[ome-users] Apple OS X 10.9 - Mavericks and LOCI question

[Curtis Rueden]

Hi Vladimir,

I am CCing the ome-users list, which is the best place to ask Bio-Formats
questions.

> it looks like LOCI is incompatible with the changes that 10.9
> introduces to Java.

Bio-Formats is working for me on OS X 10.9 with Java 1.6.0_45 as well as
Java 1.7.0_21.

> java.lang.NoClassDefFoundError: loci/formats/UpgradeChecker

That error indicates a mismatch between JAR files. Are you using the Fiji
distribution of ImageJ? If not, I suggest you do so; Fiji comes bundled
with the latest stable version of Bio-Formats, and is by far the most
convenient way of updating it. If you need to enable a development build of
Bio-Formats, you can do so as described at:

    http://fiji.sc/Bio-Formats#Daily_builds

If you use Fiji, you will not need to use the "Update LOCI plugins" command
anymore.

Regards,
Curtis


On Tue, Oct 29, 2013 at 4:46 PM, Vladimir I Gelfand <
vgelfand at northwestern.edu> wrote:

>   Hi Curtis,
>
>  I noticed that you are using LOCI with Apple OS X 10.9, I wonder if you
> can suggest to have it to work. I am trying to use it within Fiji but it
> complains every time (see the log below, for example, from my attempt to
> update LOCI).
>
>  I would very much appreciate your suggestions — it looks like LOCI is
> incompatible with the changes that 10.9 introduces to Java.
>
>  Thank you very much for your help!
>
>  Vladimir Gelfand
>
>
>  (Fiji Is Just) ImageJ 1.48e; Java 1.6.0_65 [64-bit]; Mac OS X 10.9; 81MB
> of 3713MB (2%)
>
> java.lang.NoClassDefFoundError: loci/formats/UpgradeChecker
> at loci.plugins.Updater.install(Updater.java:113)
> at loci.plugins.Updater.run(Updater.java:94)
> at ij.IJ.runUserPlugIn(IJ.java:196)
> at ij.IJ.runPlugIn(IJ.java:160)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at ij.Command.runPlugIn(Command.java:148)
> at ij.Command.runCommand(Command.java:97)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:695)
>
>
>    -----------
>  Vladimir I. Gelfand, Ph.D.
> Leslie B. Arey Professor
> Department of Cell and Molecular Biology
> Feinberg School of Medicine
> Northwestern University
> 303 E. Chicago Ave. Ward 11-100
> Chicago, IL 60611-3008
> T-(312) 503-0530
> F-(312) 503-7912
> vgelfand at northwestern.edu
>
>
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