I am a bit of a noob on Mac and my python installation is refusing to acknowledge the existence of the rpy2 module on my mac. It looks like it only sees it as a Python 2.6 module. How do I make it visible in 2.7 ? Do I need to downgrade my python ? If so, how ? On the RPy2 web page (http://rpy.sourceforge.net/rpy2_download.html) Python 2.6 is recommended. Thanks!
mayumi@MAYUMI-iMac~:/ python --version
Python 2.7.6
mayumi@MAYUMI-iMac~:/ pip install rpy2
Requirement already satisfied (use --upgrade to upgrade): rpy2 in /Library/Python/2.6/site-packages/rpy2-2.3.8-py2.6-macosx-10.6-universal.egg
Cleaning up...
mayumi@MAYUMI-iMac~:/ python
Python 2.7.6 (v2.7.6:3a1db0d2747e, Nov 10 2013, 00:42:54)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy2
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named rpy2
>>>
I also found it is difficult to successfully install rpy2
in OSX machines. Sometime it works, sometimes it doesn't, which is very annoying. I eventually settled with Anaconda
Python
distribution from https://store.continuum.io/cshop/anaconda/ to save all the troubles. Installing rpy2
never fails since the switch.
The default installation of Anaconda
does not included rpy2
, so you want to run the installation command, from Anaconda
folder, bin
subfolder
conda install rpy2
Depends on the version, you may get a bunch of warnings. Just ignore them.
Then rpy2
just works! Of course, only under the Anaconda python
, not the other python
version you may have installed on your machine.
You can run a few test to make sure rpy2
works, following this example: http://nbviewer.ipython.org/urls/raw.github.com/ipython/ipython/3607712653c66d63e0d7f13f073bde8c0f209ba8/docs/examples/notebooks/rmagic_extension.ipynb
bash
commands, run in the folder /Users/YOUR_USER_NAME/anaconda/bin/
:
user-Mac-Pro:bin user$ conda install rpy2
and it says:
Conda package not available for rpy2, attempting to install via pip
Downloading/unpacking rpy2
Downloading rpy2-2.3.8.tar.gz (185kB): 185kB downloaded
Running setup.py egg_info for package rpy2
If you don't have R
installed it will complain with a few warnings and fetch R
for you. Then there may be some other depreciation warnings dependents on what you have installed.
(I am not associated with Continuum in any way)