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Bug 488 - LOCI no longer functions after update
LOCI no longer functions after update
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Windows
: P5 critical
Assigned To: ImageJ Bugs Mailing List
: 489
Depends on:
Blocks:
 
Reported: 2012-09-12 19:30 CDT by Andrea Stout
Modified: 2012-09-13 21:58 CDT
3 users (show)

See Also:

Description Andrea Stout 2012-09-12 19:30:20 CDT
This problem occurs on all Mac OS and Windows computers in our facility and showed up around Sept. 1: after updating Fiji, LOCI no longer works at all (though it shows up in the Plugins menu).  Repeated removal of old copies of Fiji and re-installation (followed by updating) do not solve the problem.  Java is up-to-date on all machines.  Please help!

Andrea


Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86
  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) Client 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: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Public\Fiji\Fiji.app/java/win32/jdk1.6.0_24/jre/
  ij.dir => C:\Users\Public\Fiji\Fiji.app
Comment 1 Melissa Linkert 2012-09-12 19:50:44 CDT
Do you see any error messages?  If so, can you please add the complete text of the errors to this bug report?
Comment 2 Andrea Stout 2012-09-12 20:39:50 CDT
No error message appears when you go to Plugins --> LOCI --> Bio-Formats Importer, but nothing happens (you don't see the usual file selection dialog). Other items under the LOCI subheading do seem to work: the Bio-Formats Exporter is there and the LOCI configurations window opens if you try that.

If you try to open a .dv (Deltavision) file you get the error message "File is not in a supported format, a reader plugin is not available, or it was not found"  This happens with Drag & Drop or if you do File --> Open.
Comment 3 Melissa Linkert 2012-09-12 21:32:13 CDT
Thank you for the additional information; I do see the problem now too.

This is not a bug in Bio-Formats - one of the .jar files required for Bio-Formats to function is not automatically installed by the Fiji updater.  If you go to "Help > Update Fiji", click "Advanced mode" and then choose and install the "jars/slf4j-log4j12-1.5.10.jar" entry (you might need to click "View all files" first) that should solve the problem.
Comment 4 Melissa Linkert 2012-09-12 21:34:27 CDT
*** Bug 489 has been marked as a duplicate of this bug. ***
Comment 5 Johannes Schindelin 2012-09-13 21:58:11 CDT
The problem was that the update site did not list slf4j-log4j.jar as a dependency of loci-common.jar (and indeed, loci-common.jar does not reference any class of slf4j-log4j.jar directly). I fixed this.

I also fixed the updater so that it realizes when not-installed dependencies have been added to installed files and marks them for installation.