rpy2 import is not working

Question

I get an error when I try to import rpy2. Here is the code and error.

>>> import pandas.rpy.common
Traceback (most recent call last):  

File "C:\PF\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\lib\site-packages\IPython\core\interactiveshell.py", line 2828, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

File "<ipython-input-148-c258a0f70d44>", line 1, in <module>
import pandas.rpy.common

File "C:\PF\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\lib\site-packages\pandas\rpy\common.py", line 14, in <module>
from rpy2.robjects.packages import importr

ImportError: No module named 'rpy2'

What could be the issue? I'm using python version 3.3.3 and pandas version 0.13.1

EDIT

Tried to install rpy2 separately.

1. Directly using python setup.py install gave me an error that os doesn't have a module popen3.

2. Directly installing the exe (rpy2-2.3.9.win32-py3.3.exe) from Christoph Gohlke's site http://www.lfd.uci.edu/~gohlke/pythonlibs/ run fine. But if I try to do import pandas.rpy.common as com then I get the following error (issue with the loading the DLL at from rpy2.rinterface._rinterface import * :

   Traceback (most recent call last):
     File "C:\PF\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\lib\site-packages\IPython\core\interactiveshell.py", line 2828, in run_code
   exec(code_obj, self.user_global_ns, self.user_ns)
   
     File "<ipython-input-10-63ebebefea80>", line 1, in <module>
   import pandas.rpy.common as com
   
     File "C:\PF\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\lib\site-    packages\pandas\rpy\common.py", line 14, in <module>
   
   from rpy2.robjects.packages import importr
   
     File "C:\PF\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\lib\site-packages\rpy2\robjects\__init__.py", line 15, in <module>
   
       import rpy2.rinterface as rinterface
     File "C:\PF\WinPython-64bit-3.3.3.3\python-3.3.3.amd64\lib\site-packages\rpy2\rinterface\__init__.py", line 103, in <module>
   
       from rpy2.rinterface._rinterface import *
   ImportError: DLL load failed: %1 is not a valid Win32 application.
   

EDIT

Solved it finally. It seems like adding R_HOME and R_USER environment variables did the trick.

Answer 1

This might not apply directly to your question, but ever since pandas and rpy2 have upgraded, their interface has changed. In order to set it up, you must now:

from rpy2.robjects import r, pandas2ri

pandas2ri.activate()

Now, in order to change a Pandas dataframe into an R dataframe, one must use pandas2ri.py2ri(), or use pandas2ri.ri2py() if you want change an R dataframe into a Pandas dataframe. Further information can be found at https://pandas.pydata.org/pandas-docs/stable/r_interface.html.

Answer 2

In my case it initially did not wor installing it with conda. I solved it by first changing the active environment.

source activate [environment Name]
conda install -c r rpy2=2.8.5

Answer 3

Well, first you have to install rpy2. If you are using conda you can do it using the following command

conda install -c r rpy2 

Then, if you want to use R on Jupyter Notebook environment you can activate R using

%load_ext rpy2.ipython

Answer 4

In my case it worked when I installed it in Anaconda Prompt with a command:

conda install -m rpy2

After that I had to move rpy2 directory from rpy2-2.9.0-py3.6-win32.egg (folder that was installed to) cause it didn't recognized it after installation...and moved only rpy2 folder to the following path:

C:\Users..\Anaconda3\Lib\site-packages (where all packages are called from)

That solved problem for me.

Answer 5

That looks like a pandas interface to rpy2. Separately, you also need rpy2 installed on your system. I don't have rpy2, so it was easy for me to check this:

In [1]: import pandas.rpy.common
(...)
ImportError: No module named rpy2.robjects.packages


In [2]: import rpy2
(...)
ImportError: No module named rpy2

I installed it using pip:

$ pip install rpy2

In [1]: import pandas.rpy.common

It works! It import rpy2 works for you, but import pandas.rpy.common does not then the problem might be more subtle.

Answer 6

I recently ran into a similar issue. I was trying to install rpy2 using anaconda version of python(3.6.3). Below, mentioned command worked for me,

* python3 -m conda install rpy2