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

Brian Loranger brian.loranger at lifesci.dundee.ac.uk
Tue Dec 2 16:07:59 GMT 2008 

Hi Caterina,

Glad you got it working.. let us know if you need anything else,

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 15:59, Caterina Strambio De Castillia wrote:

> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
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>>>>>>>> users at lists.openmicroscopy.org.uk>
>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>
>>>>>>
>>
>>
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