Execute .R script within Python using Rscript.exe shell

Question

I have an .R file saved locally at the following path:

Rfilepath = "C:\\python\\buyback_parse_guide.r"

The command for RScript.exe is:

RScriptCmd = "C:\\Program Files\\R\\R-2.15.2\\bin\\Rscript.exe --vanilla"

I tried running:

subprocess.call([RScriptCmd,Rfilepath],shell=True)

But it returns 1 -- and the .R script did not run successfully. What am I doing wrong? I'm new to Python so this is probably a simple syntax error... I also tried these, but they all return 1:

subprocess.call('"C:\Program Files\R\R-2.15.2\bin\Rscript.exe"',shell=True)

subprocess.call('"C:\\Program Files\\R\\R-2.15.2\\bin\\Rscript.exe"',shell=True)

subprocess.call('C:\Program Files\R\R-2.15.2\bin\Rscript.exe',shell=True)

subprocess.call('C:\\Program Files\\R\\R-2.15.2\\bin\\Rscript.exe',shell=True)

Thanks!

cfeduke · Accepted Answer · 2012-11-29 16:15:04Z

0

The RScriptCmd needs to be just the executable, no command line arguments. So:

RScriptCmd = "\"C:\\Program Files\\R\\R-2.15.2\\bin\\Rscript.exe\""

Then the Rfilepath can actually be all of the arguments - and renamed:

 RArguments = "--vanilla \"C:\\python\\buyback_parse_guide.r\""

edited Nov 29, 2012 at 16:15

answered Nov 29, 2012 at 2:49

cfeduke

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6 Comments

Ray Over a year ago

It's still not working. I tried the above and did: subprocess.call([RScriptCmd,RArguments],shell=True)

cfeduke Over a year ago

what happens when you run that same command from the command prompt? Some programs incorrectly return a non-zero value on success (doubt that R would do this though)

Ray Over a year ago

C:\Program Files>C:\Program Files\R\R-2.15.2\bin\Rscript.exe --vanilla C:\python\ buyback_parse_guide.r 'C:\Program' is not recognized as an internal or external command, operable program or batch file.

Ray Over a year ago

I tried RScriptCmd = "C:\\Program Files\\R\\R-2.15.2\\bin\\Rscript.exe" and RArgs = "--vanilla C:\\python\\buyback_parse_guide.r". Didn't work either. Definitely a syntax error I'm not seeing

Ray Over a year ago

This is what works in cmd.exe: "C:\Program Files\R\R-2.15.2\bin\Rscript.exe" --vanilla C:\python\buyback_parse_guide.r

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Community · Accepted Answer · 2017-05-23 12:28:29Z

0

It looks like you have a similar problem to mine. I had to reinstall RScript to a path which has no spaces.

See: Running Rscript via Python using os.system() or subprocess()

This is how I worked out the communication between Python and Rscript:

part in Python:

from subprocess import PIPE,Popen,call
p = subprocess.Popen([ path/to/RScript.exe, path/to/Script.R, Arg1], stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE)
out = p.communicate()
outValue = out[0]

outValue contains the output-Value after executing the Script.R

part in the R-Script:

args <- commandArgs(TRUE)
argument1 <- as.character(args[1])
...
write(output, stdout())

output is the variable to send to Python

edited May 23, 2017 at 12:28

CommunityBot

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answered Feb 16, 2015 at 16:56

EikeMike

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