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Bug 777 - Error opening Fiji on Windows after updating
Error opening Fiji on Windows after updating
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Windows
: P5 enhancement
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-12 08:40 CDT by Mark Hiner
Modified: 2014-06-24 09:03 CDT
2 users (show)

See Also:
Description Mark Hiner 2014-06-12 08:40:39 CDT 
Opened on behalf of Aryeh Weiss:

> ...after upgrading today FIji would not launch.
>I used the --console option to generate the attached log, which I hope will be >helpful to you.

>BTW -- does the WIn cmd window allow redirection, especially of error output???

>As for the XP64 machine -- I "fell back" to your "safe" version for now.

Error log:

C:\Documents and Settings\confocal\Desktop\Fiji.app>ImageJ-win64.exe --console
Warning: imagej-legacy-0.5.8.jar matched multiple versions:
       imagej-legacy-0.2.0.jar
       imagej-legacy-0.5.10.jar
Picking C:\DOCUME~1\confocal\Desktop\Fiji.app\jars\imagej-legacy-0.5.10.jar
Warning: imagej-2.0.0-rc-3.jar matched multiple versions:
       imagej-2.0.0-beta-8.jar
       imagej-2.0.0-rc-4.jar
Picking C:\DOCUME~1\confocal\Desktop\Fiji.app\jars\imagej-2.0.0-rc-4.jar
Warning: imagej-legacy-0.5.9.jar matched multiple versions:
       imagej-legacy-0.2.0.jar
       imagej-legacy-0.5.10.jar
Picking C:\DOCUME~1\confocal\Desktop\Fiji.app\jars\imagej-legacy-0.5.10.jar
[ERROR] Invalid service: class='io.scif.ome.services.DefaultOMEMetadataService',
priority=0.0, enabled=true, pluginType=Service
java.lang.NoClassDefFoundError: io/scif/SCIFIOService
       at java.lang.ClassLoader.defineClass1(Native Method)
       at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
       at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
       at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:14
1)
       at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
       at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
       at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
       at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
       at java.lang.ClassLoader.defineClass1(Native Method)
       at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
       at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
       at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:14
1)
       at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
       at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
       at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
       at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
       at org.scijava.util.ClassUtils.loadClass(ClassUtils.java:198)
       at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:275)
       at org.scijava.service.ServiceHelper.findServiceClasses(ServiceHelper.ja
va:326)
       at org.scijava.service.ServiceHelper.<init>(ServiceHelper.java:100)
       at org.scijava.Context.<init>(Context.java:178)
       at org.scijava.Context.<init>(Context.java:122)
       at org.scijava.Context.<init>(Context.java:82)
       at org.scijava.Context.<init>(Context.java:71)
       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:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       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)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at fiji.Main.main(Main.java:174)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       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.ClassNotFoundException: io.scif.SCIFIOService
       at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
       at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
       ... 54 more
[ERROR] Invalid service: class='io.scif.ome.services.DefaultOMEXMLService', prio
rity=0.0, enabled=true, pluginType=Service
java.lang.NoClassDefFoundError: io/scif/SCIFIOService
       at java.lang.ClassLoader.defineClass1(Native Method)
       at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
       at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
       at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:14
1)
       at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
       at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
       at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
       at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
       at java.lang.ClassLoader.defineClass1(Native Method)
       at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
       at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
       at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:14
1)
       at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
       at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
       at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
       at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
       at org.scijava.util.ClassUtils.loadClass(ClassUtils.java:198)
       at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:275)
       at org.scijava.service.ServiceHelper.findServiceClasses(ServiceHelper.ja
va:326)
       at org.scijava.service.ServiceHelper.<init>(ServiceHelper.java:100)
       at org.scijava.Context.<init>(Context.java:178)
       at org.scijava.Context.<init>(Context.java:122)
       at org.scijava.Context.<init>(Context.java:82)
       at org.scijava.Context.<init>(Context.java:71)
       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:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       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)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at fiji.Main.main(Main.java:174)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       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.ClassNotFoundException: io.scif.SCIFIOService
       at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
       at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
       ... 54 more
[WARNING] 28 exceptions occurred during plugin discovery.
log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventSe
rvice).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more in
fo.
Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalArgumentException: Invalid service: net.imagej.lut.DefaultLUTSe
rvice
       at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.ja
va:254)
       at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:210)

       at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:173)

       at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:145
)
       at org.scijava.Context.<init>(Context.java:179)
       at org.scijava.Context.<init>(Context.java:122)
       at org.scijava.Context.<init>(Context.java:82)
       at org.scijava.Context.<init>(Context.java:71)
       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:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       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)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       at fiji.Main.main(Main.java:174)
       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
java:39)
       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:25)
       at java.lang.reflect.Method.invoke(Method.java:597)
       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.IllegalArgumentException: Invalid service: net.imagej.Defau
ltDatasetService
       at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.ja
va:254)
       at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:210)

       at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHel
per.java:305)
       at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.ja
va:244)
       ... 29 more
Caused by: java.lang.NoClassDefFoundError: io/scif/img/ImgIOException
       at java.lang.Class.getDeclaredConstructors0(Native Method)
       at java.lang.Class.privateGetDeclaredConstructors(Class.java:2389)
       at java.lang.Class.getConstructor0(Class.java:2699)
       at java.lang.Class.newInstance0(Class.java:326)
       at java.lang.Class.newInstance(Class.java:308)
       at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHel
per.java:275)
       at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.ja
va:244)
       ... 32 more
Caused by: java.lang.ClassNotFoundException: io.scif.img.ImgIOException
       at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
       at java.security.AccessController.doPrivileged(Native Method)
       at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
       at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
       at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
       ... 39 more


C:\Documents and Settings\confocal\Desktop\Fiji.app>
fijiErrors.log
Comment 1 Mark Hiner 2014-06-12 08:51:06 CDT 
Hi Aryeh,

 The various "Warning: XXX.jar matched multiple versions" suggests there is problem with your local installation. I am concerned that when enabling/disabling update sites, some unwanted jars got left behind and caused these versioning problems.

 You could try manually deleting the older versions of the jars in contention (e.g. imagej-legacy-0.2.0.jar and imagej.2.0.0-beta-8.jar), or try running:

ImageJ-win64.exe --update update-force-pristine

(although I'm not sure that will work given the state of your Fiji)

Let me know if those don't help
Comment 2 Aryeh Weiss 2014-06-12 09:01:10 CDT 
I will next see that machine next Thurs.
Most likely I will put in a clean installation and enable the sites whose
plugins I really need.
I will follow this up to let you know if that resolved the issue.
Comment 3 Curtis Rueden 2014-06-23 16:51:23 CDT 
Waiting on info from Aryeh.
Comment 4 Aryeh Weiss 2014-06-23 21:46:34 CDT 
Sorry about that...
This was probably also a problem with update sites. Re-installation 
without the problematic sites solved the problem.
Comment 5 Curtis Rueden 2014-06-24 09:03:01 CDT 
Thanks for the confirmation, Aryeh.

For anyone else interested: see also
http://fiji.sc/bugzilla/﷒0﷓