Executing R script with Python via subprocess.call

Question

I have a R script which works fine on its own but I need it to be a part of python script. So, when I run the python script the R script be executed automatically. I use the below command; there is no error but the R script output files are not created.

import subprocess

retcode = subprocess.call("C:/Program Files/R/R-3.2.2/bin/Rscript --vanilla T:/2012.R", shell=True)

Thank you so much in advance.

What happens with a simple test program: print.hw <- function() { print("hello world") }; print.hw() — IRTFM
– IRTFM, Commented Mar 3, 2016 at 0:50
Is there a syntax error with the path to the Rscript interpreter? My intuition is that you need to escape any space characters in the path. C:/Program\ Files/R/R-3.2.2/bin/Rscript — Keenan
– Keenan, Commented Mar 3, 2016 at 0:53
Does exact command run in Command Prompt or PowerShell: C:/Program Files/R/R-3.2.2/bin/Rscript --vanilla T:/2012.R? — Parfait
– Parfait, Commented Mar 3, 2016 at 2:22
Code.. code..code. Stop wasting our time vague error descriptions. — IRTFM
– IRTFM, Commented Mar 3, 2016 at 17:22

Parfait · Accepted Answer · 2016-03-04 03:02:59Z

5

Simply place your string command in brackets and break string into separate components as the first parameter of function expects a list of arguments, per the doc:

subprocess.call(args, *, stdin=None, stdout=None, stderr=None, shell=False)

import subprocess

retcode = subprocess.call(['C:/Program Files/R/R-3.2.2/bin/Rscript', '--vanilla', 
                           'T:/2012.R'], shell=True)

Alternatively, break it up into multiple strings:

command = 'C:/Program Files/R/R-3.2.2/bin/Rscript'
arg = '--vanilla'
path2script = 'T:/2012.R'

retcode = subprocess.call([command, arg, path2script], shell=True)

edited Mar 4, 2016 at 3:02

answered Mar 4, 2016 at 2:56

Parfait

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