⚠

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 790 - BioFormats Importer Error
BioFormats Importer Error
Status: RESOLVED DUPLICATE of bug 772
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-16 08:02 CDT by nantho2
Modified: 2014-06-16 08:43 CDT
2 users (show)

See Also:
Description nantho2 2014-06-16 08:02:35 CDT 
Since ImageJ2 I cannot seem to open .oib files.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\NELLYP~1\Fiji\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\NELLYP~1\Fiji\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140610174546)
Fiji: http://fiji.sc/update/ (last check:20140610180938)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20131118044144)

Files not up-to-date:
  b40c29fe (MODIFIED) 20140610144745 jars/imagej-common-0.7.2.jar
  28dd47da (MODIFIED) 20140616085853 jars/imagej-common-0.7.3.jar
  662c71b7 (MODIFIED) 20140610144745 jars/imagej-updater-0.3.6.jar
  e50da8f6 (MODIFIED) 20140616085853 jars/imagej-updater-0.3.7.jar
  1aac083b (MODIFIED) 20140611122822 jars/scifio-0.15.0.jar
  af8c5783 (MODIFIED) 20140616085852 jars/scifio-0.15.1.jar
  9c41e52c (MODIFIED) 20140611122823 jars/scijava-common-2.22.5.jar
  86b72a38 (MODIFIED) 20140616085852 jars/scijava-common-2.23.0.jar
  2eca2c1e (LOCAL_ONLY) 20140521105355 macros/BatchMacro.ijm
  728a17e6 (LOCAL_ONLY) 20131122172305 macros/Macro.ijm
  cb9e3fee (LOCAL_ONLY) 20140512131332 plugins/Differentials_m_.jar
  0bbd60b1 (LOCAL_ONLY) 20140217105204 plugins/Intravital_Microscopy_Toolbox.ijm
  94ff9125 (LOCAL_ONLY) 20140305083011 plugins/Mosaic_ToolSuite.jar
  113d8ccc (LOCAL_ONLY) 20130815165830 plugins/PhiOverlay.jar
  68fa4608 (LOCAL_ONLY) 20130814125912 plugins/Radial_Profile.class
  100e7398 (LOCAL_ONLY) 20050928181804 plugins/SurfaceJ_.class
  276637c9 (LOCAL_ONLY) 20050928181804 plugins/VolumeJ_.class
Comment 1 nantho2 2014-06-16 08:03:03 CDT 
Error details:

(Fiji Is Just) ImageJ 2.0.0-rc-4/1.49b; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 22MB of 6095MB (<1%)
 
java.lang.NoClassDefFoundError: Could not initialize class loci.common.NIOByteBufferProvider
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:129)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:138)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:147)
	at loci.common.Location.getHandle(Location.java:307)
	at loci.common.Location.getHandle(Location.java:278)
	at loci.common.Location.getHandle(Location.java:268)
	at loci.formats.ImageReader.getReader(ImageReader.java:176)
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:608)
	at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:201)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)
Comment 2 Mark Hiner 2014-06-16 08:35:23 CDT 
Hello,

 This is a duplicate of bug #772. There is a problem with the MOSAIC ToolSuite, as it ships a class that is now outdated and clashing with a Bio-Formats class.

 The MOSAIC developers will need to update their tool so that it either does not ship the conflicting class or shadows it appropriately.

Sorry for the inconvenience! Thank you for the report though.

*** This bug has been marked as a duplicate of bug 772 ***
Comment 3 Mark Hiner 2014-06-16 08:43:47 CDT 
I wanted to point out that this bug may actually be fixed on the latest MOSAIC ToolSuite.

Have you updated your Fiji? I notice that your last check for the MOSAIC ToolSuite is 20131118044144.

For me it's 20140615174137, and it looks like there have been updates to the ToolSuite in the last 3 days. When I have the ToolSuite enabled I am able to use the Bio-Formats importer again.