Problem running a R script from Python (Windows)

Question

I've recently started programming in python for my job, so I'm quite new to it. My goal is to create a graphic interface so that the user can run a program that I have been developing in R. The interface is done using the Tkinter module from python (version 3.3).

The problem comes when I have to call the R interpreter from python to run an R file that is generated (run.R file). The curious thing is that this only happens when I try to run my script in Windows, not in Linux. In both cases, I am trying to use the os module from python.

This is the code that is not working for Windows:

os.chdir(outRW) #first I change the working directory to the one where the run.R file is

os.system("C:\R-3.6.1\bin\Rscript run.R")

When I execute this, it changes the directory successfully, but when it comes to calling the R interpreter, it shows me this error:

The filename, directory name, or volume label syntax is incorrect.

However, I have tried running the "C:\R-3.6.1\bin\Rscript run.R" command in the Windows Command Prompt and it works perfectly. I have also tried adding the path to R to the environmental variables, but again I could only make it work in the Command Prompt, not with python.

I guess there is something very obvious that I am missing here, but I cannot see it.

Any help or comments are very much appreciated!

Thank you!

Try os.system("C:/R-3.6.1/bin/Rscript run.R"). \r is the escape sequence for a carriage return and by using forward slashes you avoid any escaping. I would also suggest using subprocess instead of os.system. — SitiSchu
– SitiSchu, Commented Nov 25, 2019 at 14:56

Louis · Accepted Answer · 2019-11-25 15:13:23Z

1

Use double backslashes.

In R you need to use double backslashes \\, otherwise it'll try to interpret it as an Escape Character.

Use this and it will work:

os.system("C:\\R-3.6.1\\bin\\Rscript run.R")

Hope this helps.

answered Nov 25, 2019 at 15:13

Louis

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2 Comments

MagicLettuce Over a year ago

Thank you very much! it did work for me! Now I have a different problem since R tells me that it can't find a package that this code needs, however it is installed and when I run the same command in the prompt it works. Why is this happening now?

Louis Over a year ago

You're welcome, happy it worked! I think this other problem is unrelated to the first one. Open a new question and we'll gladly help you! :)

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Use double backslashes.

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