Error when calling a file from python

Question

I want to call an R program from a python script.

I wrote the following:

os.system("cat " + variableName + " | code.R")

It returns the error: sh: 1 : code.R: not found cat: write error: Broken pipe

Yet, I am sure of the name of the R file.

Why is it not working?

I don´t know about *.R programs. But... is code.R a binary file or a script that has to be interpreted? — Raydel Miranda
– Raydel Miranda, Commented Mar 11, 2014 at 17:49
Is the code.R file in the same directory where from you are calling the python script? — vivekagr
– vivekagr, Commented Mar 11, 2014 at 17:50
Maybe this can help: stackoverflow.com/questions/4106565/… — silent
– silent, Commented Mar 11, 2014 at 18:08

Raydel Miranda · Accepted Answer · 2014-03-11 18:09:00Z

1

So, if code.R is a script that has to be interpreted you must build the pipe to the interpreter not to the script. You receive a Broken PIPE error because code.R by it self don't know how to handle command line arguments.

On the other hand if what you want is store the variable value inside code.R you have to change | by >>.

os.system("cat " + variablename + ">> code.R")

EDIT: Since it's working from terminal, try this:

import subprocess
input = open(variableName, "r")
result = suprocess.call(["code.R"], stdin=input)    # result is the return code for the command being called.

see subprocess.call for more details.

edited Mar 11, 2014 at 18:09

answered Mar 11, 2014 at 17:51

Raydel Miranda

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2 Comments

bigTree Over a year ago

Actually, code.R takes variable as input. What bothers me is that, from the terminal, cat variable | code.R worked perfectly. I would like to call this command from my python script, but for some reason it doesn't work...

bigTree Over a year ago

the problem is then solved. Thank you guys for your help

Russell Borogove · Accepted Answer · 2014-03-11 17:50:10Z

1

Is code.R in the current working directory? Is it executable? Can you run cat xxx | code.R from the shell and have it work properly, instead of running your python program?

answered Mar 11, 2014 at 17:50

Russell Borogove

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2 Comments

bigTree Over a year ago

Yes to all these questions (for the executable part, ls -lrt gives -rwxr-xr-x. I had executed the code.R from another directory before copying it to the one where my python script is located)

Russell Borogove Over a year ago

Do print os.getcwd() immediately before the os.system() call?

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