R: pass variable from R to unix

Question

I am running an R script via bash script and want to return the output of the R script to the bash script to keep working with it there.

The bash is sth like this:

#!/bin/bash
Rscript MYRScript.R
a=OUTPUT_FROM_MYRScript.R
do sth with a

and the R script is sth like this:

for(i in 1:5){
i
sink(type="message")
}

I want bash to work with one variable from R at the time, meaning: bash receives i=1 and works with that, when that task is done, receives i=2 and so on.

Any ideas how to do that?

you want to construct a pipe from your running R-script to another shell-command. is it right? — jogo
– jogo, Commented Oct 27, 2015 at 15:06
I want to use the R output (a filename) to be directly used in bash to modify another file there. Seems to me to be easier this way... ? — gugy
– gugy, Commented Oct 27, 2015 at 15:16

nrussell · Accepted Answer · 2015-10-27 15:31:55Z

3

One option is to make your R script executable with #!/usr/bin/env Rscript (setting the executable bit; e.g. chmod 0755 myrscript.r, chmod +x myrscript.r, etc...), and just treat it like any other command, e.g. assigning the results to an array variable below:

myrscript.r

#!/usr/bin/env Rscript
cat(1:5, sep = "\n")

mybashscript.sh

#!/bin/bash
RES=($(./myrscript.r))
for elem in "${RES[@]}"
do
  echo elem is "${elem}"
done

nrussell$ ./mybashscript.sh
elem is 1
elem is 2
elem is 3
elem is 4
elem is 5

edited Oct 27, 2015 at 15:31

answered Oct 27, 2015 at 15:20

nrussell

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4 Comments

gugy Over a year ago

strangely enough I get a Permission denied (for myrscript.r) error when running your solution. Any ideas why?

Dirk is no longer here Over a year ago

Do a chmod 0755 myrscript.r first,

nrussell Over a year ago

@gugy Sorry I kind of glossed over that in my answer; thank you Dirk.

MAZ Over a year ago

How to prevent printing of R startup intro in output?

DunderChief · Accepted Answer · 2015-10-27 15:28:06Z

0

Here is MYRScript.R:

for(iter in 1:5) {
  cat(iter, ' ')
}

and here is your bash script:

#!/bin/bash

r_output=`Rscript ~/MYRscript.R`

for iter in `echo $r_output`
do
    echo Here is some output from R: $iter
done

Here is some output from R: 1
Here is some output from R: 2
Here is some output from R: 3
Here is some output from R: 4
Here is some output from R: 5

edited Oct 27, 2015 at 15:28

answered Oct 27, 2015 at 15:18

DunderChief

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