Continuous Fiji releases

[ctrueden]

Hi everyone,

To make it easier to start with a more recent Fiji, and keep things up to
date, the Fiji Downloads page [1] now offers a Continuous Release bundle,
which reflects the latest version of Fiji according to the Updater.
Downloading this bundle is the most painless way to quickly get an
up-to-date Fiji from scratch.

Please let us know if you have any questions or issues with it!

Cheers,
The Fiji team

[1] http://fiji.sc/Downloads

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[Glen MacDonald-2]

If a bundled plugin, such as  LOCI, has been reinstalled in FIJI, all subsequent updates will flag that plugin as locally modified.  How can I force FIJI to update a plugin flagged aslocally modified when it runs updates?

thanks,
Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923
[phone]

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[Pariksheet Nanda]

On Mon, Oct 29, 2012 at 5:00 PM, Glen H MacDonald
<[hidden email]> wrote:
> If a bundled plugin, such as  LOCI, has been reinstalled in FIJI, all
> subsequent updates will flag that plugin as locally modified.  How can I
> force FIJI to update a plugin flagged aslocally modified when it runs
> updates?
>

Help > Update Fiji > Advanced Mode > View Options: View locally
modified files only > [Change the Status/Action] > Apply Changes

> Glen

Pariksheet

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[Glen MacDonald-2]

Yes, that should work but I've got 2 installations of FIJI that had trouble with LOCI, so I reinstalled the LOCI plugin. Then updates flagged it as locally modified.  A complete FIJI reinstall fixed the situation on 1 computer.  But, I've been trying to figure what is going with the other computer before reinstalling FIJI.  Both are MacPro, OS10.6.8. The updater will not update the this morning's Daily Build, the advanced mode only offers to leave  LOCI as is or to uninstall it.

LOCI appears in the plugins menu.  Attempting to open a file gives this exception:
java.lang.reflect.InvocationTargetException
  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:146)
  at ij.Command.runCommand(Command.java:95)
  at ij.Executer.run(Executer.java:64)
  at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NoSuchMethodError: loci.common.IniTable.get(Ljava/lang/Object;)Ljava/lang/String;
  at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:72)
  at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:66)
  at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:158)
  at loci.plugins.in.Importer.parseOptions(Importer.java:114)
  at loci.plugins.in.Importer.run(Importer.java:73)
  at loci.plugins.LociImporter.run(LociImporter.java:81)
  at ij.IJ.runUserPlugIn(IJ.java:185)
  at ij.IJ.runPlugIn(IJ.java:152)
  ... 8 more

Regards,
Glen


Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923
[phone]

On Mon, 29 Oct 2012, Pariksheet Nanda wrote:

> On Mon, Oct 29, 2012 at 5:00 PM, Glen H MacDonald
> <[hidden email]> wrote:
>> If a bundled plugin, such as  LOCI, has been reinstalled in FIJI, all
>> subsequent updates will flag that plugin as locally modified.  How can I
>> force FIJI to update a plugin flagged aslocally modified when it runs
>> updates?
>>
>
> Help > Update Fiji > Advanced Mode > View Options: View locally
> modified files only > [Change the Status/Action] > Apply Changes
>
>> Glen
>
> Pariksheet
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[dscho]

Hi Glen,

On Mon, 29 Oct 2012, Glen H MacDonald wrote:

> If a bundled plugin, such as  LOCI, has been reinstalled in FIJI, all
> subsequent updates will flag that plugin as locally modified.  How can I
> force FIJI to update a plugin flagged aslocally modified when it runs
> updates?

You can either right-click (Ctrl+click on MacOSX) the respective line and
select "Install it", or select the row by clicking on it and then clicking
the button "Install" in the lower left.

Ciao,
Johannes

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[dscho]

Hi Glen,

On Tue, 30 Oct 2012, Glen MacDonald wrote:

> that offers the 2 choices of "Locally modified" and "Uninstall it", same
> as selecting from the Advanced mode list
>
> Also, in Advanced mode, the details window says "this file is no longer
> needed"

In the particular case of loci_tools.jar: this file is an assembly of a
lot of other files, and as such very large. Therefore we switched to serve
the individual .jar files instead, most of which can stay unchanged over
the course of updates, saving a lot of bandwidth.

The .jar file containing the plugins is loci_plugins-4.4-SNAPSHOT.jar.

Ciao,
Johannes

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