Error while running R script in Python with SubProcess

Question

I am trying to run an R script that is in the same directory as the python script while executing the python script.

So far, I have:

if condition is True:
    import subprocess
    subprocess.call (["C:/Program Files/R/R-3.4.3/Rscript", "./testing.r"])
    sys.exit()

I keep getting the error:

OSError: [WinError 193] %1 is not a valid Win32 application

I've tried replacing "C:/Program Files/R/R-3.4.3/Rscript" with "/usr/bin/Rscript" but keep getting the same error. I was wondering if anybody would know why it keeps throwing this error?

Try this subprocess.call(['C:/Program Files/R/R-3.4.3/Rscript', '--vanilla', 'testing.r'], shell = True) or provide the full path to the R script file — Tung
– Tung, Commented May 18, 2018 at 4:20
I guess the it might be a path problem. (The R version and Rscript path is for sure correct?) If yes, then give the full absolute path to testing.r, so 'C:/full/absolute/path/to/testing.r' (or is it in 'D:/' even)? — Gwang-Jin Kim
– Gwang-Jin Kim, Commented May 19, 2018 at 18:54
I've tried both suggestions but get an error that "C:/Program Files/R/R-3.4.3/Rscript" is not recognized as an external or internal command. — tooty44
– tooty44, Commented May 20, 2018 at 1:07

user387832 · Accepted Answer · 2018-05-23 06:32:02Z

2

I believe the arguments of subprocess.call get passed straight to the command line, so you need to escape your quotation marks as such "\"C:/Program Files/R/R-3.4.3/Rscript\"". That being said, I get a [WinError 5] Access violation error when I use this. A workaround is to use the executable argument:

import sys
import subprocess

if True is True:
    subprocess.call(["C:/Program Files/R/R-3.4.3/Rscript.exe", "./testing.r"], 
                    executable="C:/Program Files/R/R-3.4.3/Rscript.exe")
    sys.exit()

Also, make sure that C:/Program Files/R/R-3.4.3/Rscript.exe is the location of your Rscript.exe. Mine is C:/Program Files/R/R-3.4.3/bin/Rscript.exe.

edited May 23, 2018 at 6:32

answered May 23, 2018 at 6:17

user387832

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1 Comment

tooty44 Over a year ago

Yes, I was missing the "bin" in "C:/Program Files/R/R-3.4.3/bin/Rscript.exe". Thanks!

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