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

[Renato Alves]

Yes it helps. I started directly on the OmeroPy page, and for some
reason I just assumed I should go to the svn.

Got the latest tar.gz and I've now the python code working.

Thanks again for all the help.

PS: As a close note, I would like to suggest including something like a
SDK for Omero or language specific 'client' packages (if that's
possible). It's a bit of a waste having to download a ~110Mb file
unpacking into ~340Mb when at the end ~4Mb of code was all I was looking
for.

Quoting Will Moore on 07/28/2009 12:39 PM:
> 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 <mailto: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
>>>> <mailto:ome-users at lists.openmicroscopy.org.uk>
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>
>>
>> _______________________________________________
>> 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
> 
> William Moore
> Division of Gene Regulation and Expression
> College of Life Sciences
> University of Dundee
> Scotland
> DD1 5PH
> 
> Tel 01382 386364
>