Rscript Subprocess Python

Question

By google I have found that the way to call R code is to use the following:

subprocess.call("Rscript" + " /path/Rscript.R")

# The reason there is an add statment is because in actual code I have a 
variable of where the script is.

On my home computer such code works. I am now working on a Server machine. If while in the the direcotry of my code I run

Rscript /path/Rscript.R

it works. However when I try to run it from the python code I get No such file or Directory. I have made sure Rscript was in my path (because I could Run it from command line).

Any help would be appreciated.

I have tried running from ~/path to it, ./path to it, /absolutepathtoit.

falsetru · Accepted Answer · 2014-03-16 00:54:06Z

2

There's a needless parenthesis at the end of the line:

subprocess.call("Rscript" + "/path/Rscript.R"))
                                              )

And, you need to insert a space between a command and arguments. Otherwise Rscript/path/Rscript.R is recognized as a command.

subprocess.call("Rscript" + " " + "/path/Rscript.R")
                            ^^^

Or pass a list:

subprocess.call(["Rscript", "/path/Rscript.R"])

answered Mar 16, 2014 at 0:54

falsetru

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4 Comments

1478963 Over a year ago

The parenthesis and lack of space comes from my sloppy editing to make the path smaller. It is there in the acutal code. I am going to try to use the list method.

falsetru Over a year ago

@user2100799, If passing a list also does not work, try it with shell=True argument.

1478963 Over a year ago

The list worked! Although I read on this site that using shell=True was advised against. I can only accept after waiting for 5 mins.

hrbrmstr Over a year ago

Glad you got the problem solved. Depending on exactly how the Python+R is getting executed, you should give rpy2 a go since--in certain circumstances--it could be much more efficient to use R code that way.

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