Unable to use rPython or pythoninr to import python modules

Question

When I was trying to import modules like "pymc3" or "theano", the rPython or PythoninR are not able to locate these modules even though I have already installed them. I am using Ubuntu 16.04, R 3.4.2, and python 3.5.2

It seems like these two packages fail to locate a certain folder, but it doesn't work after I append the path into sys.path, which contains all the packages I need, by using this command:

pyExec("sys.path.append('/home/lijiakai/.local/lib/python3.5/site-packages')")

Result also seems like good:

pyExec('import sys; print(sys.path)')

['', '/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/lijiakai/.local/lib/python3.5/site-packages']

I imported the packages:

pyExec('import pymc3')

Then received the following errors:

Traceback (most recent call last):   File "<string>", line 1, in
<module> **ImportError** :  No module named 'pymc3' Error in
pyExec("import pymc3") :    An error has occured while executing
Python code. See traceback above.

Totally got me crazy ... really appreciate if anyone can help me out here. Thanks

it is /usr/bin/python, but when I run python in bash, the version is 3.5.2, which should be right — jli
– jli, Commented Nov 23, 2017 at 3:10
and what does: library(rPython) python.exec(c("import sys", "\n", "print(sys.version)")) return? I suspect that rPython is using another Python version, not 3.5.2 — clemens
– clemens, Commented Nov 23, 2017 at 8:44
Yes, this is true, I got python 2.7.10 in R when using the library(rPython) T_T — jli
– jli, Commented Nov 25, 2017 at 7:39

clemens · Accepted Answer · 2017-11-23 13:47:06Z

1

If you use anaconda, you might want to turn to turn to the package reticulate, where you can specify the python version to use.

# install.packages("reticulate")
library(reticulate)
use_python("/anaconda/bin/python")

However, from my experience this is slower.

Otherwise, if you use 'standard' Python, you can start by removing rPython:

remove.packages("rPython")

And then re-install it specifying the version:

install.packages("rPython", configure.vars= "RPYTHON_PYTHON_VERSION=3.5")

This should then use Python_3.5 on your machine, see here for more details.

You can test, if it was successful by using:

library(rPython)
python.exec(c("import sys", "\n", "print(sys.version)"))

answered Nov 23, 2017 at 13:47

clemens

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2 Comments

jli Over a year ago

Thank you for your kind help, but I still got a python version of 2.7.10 after specified ""RPYTHON_PYTHON_VERSION=3.5" when install the package, which is so frustrating ...

clemens Over a year ago

Are you using anaconda?

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