How to insert an R script into a bash script?

Question

This question is similar to my previous question How to insert a python program into a bash script?. I am basically trying to achieve the same thing but with R. I tried the following

#!/bin/bash

R 1 2 3 4 << EOF 

args<-commandArgs(TRUE)

for (i in args) {

        print(i) 

}

EOF

The output (as displayed when ran in R) should be:

[1] "1"
[1] "2"
[1] "3"
[1] "4"

The method of the answer to my previous question worked fine for python but not for R (which is what I expected). Is there a way to run R code within a a bash script as there is with python?

Dirk is no longer here · Accepted Answer · 2014-07-23 18:30:45Z

2

Short version: Don't do that.

Long version: Write an R script for which you can use the Rscript executable or, if you have it, the r one from our littler package.

While shell scripts seem tempting at first, you will at some point run into issues with variable interpolation and escaping. Proper R scripts are better -- and the R sources contain a large number of examples.

Example:

/tmp$ ./rex.R 1 2 3 4
[1] "1"
[1] "2"
[1] "3"
[1] "4"
/tmp$

With this source:

/tmp$ cat rex.R 
#!/usr/bin/Rscript

args<-commandArgs(TRUE)
for (i in args) {
     print(i) 
}
tmp$

answered Jul 23, 2014 at 18:30

Dirk is no longer here

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