[ome-users] [Fwd: Problems with OMERO.importer]

Brian Loranger brian.loranger at lifesci.dundee.ac.uk
Tue Dec 2 15:29:01 GMT 2008 

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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