[ome-users] OMERO failing to build - java.lang.ClassNotFoundException: org.apache.tools.ant.util.regexp.Jdk14RegexpMatcher

[Will Moore]

Hi Renato,

  I'm not a server or python developer, but I just tried going to
http://openmicroscopy.org/site/support/omero4/downloads

downloading the server for UNIX, called:
omero-Beta4.0.3.tar.bz2

unzipped this file, which creates a folder called
omero_dist

and if I open this folder I find
omero_dist/lib/python/

with lots of stuff in it!

  Does that help?

   Will.



On 28 Jul 2009, at 12:18, Renato Alves wrote:

> Hi Bernhard,
>
> Well I though to myself, but reading on the documentation, I couldn't
> find the folders mentioned there. For instance the
> omero_folder/lib/python folder doesn't exist neither does
> omero_folder/dist/lib/python. There is also
> omero_folder/components/tools/OmeroPy/src/omero but it fails to import
> when searching for one file that is missing.
> I assumed the missing files were generated using the build-py target,
> hence my attempt to build it.
>
> With the suggestion from Mark Woodbridge I managed to progress in the
> compilation, but now I'm getting Memory errors related to garbage
> collecting. We've dealt with this error before so we are working on it
> and trying to find the relevant docs.
>
> In the meantime thanks for the help.
> Renato
>
> Quoting Bernhard Holländer on 07/28/2009 11:49 AM:
>> Hi Renato!
>>
>> AFAIK you don't have to build the python interface yourself. It comes
>> included in the release archive. The python packages and modules live
>> in /your_path_to_omero/lib/python. Put that path and the
>> path_to_Ice-3.3/python into the PYTHONPATH environment variable. This
>> should be enough to start coding against omero in python.
>>
>> For example on linux (omero unpacked to /opt/omero-4.0.3 and Ice-3.3
>> installed in /opt/Ice-3.3) one could call python like this and import
>> the omero package:
>>
>> $ PYTHONPATH=/opt/omero-4.0.3/lib/python:/opt/Ice-3.3/python python
>>>>> import  omero
>> ...
>>
>> See https://trac.openmicroscopy.org.uk/omero/wiki/OmeroPy for an
>> example how to get started.
>>
>> Cheers! Bernhard
>>
>> On Mon, Jul 27, 2009 at 7:01 PM, Renato  
>> Alves<rjalves at igc.gulbenkian.pt> wrote:
>>> Hello everyone,
>>>
>>> I'm currently trying to build the python interface. In order to  
>>> do this
>>> I fetched the code from svn (both trunk and tag omero-4.0.3) and  
>>> did:
>>>
>>> ant build-py
>>>
>>> After a couple of minutes of building, eventually it fails with  
>>> the error:
>>>
>>> icegen2:
>>>
>>> BUILD FAILED
>>> /home/rjalves/omero-python/omero-4.0.3/build.xml:171: The following
>>> error occurred while executing this line:
>>> /home/rjalves/omero-python/omero-4.0.3/build.xml:137: The following
>>> error occurred while executing this line:
>>> /home/rjalves/omero-python/omero-4.0.3/components/antlib/ 
>>> resources/global.xml:79:
>>> The following error occurred while executing this line:
>>> /home/rjalves/omero-python/omero-4.0.3/components/blitz/build.xml: 
>>> 140:
>>> The following error occurred while executing this line:
>>> /home/rjalves/omero-python/omero-4.0.3/components/blitz/build.xml: 
>>> 58:
>>> Could not create type regexpmapper due to No supported regular
>>> expression matcher found: java.lang.ClassNotFoundException:
>>> org.apache.tools.ant.util.regexp.Jdk14RegexpMatcher
>>>
>>> The versions of the software I'm using are the following:
>>>
>>> Apache Ant version 1.7.0 compiled on April 29 2008
>>> Ice - 3.3.1 (tried with and without the slice2 extras)
>>> Java - Java(TM) SE Runtime Environment (build 1.6.0_14-b08) / Java
>>> HotSpot(TM) 64-Bit Server VM (build 14.0-b16, mixed mode)
>>>
>>> this on a Debian 64-bit machine running 'testing' (aka squeeze).
>>>
>>> I also get a few other deprecation warnings and log4j giving a  
>>> non fatal
>>> error about being improperly setup.
>>>
>>> Am I missing something or maybe version mismatch?
>>>
>>> Thanks for all help,
>>> Renato
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>
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William Moore
Division of Gene Regulation and Expression
College of Life Sciences
University of Dundee
Scotland
DD1 5PH

Tel 01382 386364

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