Ubuntu
rpy package

R 2.11.1 compatibility issue?

Asked by MikeM

Running 32-bit intel maverick in xubuntu, with these versions of python-rpy and r-base:

ii python-rpy 1.0.3-14 Python interface to the GNU R language and environ
ii r-base 2.11.1-2 GNU R statistical computation and graphics system

In python code, "from rpy import r as R" is failing for me as follows:

Traceback (most recent call last):
  File "compute_error.py", line 5, in <module>
    from rpy import r as R
  File "/usr/lib/python2.6/dist-packages/rpy.py", line 134, in <module>
    """ % RVERSION)
RuntimeError: No module named _rpy2111

      RPy module can not be imported. Please check if your rpy
      installation supports R 2.11.1. 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 *

Indeed, there seems to be no such module _rpy2111 in my python-rpy package, although I do have this file:

/usr/lib/python2.6/dist-packages/_rpy2110.so

Has python-rpy gotten out of sync with the r-base package?

(On a related note, I tried downloading rpy (1.0.3) from sourceforge to build it myself, but the file "Rdevices.h" cannot be found, even though I have the current r-base-dev (2.11.1-2). Oddly, r-base-dev does not seem to have that or any other header files, and I can't find a file of that name at packages.ubuntu.com. I suppose I can move on to downloading the R source, but this starts to defeat the purpose of using apt I think.)

Question information

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Status:
Solved
For:
Ubuntu rpy Edit question
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Solved by:
Jérémy Subtil
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Revision history for this message
Jérémy Subtil (bigmadwolf) said : 		#1

Hi, this is a packaging bug introduced in Debian. The fix has been released in Debian few months ago, but it has not been synced in Ubuntu… So I reported the bug #667795.

Revision history for this message
MikeM (jmmacpherson) said : 		#2

Hi Jérémy --

Thanks much. I take it from your activity on 667795 that the remedy is to update the maverick python-rpy to 1.0.3-15 from 1.03.-14. I imagine that this update will happen when folks with the necessary permissions have the bandwidth for it. If this is accurate, would you expect the fix to be in place within, perhaps, one week's time?

Thanks again, Yours, Mike

Revision history for this message
Best Jérémy Subtil (bigmadwolf) said : 		#3

If you haven't done it yet, I advise you to click the "This bug affects me too" link at the top of the bug #667795 page. This would increase the bug "heat", and so it's more likely to get the developpers' attention.

I'm not able to provide any official fix, but I think I've completed the whole procedure to expect the bug to get fixed. However, as a temporary workaround, I've just prepared an Ubuntu python-rpy 1.0.3-15 package from Debian sources: it will be available on my PPA once Launchpad will build the binary packages from what I uploaded. I'll try to remember to tell you once it will be alright. ;)

Revision history for this message
MikeM (jmmacpherson) said : 		#4

Hi Jérémy --

I added myself as you suggested. Merci beaucoup for your help.

Yours, Mike

Revision history for this message
Jakob (jakob-g) said : 		#5

HI there,

I have exactly the dame problem. I tried to install an older version of R (v 2.10.1), then I installed rpy with all its dependencies using synaptic (I have ubuntu 10.10). Once I import rpy in python I get:

Traceback (most recent call last):
  File "<pyshell#6>", line 1, in <module>
    import rpy
  File "/usr/lib/python2.6/dist-packages/rpy.py", line 134, in <module>
    """ % RVERSION)
RuntimeError: No module named _rpy2101

      RPy module can not be imported. Please check if your rpy
      installation supports R 2.10.1. 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 *

How do I solve it? I thought that rpy 1.0.3-14 supported R2.10.1.

Any suggestion?
I have reported the bug as you suggested above!

Thanks!

Revision history for this message
Jérémy Subtil (bigmadwolf) said : 		#6

I've finally uploaded in my PPA the python-rpy 1.0.3-15 Debian package, as commented in bug #667795. ;)

Revision history for this message
MikeM (jmmacpherson) said : 		#7

Hi guys --

Thanks Jérémy!

In the meantime, my workaround was to point at the ubuntu repos hosted by CRAN, eg:

http://cran.cnr.berkeley.edu/bin/linux/ubuntu/

They have a functioning rpy, in addition to a more recent version of R than maverick's.

Cheers, Mike

Revision history for this message
Jakob (jakob-g) said : 		#8

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Revision history for this message
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Revision history for this message
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Revision history for this message
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