[ome-users] [Problems with OMERO.importer] _ SOLVED

Caterina Strambio De Castillia strambc at mail.rockefeller.edu
Tue Dec 2 15:59:08 GMT 2008 

Dear Curtis and Brian,

I looked in the /System/Library/Java/Extensions folder  and I indeed  
found a bio-formats.jar in there which I removed and:

IT SOLVED THE PROBLEM!!!!!!

Now the OMERO.importer works fine.

Thank you very much for your help

Caterina


On 2-dic-08, at 16:34, Curtis Rueden wrote:

> Also, Caterina, take a look in your /System/Library/Java/Extensions  
> folder for old versions of bio-formats.jar or loci_tools.jar. Any  
> JARs in there should be removed. To use Bio-Formats with ImageJ,  
> download a new loci_tools.jar and place in your /Applications/ 
> ImageJ/plugins folder.
>
> Oops, by "any JARs in there" I mean any JARs relating to Bio- 
> Formats. *Some* of the JARs in there are important and required, so  
> don't delete all of them.
>
>
> On Tue, Dec 2, 2008 at 9:33 AM, Curtis Rueden <ctrueden at wisc.edu>  
> wrote:
> Hi Brian & Caterina,
>
> To test for classpath issues you can launch Java with the -verbose  
> argument -- it might shed some light on where the Bio-Formats  
> classes are being loaded from.
>
> Also, Caterina, take a look in your /System/Library/Java/Extensions  
> folder for old versions of bio-formats.jar or loci_tools.jar. Any  
> JARs in there should be removed. To use Bio-Formats with ImageJ,  
> download a new loci_tools.jar and place in your /Applications/ 
> ImageJ/plugins folder.
>
> HTH,
> Curtis
>
> On Tue, Dec 2, 2008 at 9:29 AM, Brian Loranger  
> <brian.loranger at lifesci.dundee.ac.uk> wrote:
> Hi Caterina,
>
> I am still mystified by this one as we use the clients daily on  
> Power PC boxes herel. I am still of the option that the problem  
> machine has a bad java engine or bio-formats reference somewhere.
>
> Can you go into your user home directory/omero/log folder and send  
> me your importer.log file.. I am hoping that will reveal more.
>
> Cheers,
>
> Brian Loranger
> Software Developer, Open Microscopy Environment
> Division of Gene Regulation and Expression
> University of Dundee
> (The University of Dundee is a registered Scottish charity, No:  
> SC015096)
>
>
>
>
> On 2 Dec 2008, at 12:21, Caterina Strambio De Castillia wrote:
>
>> Dear Brian and bio-formats team,
>>
>> I wanted to give you an update on the OMERO.importer problem I  
>> have been having.
>> The problem presents itself when launching OMERO.importer (on a  
>> PowerBookG4 computer running MacOS X 10.4.11 that does not have  
>> the OMERO.server installed locally).
>> When I launch I get the following error message:
>>
>>> "Cannot launch Java application
>>>
>>> Uncaught exception in main method:
>>> java.lang.VeriryError: (class: loci/format/in/
>>> APNGReader, method: initFile signature: (Ljava/lang/
>>> String;)V) incompatible argument to function"
>>>
>>>
>>
>>
>> After the correspondence we have had back in November (see below)  
>> I have done the following tests:
>>
>> 1) removed the extra bio-formats.jar file I had on my computer  
>> (PowerBook G4)_ did not improve matters even after restarting the  
>> computer.
>>
>> 2) performed the OMERO.clients package download and installation  
>> (v3.1.1) on another Mac I have (iBookG4)_  in this case the  
>> OMERO.importer launched properly.
>>
>> 3) today I have downloaded and installed on the "problem" computer  
>> the new version of the OMERO.clients package (v3.2.1)_  I get  
>> exactly the same error message.
>>
>>
>> Just to remind you,
>> My Java verison is:
>>
>>>
>>> "local-ca% java -version
>>> java version "1.5.0_16"
>>> Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_16-  
>>> b06-275)
>>> Java HotSpot(TM) Client VM (build 1.5.0_16-132, mixed mode,  
>>> sharing)"
>>>
>>
>>
>> Everything else below applies.
>>
>> If you think I have to do a clean re-install of  the MacOS X I  
>> will do it but I would rather not if possible...
>>
>> Have a nice day
>>
>> Caterina
>>
>>
>>
>>
>>
>> Begin forwarded message:
>>
>>> *From: *Caterina Strambio De Castillia  
>>> <strambc at mail.rockefeller.edu <mailto:strambc at mail.rockefeller.edu>>
>>> *Date: *5 novembre 2008 12:03:34 GMT+01:00
>>> *To: *Brian Loranger <brian.loranger at lifesci.dundee.ac.uk  
>>> <mailto:brian.loranger at lifesci.dundee.ac.uk>>
>>> *Subject: **Re: [ome-users] Problems with OMERO.importer*
>>>
>>> Dear Brian and the whole team,
>>> thank you for your help on this.
>>>
>>> To answer your questions:
>>>
>>> 1. Yes, I have bio-formats.jar also in the ImageJ folder.
>>> 2. Yes, I have downloaded the MacOS X package from your website  
>>> (http://www.openmicroscopy.org/site/downloads/omero-downloads).
>>> 3. The OMERO.clients is in /Applications, which in a Mac is the  
>>> default directory for applications.
>>> 4. Yes I believe I do.
>>>
>>> I am using Mac OS X 10.4.11
>>> on a Power PC G4
>>>
>>> Hope this can help you figure it out.
>>>
>>> In any event I have a feeling I have to rebuild my System from  
>>> scratch. Hopefully not.
>>>
>>> CIAO and thank you
>>> Caterina
>>>
>>>
>>>
>>> On 4-nov-08, at 17:29, Brian Loranger wrote:
>>>
>>>> Hi again Caterina,
>>>>
>>>> This is the first time any of us have seen that error so it is a  
>>>> real mystery for us. Let me try to get a bit more information if  
>>>> I can to track it down:
>>>>
>>>> 1. Do you use the bio-formats package anywhere else? I'm  
>>>> wondering if perhaps your classpath is referencing a different  
>>>> version of bio-formats somewhere.
>>>> 2. You downloaded the macintosh client bundle and are using the  
>>>> OMERO.importer application? (as opposed to something like the  
>>>> linux bundle, where you would call the application using the  
>>>> importer.sh script).
>>>> 3. You have the importer and insight in the default directly  
>>>> (although it should give you a warning message if its not in  
>>>> that folder).
>>>> 4. You have write permission to your user home directly (the  
>>>> clients create a directly called 'omero' there to store log and  
>>>> ini files).
>>>>
>>>> Also, can you tell me what version of macintosh you're using?
>>>> If possible, can you send me the importer.log file located in  
>>>> your ~/omero/log/ directory (there may be additional debug  
>>>> information located in there).
>>>>
>>>> Cheers and hopefully we can track this down for you,
>>>>
>>>> Brian Loranger
>>>> Software Developer, Open Microscopy Environment
>>>> Division of Gene Regulation and Expression
>>>> University of Dundee
>>>> (The University of Dundee is a registered Scottish charity, No:  
>>>> SC015096)
>>>>
>>>>
>>>>
>>>>
>>>> On 4 Nov 2008, at 16:00, Caterina Strambio De Castillia wrote:
>>>>
>>>>> Hi Brian and thank you for your fast reply.
>>>>>
>>>>> The answer is yes to both questions:
>>>>> the OMERO.importer is the version that came in the latest  
>>>>> download  bundle, and I have double checked it is the right  
>>>>> version Beta 3.1.1;
>>>>>
>>>>>   the Java version is as follows:
>>>>>
>>>>> "local-ca% java -version
>>>>> java version "1.5.0_16"
>>>>> Java(TM) 2 Runtime Environment, Standard Edition (build  
>>>>> 1.5.0_16- b06-275)
>>>>> Java HotSpot(TM) Client VM (build 1.5.0_16-132, mixed mode,  
>>>>> sharing)"
>>>>>
>>>>> Any idea?
>>>>>
>>>>> CIAO
>>>>> Caterina
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 4-nov-08, at 16:16, Brian Loranger wrote:
>>>>>
>>>>>> Hi Caterina,
>>>>>>
>>>>>> This one is new to me, are you using the default install of  
>>>>>> the  3.1.1 importer and java version 1.5 or better?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Brian Loranger
>>>>>> Software Developer, Open Microscopy Environment
>>>>>> Division of Gene Regulation and Expression
>>>>>> University of Dundee
>>>>>> (The University of Dundee is a registered Scottish charity,  
>>>>>> No:  SC015096)
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 4 Nov 2008, at 14:57, Caterina Strambio De Castillia wrote:
>>>>>>
>>>>>>> Dear All,
>>>>>>> Mario and I are proceeding with our OMERO installation. After  
>>>>>>> some  glitches this morning, the OMERO.server 3.1.1 is up an  
>>>>>>> running.
>>>>>>> I have now installed the clients on my laptop and while the  
>>>>>>> editor  and the insight work well, the importer does not  
>>>>>>> launch. It gives  me a Java error as follows:
>>>>>>>
>>>>>>> <2008-11-04_OMERO.importer_error.tiff>
>>>>>>>
>>>>>>> "Cannot launch Java application
>>>>>>>
>>>>>>> Uncaught exception in main method:
>>>>>>> java.lang.VeriryError: (class: loci/format/in/
>>>>>>> APNGReader, method: initFile signature: (Ljava/lang/
>>>>>>> String;)V) incompatible argument to function"
>>>>>>>
>>>>>>> Can anybody help me figure this out?
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>> Caterina
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ____________________________
>>>>>>> Caterina Strambio De Castillia, Dottore in Biologia, PhD
>>>>>>> Senior Research Scientist
>>>>>>> Laboratory of Viral replication, pathogenesis, and immunity
>>>>>>>
>>>>>>> http://www.mimo.unige.ch/luban_lab/
>>>>>>>
>>>>>>> Department of Microbiology and Molecular Medicine
>>>>>>> University of Geneva
>>>>>>> Switzerland
>>>>>>>
>>>>>>>
>>>>>>> ****
>>>>>>> Visiting Scientist
>>>>>>> Laboratory of Cellular and Structural Biology
>>>>>>> The Rockefeller University
>>>>>>> 1230 York Avenue
>>>>>>> New York NY 10065
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> ome-users mailing list
>>>>>>> ome-users at lists.openmicroscopy.org.uk <mailto:ome- 
>>>>>>> users at lists.openmicroscopy.org.uk>
>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>
>>>>>
>
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