I use Ubuntu 16.04. I'm trying to run a simple python script from R. The script is
import numpy as np
 "['/home/user/Desktop', '/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/usr/local/lib/python3.5/dist-packages', '/usr/lib/python3/dist-packages']"
['/home/user/Desktop', '/home/user/anaconda3/lib/python35.zip', '/home/user/anaconda3/lib/python3.5', '/home/user/anaconda3/lib/python3.5/plat-linux', '/home/user/anaconda3/lib/python3.5/lib-dynload', '/home/user/anaconda3/lib/python3.5/site-packages', '/home/user/anaconda3/lib/python3.5/site-packages/Sphinx-1.4.1-py3.5.egg', '/home/user/anaconda3/lib/python3.5/site-packages/setuptools-23.0.0-py3.5.egg']
The problem is that you have two versions of python3 on your computer: The system default (Ubuntu, I'm assuming), and the one you installed (Anaconda3).
When you run it from the command-line, you are using the Anaconda3 environment (which includes numpy and all the other anaconda modules). When you run it from R, it doesn't know to use the Anaconda environment, and so it just uses your default python paths (which doesn't include numpy).
To fix this, invoke your python script in R using the Anaconda python, not the system one:
Alternatively, you could add
/home/user/anaconda3/bin/ to your
PATH environment variable in
~/.bashrc so that it chooses anaconda over the system binary.