referenceError(ECMAErrors.java:291)
	at jdk.nashorn.internal.objects.Global.__noSuchProperty__(Global.java:1432)
	at jdk.nashorn.internal.scripts.Script$38$\^eval\_.:program(<eval>:1)
	at jdk.nashorn.internal.runtime.ScriptFunctionData.invoke(ScriptFunctionData.java:640)
	at jdk.nashorn.internal.runtime.ScriptFunction.invoke(ScriptFunction.java:228)
	at jdk.nashorn.internal.runtime.ScriptRuntime.apply(ScriptRuntime.java:393)
	at jdk.nashorn.api.scripting.NashornScriptEngine.evalImpl(NashornScriptEngine.java:446)
	... 11 more

best regards,

Sorry for your troubles, @Vytas.

It looks like maybe the db.xml.gz file in your Fiji.app folder became malformed somehow. Try deleting/renaming it, and see if the updater works better.

Falling back to remote updater at http://update.imagej.net/bootstrap.js
javax.script.ScriptException: ReferenceError: “importPackage” is not defined in at line number 1

This is an unfortunate consequence of the migration to Java 8, which has a new JavaScript engine (“Nashorn”) incompatible with some old JavaScript scripts, including the one which launches the remote updater (a fallback updater which is used when the regular updater has problems).

Hopefully, deleting the db.xml.gz will avoid the issue.

1 Like

Ok, deleting the .gz file did allow the updater to launch.
Thanks! much faster than a reload.
cheers

1 Like