Reticulate: using conda python 3.6 environment

[joeymizrahi]

I have a python 3.6 anaconda environment.
I tried using use_python and giving it the path to the environment which did not work.
I also tried using use_condaenv which did not work, once I run py_config I get the following output:

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, Feb 7 2017, 00:08:15) [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
numpy: /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy
numpy_version: 1.8.0

python versions found:
/usr/bin/python
/anaconda3/envs/my-r-env/bin/python
/anaconda3/envs/py27/bin/python

/anaconda3/envs/py36/bin/python

[koverholt]

I was able to get things working by creating an .Rprofile file (either in your home dir or in the project dir) with the following:

Sys.setenv(RETICULATE_PYTHON = '/anaconda3/bin/python3')

or whichever python executable you want to use, as mentioned in #216.

[joeymizrahi]

did not seem to work.
I also have numpy installed in my environment

[koverholt]

Is your output of reticulate::py_config() the same when you set the RETICULATE_PYTHON env. var?

Mine changes from what you posted to:

python:         /anaconda3/bin/python3
libpython:      /anaconda3/lib/libpython3.7m.dylib
pythonhome:     /anaconda3:/anaconda3
version:        3.7.0 (default, Jun 28 2018, 07:39:16)  [Clang 4.0.1 (tags/RELEASE_401/final)]
numpy:          /anaconda3/lib/python3.7/site-packages/numpy
numpy_version:  1.15.1

NOTE: Python version was forced by RETICULATE_PYTHON

And did you point to the python in the root conda env, or did you also try pointing to one of the python binaries in the envs (e.g., /anaconda3/envs/my-r-env/bin/python)?

[joeymizrahi]

This is what I tried as well as the output:

 py_config()
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, Feb  7 2017, 00:08:15)  [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
numpy:          /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy
numpy_version:  1.8.0

python versions found: 
 /usr/bin/python
 /anaconda3/envs/my-r-env/bin/python
 /anaconda3/envs/py27/bin/python
 /anaconda3/envs/py36/bin/python
> Sys.setenv(RETICULATE_PYTHON = '/anaconda3/envs/py36/bin/python')
> py_config()
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, Feb  7 2017, 00:08:15)  [GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]
numpy:          /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy
numpy_version:  1.8.0

python versions found: 
 /usr/bin/python
 /anaconda3/envs/my-r-env/bin/python
 /anaconda3/envs/py27/bin/python
 /anaconda3/envs/py36/bin/python
>

[koverholt]

Instead of setting that env in the console, try putting Sys.setenv(RETICULATE_PYTHON = '/anaconda3/bin/python3') in an .Rprofile file in your home dir or project dir and restart your R session.

[joeymizrahi]

I entered this into the r studio console.
I am sorry is did not really understand what you are recommending I do

[koverholt]

Use your favorite text editor to create a new file with the following contents:

Sys.setenv(RETICULATE_PYTHON = '/anaconda3/bin/python3')

Save the text file (or edit an existing file if it's already there) to your home directory (e.g., /Users/cs4242/ if you are on macOS) called .Rprofile. So the full path of the file will be /Users/cs4242/.Rprofile.

You can verify the contents of this file by running the following command in a terminal window, which should return the contents of the file, as shown on the second line.:

$ cat ~/.Rprofile
Sys.setenv(RETICULATE_PYTHON = '/anaconda3/bin/python3')

Now, start a fresh instance of RStudio and check the version of Python being used by inputting the following command in a console:

py_config()

If it's picking up the .Rprofile file properly, it should now be configured to use the Python binary you specified.

[joeymizrahi]

hi, I created an r script in R studio and did what you told me to.
seems that its still not working.
am I supposed to add this .Rprofile file into my current project workspace. I think I am not adding it into the right place

[joeymizrahi]

Thanks @koverholt I ended up adding Sys.setenv(RETICULATE_PYTHON = '/anaconda3/bin/python3') into the already existing .Rprofile and it worked!!
Thanks again

[martijnvanattekum]

Use your favorite text editor to create a new file with the following contents:

Sys.setenv(RETICULATE_PYTHON = '/anaconda3/bin/python3')

Save the text file (or edit an existing file if it's already there) to your home directory (e.g., /Users/cs4242/ if you are on macOS) called .Rprofile. So the full path of the file will be /Users/cs4242/.Rprofile.

You can verify the contents of this file by running the following command in a terminal window, which should return the contents of the file, as shown on the second line.:

$ cat ~/.Rprofile
Sys.setenv(RETICULATE_PYTHON = '/anaconda3/bin/python3')

Now, start a fresh instance of RStudio and check the version of Python being used by inputting the following command in a console:

py_config()

If it's picking up the .Rprofile file properly, it should now be configured to use the Python binary you specified.

Also don't forget to end the .Rprofile file with a newline character or the last line will be ignored.