Calling Python from R with reticulate package

Question

I want to execute a Python script in R. I've installed reticulate and tested that a Python version has correctly initialized in my R session.

py_config()

returns the following

python:         C:/Users/username/AppData/Local/r-miniconda/envs/r-reticulate/python.exe
libpython:      C:/Users/username/AppData/Local/r-miniconda/envs/r-reticulate/python36.dll
pythonhome:     C:/Users/username/AppData/Local/r-miniconda/envs/r-reticulate
version:        3.6.10 |Anaconda, Inc.| (default, Jan  7 2020, 15:18:16) [MSC v.1916 64 bit (AMD64)]
Architecture:   64bit
numpy:          C:/Users/username/AppData/Local/r-miniconda/envs/r-reticulate/Lib/site-packages/numpy
numpy_version:  1.18.1

Now, when I call the Python script

py_run_file("PythonScript.py")

I hit the following error in R

Error in py_run_file_impl(file, local, convert) : 
  ModuleNotFoundError: No module named 'requests'

I understand that I need to install requests package but how do I make this in the specific Python version I've initialized?

If you look under ~/AppData/Local/r-miniconda for the conda executable, can you then run conda install requests? I don't have that distro of miniconda here so I cannot test it easily, but that seems like one reasonable approach. Another (perhaps more of a "best practice") would be to use a virtual environment and make sure the packages you need are installed and maintained. — r2evans
– r2evans, Commented Feb 13, 2020 at 17:05
@Onyambu Windows, since I think C:/... is exclusive to Windows. Correct me if I am wrong. — Gainz
– Gainz, Commented Feb 13, 2020 at 17:06
I suggest that you need to read rstudio.github.io/reticulate/articles/python_packages.html, where they discuss (with examples) how to deal with python packages when using reticulate. — r2evans
– r2evans, Commented Feb 13, 2020 at 17:44

Onyambu · Accepted Answer · 2020-02-13 17:47:12Z

2

You could write a function that collects the missing packages and installs them:

run_python_file <- function(python_file){
    a = try(reticulate::py_run_file(python_file),silent=TRUE)
    if(inherits(a,"try-error")& grepl("ModuleNotFoundError",a)){
        system(sprintf("python -m pip install %s",gsub(".* |\\W","",c(a))))
        run_python_file(python_file)
      }
    else a
   }
run_python_file("PythonScript.py")

edited Feb 13, 2020 at 17:47

answered Feb 13, 2020 at 17:32

Onyambu

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1 Comment

nba2020 Over a year ago

Seems futureproof, will try it tomorrow

Jrm_FRL · Accepted Answer · 2020-02-13 17:06:18Z

1

You need to install the python module requests before.

If you have installed python, you should have installed pip with it. You can install the module by running pip install requests in command line.

answered Feb 13, 2020 at 17:06

Jrm_FRL

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