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Bug 660 - bioformats import don't work
bioformats import don't work
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-09-05 04:16 CDT by julie
Modified: 2014-06-16 14:46 CDT
3 users (show)

See Also:

Description julie 2013-09-05 04:16:25 CDT
java.lang.NoClassDefFoundError: Could not initialize class loci.common.ReflectedUniverse
	at loci.common.DebugTools.enableLogging(DebugTools.java:83)
	at loci.plugins.LociImporter.run(LociImporter.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:196)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:680)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_51
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_51-b11-457-10M4509
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.51-b01-457
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2013-09-05 10:14:44 CDT
I see that at least one file is missing: jars/slf4j-log4j12.jar (which I have locally and I do not get that error). However, when I remove that file, I get another error than you did.

Could you please run the updater in advanced mode, View mode "all files" and find out what other files might be missing?
Comment 2 Curtis Rueden 2013-09-05 10:25:01 CDT
Thanks for the report. Looks like you're using the Bio-Formats daily builds, correct?

Unfortunately, I cannot reproduce this error on any of three OS X systems here. However, there was one recent change to Bio-Formats which might be related. It gave me an idea for a potential fix, which I have now uploaded.

Could you please update and try again?

If you still receive the error, try the following:

* Help > Update Fiji
* Advanced Mode
* View uninstalled files only

If any of the following files are present as "Not installed" (with or without a version suffix), install them:

* jars/bio-formats
* jars/bio-formats/scifio
* jars/loci-common
* jars/log4j
* jars/mdbtools-java
* jars/metakit
* jars/ome-xml
* jars/poi-loci
* jars/slf4j-api
* jars/slf4j-log4j12
* plugins/loci_plugins

Then check the same with "View modified files only". If any of those files are marked as "Locally modified", tell the updater to update them.

Afterwards, restart Fiji and see if it works.
Comment 3 Curtis Rueden 2013-09-05 11:00:34 CDT
In discussing this bug with between developers here, one other thing occurred to us: did you try to upgrade Bio-Formats using the "Plugins > LOCI > Update LOCI Plugins" command?

If so, that command does not work properly in Fiji. To enable Bio-Formats daily builds, you should instead run:

* Help > Update Fiji
* Manage update sites
* Tick the "Bio-Formats daily builds" box
* Click "Close"
* Click "Apply changes"
* Restart Fiji

Note, however, that if you run the "Update LOCI Plugins" command, some of those JAR files will be marked "Locally modified" by the ImageJ updater, and you will need to manually "Update" them again back to known versions.

Apologies for the confusion with this. To avoid such problems in the future, I have disabled the "Update LOCI Plugins" command in Fiji from now on. If you try to run it, it will now simply launch the ImageJ updater instead. I also disabled Bio-Formats's own built-in update check, since Fiji manages its own update checking.
Comment 4 Curtis Rueden 2014-06-16 14:46:31 CDT
I assume that updating your Fiji fixed the issue, so closing this bug as fixed. Please reopen with details if you are still having problems.