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Unable to determine R library path

I am new to R. I am running Jupyter Lab on a Windows 11 machine, and have created a virtual environment where I installed some packages and irkernel. I get the following message when I execute %load_ext rpy2.ipython:

Unable to determine R library path: Command '('C:\Users\ephra\miniconda3\envs\cde\Lib\R\bin\Rscript', '-e', 'cat(Sys.getenv("LD_LIBRARY_PATH"))')' returned non-zero exit status 1.

Here is my complete code:

import os
os.environ['R_HOME'] = 'C:\Users\ephra\miniconda3\envs\cde\Lib\R'
os.environ['R_USER'] = 'C:\Users\ephra\miniconda3\envs\cde\Lib\site-packages\rpy2' 

from src.setup import *

%load_ext rpy2.ipython


Apart from the environment variables, the above code comes from David Mertz book “Cleaning Data for Effective Data Science”. I need your help.



Note: This is a speculative answer as I don’t use Jupyter

That os.environ trick works for me in plain Python but Jupyter’s magic routine %load_ext rpy2.ipython utilizes LD_LIBRARY_PATH to set itself up. The error comes from the fact that LD_LIBRARY_PATH is Linux/Unix thing hence the trouble.

Failed Attempt #1 What you may be able to do is to add the following line to your os.environ calls:

os.environ['LD_LIBRARY_PATH'] = 'C:\Users\ephra\miniconda3\envs\cde\Lib\R\bin\x64'

Assuming ‘C:Usersephraminiconda3envscdeLibRbin’ exists. If not, look for a R subfolder with bunch of exe and dll files.

Attempt #2

Surveying further, I noticed that LD_LIBRARY_PATH itself is never used by rpy2, and it appears to be a Linux workaround. So, what happens if you comment out Lines 26-28 of

The lines should read

LD_LIBRARY_PATH = (rpy2.situation.r_ld_library_path_from_subprocess(R_HOME)
                   if R_HOME is not None
                   else '')

If this hack succeeds, let me know and I can file a PR.

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