Calling R from Python with Rscript on OS X – "No such file or directory: /usr/bin/Rscript"

Question

I'm trying to automate a workflow with Python on a Mac, which involves calling R to generate image files.

Following the answer to this question, I'm using subprocess.Popen to try calling Rscript and execute my image-generating R file.

However, I'm not sure where Rscript would be located on my machine.

Here's code I borrowed from the referenced question, and the error it returns:

def make_plot():
command = '/usr/bin/Rscript'
arg = '--vanilla' 


try: 
     p = subprocess.Popen([command, arg,
                          "r_script_for_python.R"],
                          cwd = os.getcwd(),
                          stdin = subprocess.PIPE, 
                          stdout = subprocess.PIPE, 
                          stderr = subprocess.PIPE) 

     output, error = p.communicate() 

     if p.returncode == 0: 
        print('R OUTPUT:\n {0}'.format(output.decode("utf-8"))) 
     else: 
        print('R ERROR:\n {0}'.format(error.decode("utf-8"))) 

     return True

except Exception as e: 
     print(e)

     return False

Running make_plot() returns an error: No such file or directory: '#!/usr/bin/Rscript'

Is it necessary to specify the full path? Would it work if you replaced `/usr/bin/Rscript` with `Rscript`? — Damian, Apr 12 '21 at 16:12
Is R installed? What does `which R` say when you run it in Terminal? — Damian, Apr 12 '21 at 16:49
Ah! `which R` returns `R not found` – this is very mysterious to me because I run R (via RStudio) all day — Thalecress, Apr 12 '21 at 18:36
Running `file.path(R.home("bin"), "R")` in R should tell you where RStudio is finding it. Refer to: https://stackoverflow.com/questions/33798115/command-to-see-r-path-that-rstudio-is-using — Damian, Apr 12 '21 at 21:14

Calling R from Python with Rscript on OS X – "No such file or directory: /usr/bin/Rscript"

0 Answers0