⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 76 - Odd plugin folder behavior
Odd plugin folder behavior
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: Johannes Schindelin
Depends on:
Blocks:
 
Reported: 2009-09-02 20:09 CDT by nodice73@yahoo.com
Modified: 2011-03-23 12:35 CDT
2 users (show)

See Also:
Description nodice73@yahoo.com 2009-09-02 20:09:32 CDT 
Useful Java System Properties:
  os.arch => i386
  os.name => Linux
  os.version => 2.6.28-15-generic
  java.version => 1.6.0_10
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_10-b33
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 11.0-b15
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

Bug Report Text:

Hello,

I have a folder where I keep my plugins:

/home/nodice/Documents/Code/ImageJ/plugins

If I make a link to this folder in the Fiji plugins folder:

ln -s /home/nodice/Documents/Code/ImageJ/plugins aw_plugins

and restart Fiji, a menu item 'aw plugins' appears in the 'Plugins' menu, as expected.  Clicking on it reveals each of my plugins, and they run as expected.  However, an additional 'aw plugins' entry is also created which is empty.

If instead I copy my plugins folder to the Fiji plugins folder, only one menu item appears, but I cannot run any of the plugins, as they all result in the error:

java.lang.NoSuchMethodError: ij.io.PluginClassLoader.loadClass(Ljava/lang/String;ZZ)Ljava/lang/Class;
at Refresh_Javas.compile(Refresh_Javas.java:83)
at Refresh_Javas.runScript(Refresh_Javas.java:39)
at common.RefreshScripts.run(RefreshScripts.java:323)
at Refresh_Javas.run(Refresh_Javas.java:30)
at ij.IJ.runUserPlugIn(IJ.java:179)
at ij.IJ.runPlugIn(IJ.java:146)
at ij.Executer.runCommand(Executer.java:122)
at ij.Executer.run(Executer.java:59)
at java.lang.Thread.run(Thread.java:619)

Neither of these problems occur when I use a fresh install of ImageJ from the ImageJ website.

Thanks,
Adam
Comment 1 nodice73@yahoo.com 2009-09-03 19:39:11 CDT 
Going to 'Help' -> 'Update Menus' gets rid of the extra entry, but it reappears after restarting Fiji.
Comment 2 Johannes Schindelin 2009-09-11 07:33:15 CDT 
Could you please provide more details as to what is in your plugins folder? Are there .class, .java, .jar, other files?
Comment 3 nodice73@yahoo.com 2009-09-11 23:48:34 CDT 
(In reply to comment #2)
> Could you please provide more details as to what is in your plugins folder? Are
> there .class, .java, .jar, other files?

Currently, there are .class and .java files.
Comment 4 Johannes Schindelin 2009-11-12 02:31:15 CST 
Sorry for the long delay.  It appears that there is a problem due to the presence of the .java files, and I suspect that you are not running Fiji's version of ImageJ (which makes compiling .java files on-the-fly break).  Am I correct?
Comment 5 nodice73@yahoo.com 2009-11-22 01:11:22 CST 
(In reply to comment #4)
> Sorry for the long delay.  It appears that there is a problem due to the
> presence of the .java files, and I suspect that you are not running Fiji's
> version of ImageJ (which makes compiling .java files on-the-fly break).  Am I
> correct?

I have both Fiji and ImageJ independently installed on my computer.  Not sure if that counts as "not running Fiji's version of ImageJ".

I tested removing the .java files, and this makes the issue go away.  Do they need to be in a different place?
Comment 6 Johannes Schindelin 2010-03-13 12:04:09 CST 
Again, very sorry for the delay!

(In reply to comment #5)
> I tested removing the .java files, and this makes the issue go away.  Do they
> need to be in a different place?

The problem is that we used to be able to only run .java plugins (which are compiled transparently, i.e. if you change the .java file, the plugin is compiled before it is launched) with Fiji's own version of ImageJ.

This should be fixed with recent changes, though, as well as the duplicate menu entry.

Could you please try again?
Comment 7 Johannes Schindelin 2011-03-23 12:35:33 CDT 
Assuming that no answer means that this bug is indeed fixed.