On 2011-04-22 17:22, Brent Pedersen wrote:
> On Fri, Apr 22, 2011 at 9:03 AM, Brent Pedersen<bpede...@gmail.com> wrote:
>> On Fri, Apr 22, 2011 at 8:34 AM, Brent Pedersen<bpede...@gmail.com> wrote:
>>> hi, I am getting some errors with the latest version of rpy2, any ideas?
>>>
>>>
>>>
>>> $ python rpy/tests.py
>>> Error in sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp) :
>>> 7 arguments passed to .Internal(sub) which requires 8
>>> Traceback (most recent call last):
>>> File "rpy/tests.py", line 3, in<module>
>>> import rpy2.robjects.tests
>>> File
>>> "/home/brentp/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py",
>>> line 17, in<module>
>>> from rpy2.robjects.robject import RObjectMixin, RObject
>>> File
>>> "/home/brentp/local/lib/python2.7/site-packages/rpy2/robjects/robject.py",
>>> line 9, in<module>
>>> class RObjectMixin(object):
>>> File
>>> "/home/brentp/local/lib/python2.7/site-packages/rpy2/robjects/robject.py",
>>> line 22, in RObjectMixin
>>> __show = rpy2.rinterface.baseenv.get("show")
>>> LookupError: 'show' not found
>>>
>>>
>>> $ uname -a
>>> Linux ilmn-qm.ucdenver.pvt 2.6.18-194.3.1.el5 #1 SMP Sun May 2
>>> 04:17:42 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
>>> $ python --version
>>> Python 2.7.1
>>> $ python -c "import rpy2; print rpy2.__version__"
>>> 2.2.0beta # (it's revision aad34041491f)
>>> $ R --version | head -n 1
>>> R version 2.13.0 (2011-04-13)
>>>
>> this also happens with R version 2.12.2
>>
> Sorry for the noise. I fixed this my messing with my LD_LIBRARY_PATH
> and saw this:
> https://bitbucket.org/lgautier/rpy2/issue/46/lookuperror-show-not-found
>
> I do find that with 2.2 (aad34041491f), i get
> ValueError: Nothing can be done for the type<type 'numpy.ndarray'> at
> the moment.
>
> even after import numpy2ri whereas the same code works fine in 2.19
> (0e5a13fa842e)
The conversion is no longer implicit with the import:
http://rpy.sourceforge.net/rpy2/doc-2.2/html/numpy.html#from-numpy-to-rpy2
(I am noting now that the documentation is lacking /how/ to perform the
conversion... because I left this part undecided about how to have it.
That's what betas are for ;-) )
In the meanwhile, add the following in the beginning of your main Python
file(s):
import rpy2.robjects as robjects
import rpy2.robjects.numpy2ri as rpyn
robjects.conversion.py2ri = rpyn.numpy2ri
robjects.conversion.ri2numpy = rpyn.ri2numpy
Sorry for the inconvenience.
L.
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