Hi Nate,

thank you very much for your help! I managed to figure out the problem. There seemed to be an old version of R and somehow (I still don't know how) the rpy installation did only find the old one. I hard-coded the directory of the new R in the setup.py (everything else failed) and then it compiled against the new R version.

Best regards,
Sarah


On 03/03/2011 05:11 PM, Nate Coraor wrote:
Sarah Diehl wrote:
Hi all,

I'm currently working on setting up a fresh Galaxy server at our
institute. I'm going through the tool dependencies list and install
everything on it. I installed the latest R version (2.12.2) and now
I'm trying to install rpy. With some workarounds I managed to
compile rpy, but when I try to import it in python, I get the
following error:

import rpy
Traceback (most recent call last):
   File "<stdin>", line 1, in<module>
   File "rpy.py", line 134, in<module>
     """ % RVERSION)
RuntimeError: No module named _rpy2122

       RPy module can not be imported. Please check if your rpy
       installation supports R 2.12.2. If you have multiple R versions
       installed, you may need to set RHOME before importing rpy. For
       example:

       >>>  from rpy_options import set_options
       >>>  set_options(RHOME='c:/progra~1/r/rw2011/')
       >>>  from rpy import *

It looks like my version of R isn't supported by rpy. Does anybody
know which version of R still works with rpy? I couldn't find
anything about it. What about rpy2? Is it not supported by Galaxy?

Hi Sarah,

Although I haven't tested with 2.12.2, I know it works with at least
2.11.0.  The error above is indicating that rpy is installed somewhere
on python's path but the C-extension module for the version of R found
on your $PATH (2.12.2) is not present.  Most likely this is because rpy
was already installed, and is being found earlier on python's path than
the version of rpy that you installed.  The older rpy was built against
a different version of R.

If you find the original installation of rpy you should be able to
determine from _rpy<version>.so what version of R it was built against,
and put that version of R ahead of 2.12.2 in your $PATH.

Alternatively, you can find and uninstall the old version of rpy, which
should allow your newer version to be found and used.

python's path can be determined with:

   python -c 'import sys; print "\n".join( sys.path )'

There is some effort underway in the community to rewrite rpy tools to
use rpy2, but this work is not yet complete.

Hope this helps,
--nate


Thanks very much in advance for your help!

Best regards,
Sarah Diehl
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