pycharm上的rpy2生成分段错误错误

Question

I am using (osx) pycharm as ide and anaconda as python (2.7.10) distribution. Recently I have installed rpy2 which works quite well on notebook eg

In [5]:import rpy2.robjects as robjects
In [7]:robjects.r.pi[0]
Out[7]:3.141592653589793

But on pycharm I get a segmentation fault error.

import rpy2.robjects as robjects
/Users/xxx/anaconda/envs/analytics3/bin/python.app: line 3: 695 Segmentation fault: 11 /Users/xxx/anaconda/envs/analytics3/python.app/Contents/MacOS/python "$@"

PYcharm support claims that this is a bug in the code.

any ideas what that might be?

many thanks

Answer 1

Reinstalling rpy2 from

conda install -c conda.anaconda.org/rpy2

solved the issue.

Answer 2

If you install rpy2 via conda, and also have a system installation of R on the same machine (eg 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'