IPython notebook and rmagic/rpy2: cannot find modu

Question

I'm trying to use the rmagic extension for the IPython notebook, using Python 2.7.6 via Enthought Canopy.

When I try the following example:

import numpy as np  
import pylab  
X = np.array([0,1,2,3,4])  
Y = np.array([3,5,4,6,7])  
pylab.scatter(X, Y)

%Rpush X Y  
%R lm(Y~X)$coef  

I get an error:

AttributeError                            Traceback (most recent call last)  
<ipython-input-7-96dff2c70ba0> in <module>()
      1 get_ipython().magic(u'Rpush X Y')
----> 2 get_ipython().magic(u'R lm(Y~X)$coef')
…  

/Users/hrob/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in eval(self, line)  
    212             res = ro.r("withVisible({%s})" % line)  
    213             value = res[0] #value (R object)  
--> 214             visible = ro.conversion.ri2py(res[1])[0] #visible (boolean)  
    215         except (ri.RRuntimeError, ValueError) as exception:  
    216             warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error  

AttributeError: 'module' object has no attribute 'ri2py'  

I can't find anyone else who's had the same problem and don't know enough to solve it myself. There is no definition for ri2py in conversion.py though.
I initially had installed Anaconda and was running python notebook through that, with exactly the same results.

rpy2 (version 2.4.0) installed successfully but when I test it I get 1 expected failure as follows:

python -m 'rpy2.robjects.tests.__init__'  
…  
testNewWithTranslation (testFunction.SignatureTranslatedFunctionTestCase) ... expected failure

I don't know if that's related.

Can anyone suggest what the problem might be and how I might fix it? Are the versions of python, R, etc. that I'm using compatible or do I need to re-install/update something?

Answer 1

Are you using %load_ext rmagic?

If so, try using %load_ext rpy2.ipython instead.

This is one of the new features in version 2.4.0.