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

Tue Dec 2 12:21:34 GMT 2008

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
>>>>
>>>