Reticulate: use_python still not working

[sahil-kumar]

I just did a clean install of OSX and completely wiped everything. From there, I reinstalled Homebrew, installed Python 3, then R and RStudio with the reticulate package. I am still unable to get the python version in use to switch from the default OSX installed Python to use Python 3 instead. After opening up a brand new R Markdown file, I ran the following:

library(reticulate)
use_python("/usr/local/bin/python3", required = T)
py_config()

with these results:

python:         /usr/bin/python
libpython:      /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib
pythonhome:     /System/Library/Frameworks/Python.framework/Versions/2.7:/System/Library/Frameworks/Python.framework/Versions/2.7
version:        2.7.10 (default, Oct  6 2017, 22:29:07)  [GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.31)]
numpy:          /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy
numpy_version:  1.8.1

python versions found: 
 /usr/local/bin/python3
 /usr/bin/python

Can anyone help?

[jjallaire]

reticulate will always prefer a version of Python that includes NumPy to one that doesn't. Does the version at /usr/local/bin/python3 have NumPy?

[sahil-kumar]

Yup. I forgot to mention that, sorry!

[smilesun]

@jjallaire , that means if we want to use use_python or other function to specify python path or virtual environment, we must install numpy to that directory first? Otherwise it won't work?

[jjallaire]

Yes, NumPy is always preferred (without that we can't convert matrices nor data frames between Python and R).

[wush978]

Dear all,

I try reticulate today and feel very frustrated.
I follow the vignettes of Python Version Configuration but both functions use_python and use_virtualenv do not work as expected.
Finally, I find this issue and make thing works.

Is it possible to raise an error if use_python and use_virtualenv does not find numpy?
Then users will quickly know why use_python and use_virtualenv does not work and correct it accordingly.

This is just my two cents.

[kevinushey]

You likely want reticulate::use_python("/path/to/python", required = TRUE).

[ras44]

In my case, I was able to use_virtualenv without numpy installed. Output of py_config():

python:         /home/xxx/pylift/bin/python
libpython:      /home/xxx/opt/python-3.6.2/lib/libpython3.6m.so
pythonhome:     /home/xxx/opt/python-3.6.2:/home/xxx/opt/python-3.6.2
virtualenv:     /home/xxx/pylift/bin/activate_this.py
version:        3.6.2 (default, Apr  2 2019, 11:53:38)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-36)]
numpy:           [NOT FOUND]

In order to get the above to work, I had to:

• compile python with --enable-shared (as mentioned in the docs)
• Sys.setenv(LD_LIBRARY_PATH = "<PATH_TO_PYTHON_INSTALL>/lib") so that R can find the shared libraries (otherwise error is: "error while loading shared libraries")

[RobertMyles]

@wush978 Mine worked well on a Mac by adding:

RETICULATE_PYTHON="/usr/local/bin/python3"

to my .Renviron file. As soon as you restart R, it will find the correct version (I'm assuming you're using Python3).

[jwhendy]

I don't think this is worth a new issue, but will create one if you prefer.

Does reticulate require name-spacing? I'm brand new and these instructions failed:

` ` `{R}
library(reticulate)
use_python("/usr/bin/python3")
` ` `
Error in use_python("/usr/bin/python3") : 
  could not find function "use_python"

But this (idea taken from above), worked:

` ` `{R}
library(reticulate)
reticulate::use_python("/usr/bin/python3")
` ` `

If name-spacing is required, could the documentation be updated?