CODEWITHSUNDEEP
pythonrrpy2
Sahil Thakur
Sahil Thakur

Reputation: 51

Getting Segmentation fault Core dumped error while importing robjects from rpy2

Installed R and rpy2 manually

Installation is successful but getting the above mentioned error. Please help me out?

Outputs of some useful commands:

>>> import rpy2
>>> rpy2.__path__
['/home/ashish/miniconda2/lib/python2.7/site-packages/rpy2-2.8.2-py2.7-linux-x86_64.egg/rpy2']
>>> import rpy2.robjects
cannot find system Renviron
/home/ashish/miniconda2/lib/python2.7/site-packages/rpy2-2.8.2-py2.7-linux- x86_64.egg/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Fatal error: unable to open the base package


warnings.warn(x, RRuntimeWarning)
Segmentation fault (core dumped)

Thanks in advance..

Upvotes: 5

Views: 4422

Answers (1)

Eitan Rousso
Eitan Rousso

Reputation: 181

If you install rpy2 via conda, and also have a system installation of R on the same machine (e.g with RStudio), the system's R installation will be used. Since this R version doesn't match the one that rpy2 needs, segmentation faults occur.

1) remove any existing system installations of R (see here). Verify that you don't have any installations of R: 

$>which R
R not found

2) define R_HOME env variable, either in your .rc file:

export R_HOME=/Users/<your user>/anaconda3/envs/<env name>/lib/R

or dynamically in the python project:

import os
os.environ['R_HOME'] = '/Users/<your user>/anaconda3/envs/<env name>/lib/R'

Upvotes: 15

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