ImageJ searchbar issue

imagej
search

#1

Hi guys,

my Fiji is up-to-date (Windows7 64 bit) but as soon as I start typing anything inside the new search bar the console open up and shows error messages.

Is anyone else also experiencing this issue and what info do you need to find the reason for this?

Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: org.scijava.plugin.PluginService.sort(Ljava/util/List;Ljava/lang/Class;)V
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.rebuild(SwingSearchBar.java:634)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.update(SwingSearchBar.java:563)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.lambda$null$0(SwingSearchBar.java:338)
	at org.scijava.thread.DefaultThreadService$2.run(DefaultThreadService.java:221)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: org.scijava.plugin.PluginService.sort(Ljava/util/List;Ljava/lang/Class;)V
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.rebuild(SwingSearchBar.java:634)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.update(SwingSearchBar.java:563)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.lambda$null$0(SwingSearchBar.java:338)
	at org.scijava.thread.DefaultThreadService$2.run(DefaultThreadService.java:221)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: org.scijava.plugin.PluginService.sort(Ljava/util/List;Ljava/lang/Class;)V
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.rebuild(SwingSearchBar.java:634)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.update(SwingSearchBar.java:563)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.lambda$null$0(SwingSearchBar.java:338)
	at org.scijava.thread.DefaultThreadService$2.run(DefaultThreadService.java:221)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: org.scijava.plugin.PluginService.sort(Ljava/util/List;Ljava/lang/Class;)V
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.rebuild(SwingSearchBar.java:634)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.update(SwingSearchBar.java:563)
	at org.scijava.ui.swing.search.SwingSearchBar$SwingSearchPanel.lambda$null$0(SwingSearchBar.java:338)
	at org.scijava.thread.DefaultThreadService$2.run(DefaultThreadService.java:221)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Fiji updates break plugins distributed through the Fiji update mechanism
#2

It seems that you have an outdated version of scijava-common.jar in your installation. The current one, being shipped by the Java-8 update site, should be scijava-common-2.69.0.jar. (The sort method was introduced in this commit.)

Can you check if you’ve enabled any third-party update site(s) that ship(s) an outdated scijava-common, and try if deactivating this update site helps?


#3

I deactivated Tr2D, then TensorFlow and Hadim. The last one was using jars/scijava-common-2.65.0.jar …

And now Fiji does not start anymore …


#4

And I downloaded jars/scijava-common-2.65.0.jar from the internet and put i back inside the respective folder, since deactivating those sites completely removed the jar.

And know it works. Strange, but fine.


#5

Glad to read that it works for you.

I suppose you meant scijava-common-2.69.0.jar, right?

That is strange. Removing the update sites should have resulted in the jar file from the Java-8 site being shipped (and it did so in my tests here). If not, this is a bug in imagej-updater.

Now it’s in the hands of @fjug (Tr2D), @ctrueden (TensorFlow) and @hadim (Hadim) to ensure that their update sites (which were primarily intended for testing anyways) will stop shipping their own scijava-common.jar and work with an up-to-date Fiji.


How can I remove a core Fiji JAR from my update site?
#6

I fixed the TensorFlow update site such that it does not override scijava-common or scijava-ui-swing anymore. Updating your Fiji via Help :arrow_forward: Update… should result in a working search bar with working TensorFlow-related plugins at the same time. Please let me know if not.

The TensorFlow update site is a production-ready update site which I am actively maintaining. A paper will be published soon about the main plugin it offers currently (1). So if it does not work, please do let me know!