Re: Problems with added plugins after recent update

[gankaku]

Hi Amsha, hi list,


2014-06-12 16:46 GMT+02:00 AmshaP <[hidden email]>:

> Hello,
>
> Following an update this morning, Fiji does not run the plugins that I had
> once downloaded into the /plugins folder, and I get the error "Plugin or
> Class not found" (in this case, for Mexican_Hat_Filter and MultiStackRegFix
> which are both .class files).
>


I can confirm that behaviour. None of my own and downloaded custom plugins
runs while showing the same warning as mentioned by Amsha for all of them.



>
> When I install these plugins from Plugins>Install, the Log shows: "WARNING:
> The PluginClassLoader cannot be reset." while a message says the plugin was
> installed correctly; but then I get the same error as above when I try to
> run them.
>

I can also confirm this behaviour while trying to separately intall any
custom plugin .



> As these plugins worked well until yesterday and are unrelated, I was
> wondering whether the update had modified something which clashes with
> exterior plugins...?
>

Updating to ImageJ 2.0.0-rc4 / 1.49b caused this behaviour in my case as
well

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Stoyan Pavlov]

Hi all,
Same here.
I was just about to write to the list about the same issues. Problem
plugins in my case are the ones from Landini's Morphology package.
Stoyan

---
Dr. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 052
e-mail: [hidden email]
           [hidden email]


2014-06-12 17:46 GMT+03:00 AmshaP <[hidden email]>:

> Hello,
>
> Following an update this morning, Fiji does not run the plugins that I had
> once downloaded into the /plugins folder, and I get the error "Plugin or
> Class not found" (in this case, for Mexican_Hat_Filter and MultiStackRegFix
> which are both .class files).
>
> When I install these plugins from Plugins>Install, the Log shows: "WARNING:
> The PluginClassLoader cannot be reset." while a message says the plugin was
> installed correctly; but then I get the same error as above when I try to
> run them.
>
> As these plugins worked well until yesterday and are unrelated, I was
> wondering whether the update had modified something which clashes with
> exterior plugins...?
>
> (I have tried re-installing Fiji from the website in case the Updater was
> faulty, but the behavior of the re-installed Fiji is the same.)
>
> Has someone got an idea ?
>
> Thank you,
> Amsha
>
> PS : I'm not sure this is related, but the icon of ImageJ-win64.exe has
> also
> changed from the blue FIJI to a black and gold ImageJ logo after the same
> update.
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Problems-with-added-plugins-after-recent-update-tp5008164.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

On 6/12/14, 8:06 PM, Stoyan Pavlov wrote:

> Hi all,
> Same here.
> I was just about to write to the list about the same issues. Problem
> plugins in my case are the ones from Landini's Morphology package.
> Stoyan
>
> ---
> Dr. Stoyan P. Pavlov, MD, PhD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
>   Bulgaria
> Tel: +359 (0) 52 - 677 - 052
> e-mail: [hidden email]
>             [hidden email]
>
>
> 2014-06-12 17:46 GMT+03:00 AmshaP <[hidden email]>:
>
>> Hello,
>>
>> Following an update this morning, Fiji does not run the plugins that I had
>> once downloaded into the /plugins folder, and I get the error "Plugin or
>> Class not found" (in this case, for Mexican_Hat_Filter and MultiStackRegFix
>> which are both .class files).
>>
>> When I install these plugins from Plugins>Install, the Log shows: "WARNING:
>> The PluginClassLoader cannot be reset." while a message says the plugin was
>> installed correctly; but then I get the same error as above when I try to
>> run them.
>>
>> As these plugins worked well until yesterday and are unrelated, I was
>> wondering whether the update had modified something which clashes with
>> exterior plugins...?
>>
>> (I have tried re-installing Fiji from the website in case the Updater was
>> faulty, but the behavior of the re-installed Fiji is the same.)
>>
>> Has someone got an idea ?
>>
>> Thank you,
>> Amsha
>>
>> PS : I'm not sure this is related, but the icon of ImageJ-win64.exe has
>> also
>> changed from the blue FIJI to a black and gold ImageJ logo after the same
>> update.
>>
>>
>>
>> --
>> View this message in context:
>> http://imagej.1557.x6.nabble.com/Problems-with-added-plugins-after-recent-update-tp5008164.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>>

I have also experience some issues associated with updates of Fiji. the
most serious of which was when the ImageJ window failed to open. Here is
some of my experience that may be of assistance:

1. If you can , use the the Fiji Help>Report a Bug . The response from
is often close to real time.

2. Many (perhaps all) of the problems seem to be associated with 3rd
party update sites. Try to limit those to the ones you really need.
Apparently some of them replace libraries which then cause inconsistency
in FIji. I found issues with Trackmate, LLTT, and Mosaic.

3. I use the morphology suite of Gabriel Landini -- so far, no problems
with it.

4. I cannot cut and paste out of the recorder on OSX 10.9 (on Linux I
can). I instead use the "create" button to move the recorder text to a
script, and cut-and-paste from there. I guess I should report that, but
it is just a minor annoyance, mac specific, and the support people have
enough to do.

5. Make regular backups of your working Fiji.app. Then you can always
fall back to it without losing your custom configuration.

This is my experience -- I hope it will be of use to others running this
distribution.

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner-2]

Hi all,

 I just wanted to let you know that I could only confirm this with .class
plugins. As far as I can tell, all the .jar plugins I tried were still
working. (e.g. the BioVoxxel plugins don't work, but I could run the SLIM
Curve plugin).

 If anyone can find an example of a plugin in a .jar not working, please
let us know right away.

 I believe Johannes is looking into this issue right now; it seems
reasonable to expect this is an issue with class loading within Fiji.

Thanks all for the reports,
Mark


On Thu, Jun 12, 2014 at 1:02 PM, Aryeh Weiss <[hidden email]> wrote:

> On 6/12/14, 8:06 PM, Stoyan Pavlov wrote:
>
>> Hi all,
>> Same here.
>> I was just about to write to the list about the same issues. Problem
>> plugins in my case are the ones from Landini's Morphology package.
>> Stoyan
>>
>> ---
>> Dr. Stoyan P. Pavlov, MD, PhD
>> Departament of Anatomy, Histology and Embryology
>> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
>> Prof. Marin Drinov Str.55
>> 9002 Varna
>>   Bulgaria
>> Tel: +359 (0) 52 - 677 - 052
>> e-mail: [hidden email]
>>             [hidden email]
>>
>>
>> 2014-06-12 17:46 GMT+03:00 AmshaP <[hidden email]>:
>>
>>  Hello,
>>>
>>> Following an update this morning, Fiji does not run the plugins that I
>>> had
>>> once downloaded into the /plugins folder, and I get the error "Plugin or
>>> Class not found" (in this case, for Mexican_Hat_Filter and
>>> MultiStackRegFix
>>> which are both .class files).
>>>
>>> When I install these plugins from Plugins>Install, the Log shows:
>>> "WARNING:
>>> The PluginClassLoader cannot be reset." while a message says the plugin
>>> was
>>> installed correctly; but then I get the same error as above when I try to
>>> run them.
>>>
>>> As these plugins worked well until yesterday and are unrelated, I was
>>> wondering whether the update had modified something which clashes with
>>> exterior plugins...?
>>>
>>> (I have tried re-installing Fiji from the website in case the Updater was
>>> faulty, but the behavior of the re-installed Fiji is the same.)
>>>
>>> Has someone got an idea ?
>>>
>>> Thank you,
>>> Amsha
>>>
>>> PS : I'm not sure this is related, but the icon of ImageJ-win64.exe has
>>> also
>>> changed from the blue FIJI to a black and gold ImageJ logo after the same
>>> update.
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://imagej.1557.x6.nabble.com/Problems-with-added-
>>> plugins-after-recent-update-tp5008164.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>> --
>>>
>>>
> I have also experience some issues associated with updates of Fiji. the
> most serious of which was when the ImageJ window failed to open. Here is
> some of my experience that may be of assistance:
>
> 1. If you can , use the the Fiji Help>Report a Bug . The response from is
> often close to real time.
>
> 2. Many (perhaps all) of the problems seem to be associated with 3rd party
> update sites. Try to limit those to the ones you really need. Apparently
> some of them replace libraries which then cause inconsistency in FIji. I
> found issues with Trackmate, LLTT, and Mosaic.
>
> 3. I use the morphology suite of Gabriel Landini -- so far, no problems
> with it.
>
> 4. I cannot cut and paste out of the recorder on OSX 10.9 (on Linux I
> can). I instead use the "create" button to move the recorder text to a
> script, and cut-and-paste from there. I guess I should report that, but it
> is just a minor annoyance, mac specific, and the support people have enough
> to do.
>
> 5. Make regular backups of your working Fiji.app. Then you can always fall
> back to it without losing your custom configuration.
>
> This is my experience -- I hope it will be of use to others running this
> distribution.
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi all,

> Fiji does not run the plugins that I had once downloaded into the
> /plugins folder, and I get the error "Plugin or Class not found"

Just wanted to let everyone know that Johannes has a fix for this problem,
but it needs a little more cleanup first before we upload it. We'll take
care of it by the end of the day. (Blame the World Cup for the delay... ;-)

Regards,
Curtis


On Thu, Jun 12, 2014 at 2:02 PM, Mark Hiner <[hidden email]> wrote:

> Hi all,
>
>  I just wanted to let you know that I could only confirm this with .class
> plugins. As far as I can tell, all the .jar plugins I tried were still
> working. (e.g. the BioVoxxel plugins don't work, but I could run the SLIM
> Curve plugin).
>
>  If anyone can find an example of a plugin in a .jar not working, please
> let us know right away.
>
>  I believe Johannes is looking into this issue right now; it seems
> reasonable to expect this is an issue with class loading within Fiji.
>
> Thanks all for the reports,
> Mark
>
>
> On Thu, Jun 12, 2014 at 1:02 PM, Aryeh Weiss <[hidden email]> wrote:
>
> > On 6/12/14, 8:06 PM, Stoyan Pavlov wrote:
> >
> >> Hi all,
> >> Same here.
> >> I was just about to write to the list about the same issues. Problem
> >> plugins in my case are the ones from Landini's Morphology package.
> >> Stoyan
> >>
> >> ---
> >> Dr. Stoyan P. Pavlov, MD, PhD
> >> Departament of Anatomy, Histology and Embryology
> >> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> >> Prof. Marin Drinov Str.55
> >> 9002 Varna
> >>   Bulgaria
> >> Tel: +359 (0) 52 - 677 - 052
> >> e-mail: [hidden email]
> >>             [hidden email]
> >>
> >>
> >> 2014-06-12 17:46 GMT+03:00 AmshaP <[hidden email]>:
> >>
> >>  Hello,
> >>>
> >>> Following an update this morning, Fiji does not run the plugins that I
> >>> had
> >>> once downloaded into the /plugins folder, and I get the error "Plugin
> or
> >>> Class not found" (in this case, for Mexican_Hat_Filter and
> >>> MultiStackRegFix
> >>> which are both .class files).
> >>>
> >>> When I install these plugins from Plugins>Install, the Log shows:
> >>> "WARNING:
> >>> The PluginClassLoader cannot be reset." while a message says the plugin
> >>> was
> >>> installed correctly; but then I get the same error as above when I try
> to
> >>> run them.
> >>>
> >>> As these plugins worked well until yesterday and are unrelated, I was
> >>> wondering whether the update had modified something which clashes with
> >>> exterior plugins...?
> >>>
> >>> (I have tried re-installing Fiji from the website in case the Updater
> was
> >>> faulty, but the behavior of the re-installed Fiji is the same.)
> >>>
> >>> Has someone got an idea ?
> >>>
> >>> Thank you,
> >>> Amsha
> >>>
> >>> PS : I'm not sure this is related, but the icon of ImageJ-win64.exe has
> >>> also
> >>> changed from the blue FIJI to a black and gold ImageJ logo after the
> same
> >>> update.
> >>>
> >>>
> >>>
> >>> --
> >>> View this message in context:
> >>> http://imagej.1557.x6.nabble.com/Problems-with-added-
> >>> plugins-after-recent-update-tp5008164.html
> >>> Sent from the ImageJ mailing list archive at Nabble.com.
> >>>
> >>> --
> >>>
> >>>
> > I have also experience some issues associated with updates of Fiji. the
> > most serious of which was when the ImageJ window failed to open. Here is
> > some of my experience that may be of assistance:
> >
> > 1. If you can , use the the Fiji Help>Report a Bug . The response from is
> > often close to real time.
> >
> > 2. Many (perhaps all) of the problems seem to be associated with 3rd
> party
> > update sites. Try to limit those to the ones you really need. Apparently
> > some of them replace libraries which then cause inconsistency in FIji. I
> > found issues with Trackmate, LLTT, and Mosaic.
> >
> > 3. I use the morphology suite of Gabriel Landini -- so far, no problems
> > with it.
> >
> > 4. I cannot cut and paste out of the recorder on OSX 10.9 (on Linux I
> > can). I instead use the "create" button to move the recorder text to a
> > script, and cut-and-paste from there. I guess I should report that, but
> it
> > is just a minor annoyance, mac specific, and the support people have
> enough
> > to do.
> >
> > 5. Make regular backups of your working Fiji.app. Then you can always
> fall
> > back to it without losing your custom configuration.
> >
> > This is my experience -- I hope it will be of use to others running this
> > distribution.
> >
> > --aryeh
> >
> > --
> > Aryeh Weiss
> > Faculty of Engineering
> > Bar Ilan University
> > Ramat Gan 52900 Israel
> >
> > Ph:  972-3-5317638
> > FAX: [phone]
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Curtis,

On Thu, 12 Jun 2014, Curtis Rueden wrote:

> > Fiji does not run the plugins that I had once downloaded into the
> > /plugins folder, and I get the error "Plugin or Class not found"
>
> Just wanted to let everyone know that Johannes has a fix for this
> problem, but it needs a little more cleanup first before we upload it.
> We'll take care of it by the end of the day. (Blame the World Cup for
> the delay... ;-)

Thanks for keeping everybody in the loop. In particular about where I
spent my afternoon, fixing the bug through my phone (no joke, I have
witnesses).

I also added some regression tests that should help avoid the problem in
the future.

The resulting new version of the ij1-patcher was uploaded to the update
site, after an update everybody should be able to enjoy the fix.

By the way, I got asked today why Fiji has an "Update..." and an "Update
Fiji" menu item in the Help menu. It's easy: "Update..." is the ImageJ2
plugin, "Update Fiji" is a simple ImageJ 1.x plugin adapter for exactly
the same code (but with a little bit more of a fallback strategy at the
moment). We will remove the "Update Fiji" entry once we have enough
fallbacks in place so that "Update..." is reasonably safe.

Ciao,
Johannes

P.S.: Brazil won. But Croatia played really well, I thought that a draw
would have been the most appropriate outcome. Just in case anybody is
interested in my opinion...

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[lindaP]

Hi there,

I also experienced problems with plugins in Fiji after the recent update. I downloaded the patch and it fixed the problem in some cases. However, I'm still experiencing issues with Figure Calibration plugin.

This is the message that I get when I try to run it:

(Fiji Is Just) ImageJ 2.0.0-rc-4/1.49b; Java 1.6.0_24 [32-bit]; Windows NT (unknown) 6.2; 32MB of 1223MB (2%)
 
java.lang.ClassFormatError: Truncated class file
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:296)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        at ij.IJ.runUserPlugIn(IJ.java:199)
        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)

I also tried to install the plugin again but then I got the following error message: error in opening zip file, WARNING: The PluginClassLoader cannot be reset.

What can I do to be able to keep using this useful plugin. I'm not a java programmer, only a user of Fiji.

Thanks!

Linda
 

 

[dscho]

Hi Linda,

On Fri, 13 Jun 2014, lindaP wrote:

> java.lang.ClassFormatError: Truncated class file

This means that the download from the update site did not quite work. Can
you start Help>Update... and switch to the advanced mode? You should be
able to select the "locally-modified" view mode and see that there are
files that are not up-to-date...

If that is the case, just select those files and mark them for update,
then click the "Apply changes" button.

> I also tried to install the plugin again but then I got the following
> error message: error in opening zip file, WARNING: The PluginClassLoader
> cannot be reset.

Yes, for the moment, plugins cannot be installed in Fiji without a
restart. Please excuse the inconvenience!

> What can I do to be able to keep using this useful plugin. I'm not a java
> programmer, only a user of Fiji.

Hopefully the advice above will get you back on track. If not, please
consider using Plugins>Utilities>Make Fiji Package to make a .zip package
of your installation, then upload it via Help>Upload Sample Image and get
back to me. I will then try to analyze what is wrong and how to fix it
directly in your setup (that is packaged into the .zip file).

Ciao,
Johannes

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[lindaP]

Hi Johannes,

Thanks a lot for your reply. I tried to perform the update as you suggested but it seems that all my files are up to date. The plugin still doesn't work. So I uploaded the zip archive via the Help menu.

Thanks for your help!

Lenka  

[dscho]

Hi Linda,

On Fri, 13 Jun 2014, lindaP wrote:

> I also experienced problems with plugins in Fiji after the recent update. I
> downloaded the patch and it fixed the problem in some cases. However, I'm
> still experiencing issues with Figure Calibration plugin.
>
> This is the message that I get when I try to run it:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-4/1.49b; Java 1.6.0_24 [32-bit]; Windows NT
> (unknown) 6.2; 32MB of 1223MB (2%)
>  
> java.lang.ClassFormatError: Truncated class file

I finally got a chance to have a look. The file
Fiji.app/plugins/Figure_Calibration.class is empty! It is not managed in
any update site you have enabled, therefore I assume that you downloaded
it yourself.

It may be the best idea to re-download the file from
http://www.astro.physik.uni-goettingen.de/~hessman/ImageJ/Figure_Calibration/
and overwrite the 0-byte file.

Ciao,
Johannes

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[lindaP]

You're right. I don't know how it happened. I downloaded the plugin again and it works fine now. Thanks for you help!

[dscho]

Hi Linda,

On Tue, 24 Jun 2014, lindaP wrote:

> You're right. I don't know how it happened. I downloaded the plugin
> again and it works fine now. Thanks for you help!

Thanks for your feedback, and happy that you have a working system again!
Johannes

--
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[Luisa de Vivo]

Hi list,

I had this error message in a mac mahcine after the update this morning. I
updated again FIJI after Johannes fix (I also selected locally modified
files...), but I still get the same error when I try to use the 3D viewer
plugin.
Do you have any suggestion?
thank you
==================
ERROR:
java.lang.reflect.InvocationTargetException
 at java.awt.EventQueue.invokeAndWait(EventQueue.java:1126)
at java.awt.EventQueue.invokeAndWait(EventQueue.java:1103)
 at javax.swing.SwingUtilities.invokeAndWait(SwingUtilities.java:1326)
 at ini.trakem2.display.Display3D.get(Display3D.java:321)
at ini.trakem2.display.Display3D$6.call(Display3D.java:470)
 at ini.trakem2.display.Display3D$6.call(Display3D.java:405)
 at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
 at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
 at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.SecurityException: sealing violation: package
javax.media.j3d is sealed
at java.net.URLClassLoader.defineClass(URLClassLoader.java:234)
 at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
 at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
 at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
 at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
 at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
 at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
 at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
 at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at ij3d.ImageWindow3D.<init>(ImageWindow3D.java:64)
 at ini.trakem2.display.d3d.Display3DGUI.init(Display3DGUI.java:70)
 at ini.trakem2.display.Display3D.<init>(Display3D.java:108)
at ini.trakem2.display.Display3D.<init>(Display3D.java:56)
 at ini.trakem2.display.Display3D$2.run(Display3D.java:322)
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:199)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
 at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
 at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
 at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
==> Caused by:
java.lang.SecurityException: sealing violation: package javax.media.j3d is
sealed
at java.net.URLClassLoader.defineClass(URLClassLoader.java:234)
 at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
 at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
 at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.ClassLoader.defineClass1(Native Method)
 at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
 at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
 at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
 at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
 at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at ij3d.ImageWindow3D.<init>(ImageWindow3D.java:64)
 at ini.trakem2.display.d3d.Display3DGUI.init(Display3DGUI.java:70)
 at ini.trakem2.display.Display3D.<init>(Display3D.java:108)
at ini.trakem2.display.Display3D.<init>(Display3D.java:56)
 at ini.trakem2.display.Display3D$2.run(Display3D.java:322)
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:199)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
 at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
 at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
 at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
==================



On Tue, Jun 24, 2014 at 1:18 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Linda,
>
> On Tue, 24 Jun 2014, lindaP wrote:
>
> > You're right. I don't know how it happened. I downloaded the plugin
> > again and it works fine now. Thanks for you help!
>
> Thanks for your feedback, and happy that you have a working system again!
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Luisa de Vivo, PhD
Department of Psychiatry
University of Wisconsin
6001 Research Park Boulevard
Madison WI 53719

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Luisa,

On Tue, 24 Jun 2014, Luisa de Vivo wrote:

> Caused by: java.lang.SecurityException: sealing violation: package
> javax.media.j3d is sealed

This suggests that the problem lies with obscure class loader issues
related to Java 3D.

Can you run the "Fiji Cube" demo?

Ciao,
Johannes

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html