R SIG Debian - Jul 2012 - python-rpy DEB broken - but hopefully easy to fix

Hi CRAN people,

There is an issue with python-rpy on Ubuntu, when installed from the
CRAN repository. (I read the info on
http://cran.r-project.org/bin/linux/ubuntu/ and saw the note that this
package is experimental but you are happy to receive feedback on it.)
After adding the appropriate CRAN repo:

% sudo apt-get install python-rpy
[ ... installs various dependencies ... ]
% echo import rpy | python
RuntimeError: No module named _rpy2151

      RPy module can not be imported. Please check if your rpy
      installation supports R 2.15.1. 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 *
      

This is simply because the module needs recompiling with each new R release:

% apt-get -b source python-rpy
% sudo dpkg -i *.deb

And it all works fine.

Would it be possible to get this module rebuilt automatically in line
with new releases of r-base-core?  Right now I have to hold back updates
of R on my server until I can do the rebuild manually, but it would be
nice not to have this job as it's yet one more bit of server admin for me.

I'm aware that python-rpy is superseded, but as the software I'm needing
to run is the Galaxy server (galaxy.psu.edu) it's not trivial to get it
using the new python-rpy2.  (I'm working on it!)

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

-- 
This message (and any attachments) is for the recipient ...{{dropped:23}}

On 17 July 2012 at 12:37, Tim Booth wrote:
| Hi CRAN people,
| 
| There is an issue with python-rpy on Ubuntu, when installed from the
| CRAN repository. (I read the info on
| http://cran.r-project.org/bin/linux/ubuntu/ and saw the note that this
| package is experimental but you are happy to receive feedback on it.)
| After adding the appropriate CRAN repo:
| 
| % sudo apt-get install python-rpy
| [ ... installs various dependencies ... ]
| % echo import rpy | python
| RuntimeError: No module named _rpy2151
| 
|       RPy module can not be imported. Please check if your rpy
|       installation supports R 2.15.1. 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 *
|       
| 
| This is simply because the module needs recompiling with each new R release:
| 
| % apt-get -b source python-rpy
| % sudo dpkg -i *.deb

Yes, there is code in the package which hardcodes the then-current
version. It is a pretty brain-dead scheme as it forces a rebuild on
major.minor changes.

| And it all works fine.
| 
| Would it be possible to get this module rebuilt automatically in line
| with new releases of r-base-core?  Right now I have to hold back updates

Your maintainer is guilty as charged. This time I simply forgot to rebuild rpy.

Dirk

| of R on my server until I can do the rebuild manually, but it would be
| nice not to have this job as it's yet one more bit of server admin for me.
| 
| I'm aware that python-rpy is superseded, but as the software I'm
needing
| to run is the Galaxy server (galaxy.psu.edu) it's not trivial to get it
| using the new python-rpy2.  (I'm working on it!)
| 
| Cheers,
| 
| TIM
| 
| -- 
| Tim Booth <tbooth at ceh.ac.uk>
| NERC Environmental Bioinformatics Centre 
| 
| Centre for Ecology and Hydrology
| Maclean Bldg, Benson Lane
| Crowmarsh Gifford
| Wallingford, England
| OX10 8BB 
| 
| http://nebc.nerc.ac.uk
| +44 1491 69 2705
| 
| -- 
| This message (and any attachments) is for the recipient ...{{dropped:23}}
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com