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Bug 283 - Log error on startup
Log error on startup
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2011-02-04 10:48 CST by G. Landini
Modified: 2011-02-04 21:12 CST
1 user (show)

See Also:
Description G. Landini 2011-02-04 10:48:21 CST 
I get this error in the log window at startup

"The script Temporal-Color_Code.ijm would override an existing menu entry; skipping"

That is all.

  os.arch => amd64
  os.name => Linux
  os.version => 2.6.34.7-0.7-desktop
  java.version => 1.6.0_23
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_23-b05
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.0-b09
  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 => null
  file.separator => /

The up-to-date check says: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/lib64/jvm/java/jre
  fiji.dir => /home/gabriel/fiji

Information about the version of each plugin:

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  91bf372e9c531a68d08cb158239df303c0a37fb1 20110204094429 plugins/register_virtual_stack_slices.jar
  4d7eaf239c033d305a464a06c3e64c68d096c7e1 20110204094429 plugins/registration_3d.jar
  e6e0879f5d50afa8d0dd213b4b66e396a39a47b7 20100614090832 retro/backport-util-concurrent-3.1.jar
  e250f0c40b768e90ed7d3910d9869075f3e438cd 20100614090832 retro/retrotranslator-runtime-1.2.7.jar
  eea1390da8fac38763ed4c03f1acb3342b942717 20100614090832 retro/retrotranslator-transformer-1.2.7.jar
  21e7b7ec24eff575a502e3ac5089de5b3745af15 20110106121108 scripts/Miji.m
  3daabf6b3c20f374cf42b672eb29035003dbc40e 20101203120025 scripts/Miji_Test.m
  d326018044a582f5106efc6fc90ad09f98a6a822 20100614090832 scripts/Record_Desktop.py
  0ea7f8fc6683e74065ae7fd82c1b92676e069526 20100614090832 scripts/Record_Window.py
  af954bdff6392779e47e43fb4063f255a8a5ec6b 20101203120025 scripts/bfopen.m
Comment 1 Johannes Schindelin 2011-02-04 15:29:22 CST 
This looks like a developer version which rolled back one or two files via the updater. Possible? (I updated a clean non-developer install of Fiji, and did not encounter the problem.)
Comment 2 Johannes Schindelin 2011-02-04 16:10:33 CST 
In addition, I now uploaded all of the files implementing the new special-handling of plugins/Scripts/, including all the fixes necessary to override/run macros and javascripts via Fiji's scripting framework.
Comment 3 G. Landini 2011-02-04 16:59:27 CST 
Hm... if I git pull origin master
I get Already up-to-date, but the problem persists
Comment 4 Johannes Schindelin 2011-02-04 17:59:40 CST 
I fear that the problem is an old-couple fight between the developer version and the version the Updater thinks is current.

So my guess is that either a ./Build.sh would fix things, or that Help>Update Fiji would mark a few files as locally-modified which you might want to mark for update to fix things.

In particular, I think that plugins/CLI_.jar, jars/Fiji.jar and jars/fiji-scripting.jar must conform to what the Fiji Updater thinks is current.
Comment 5 G. Landini 2011-02-04 18:26:30 CST 
I am afraid that neither resolve it.
Is the Temporal-Color_Code.ijm part of the current Fiji?
There is a jar file (menu entry in the Hyperstack submenu) as well as that macro with the same name.
Cheers
G.
Comment 6 Johannes Schindelin 2011-02-04 18:43:44 CST 
I think I understand it now. The Temporal_Color_Coder.jar was removed, since we no longer need a Java wrapper around the macro. But you still had that stale file lying around, since the Fiji Updater thinks it is current (and does not know about Temporal-Color_Code.ijm).

So it _was_ an old-couple misunderstanding between developer and user version of Fiji.

Take-home message: check "git status" from time to time to remove obsoleted .jar files.

I uploaded the macro and removed the .jar file from the updater (which I wanted to do later when I tested more, but hey, this is the way things go).
Comment 7 G. Landini 2011-02-04 21:12:14 CST 
Yup, that seems to have resolved it.
Thanks Dscho!

Cheers

G.