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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..
917
Core Dump/Segmentation fault is a specific kind of error caused by accessing memory that “does not belong to you.” When a piece of code tries to do read and write operation in a read only location in memory or freed block of memory, it is known as core dump. It is an error indicating memory corruption.
A segmentation fault (aka segfault) is a common condition that causes programs to crash; they are often associated with a file named core . Segfaults are caused by a program trying to read or write an illegal memory location.
A segmentation fault occurs when a program attempts to access a memory location that it is not allowed to access, or attempts to access a memory location in a way that is not allowed (for example, attempting to write to a read-only location, or to overwrite part of the operating system).
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'
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