Calling Rscript from linux shell script

Question

Can anyone suggest how I might get this working....

I have an R script that takes several minutes to run and writes a few hundred lines of output. I want to write a shell script wrapper around this R script which will launch the R script in the background, pipe its output to a file and start following the bottom of that file. If the user then enters CTRL-C I want that to kill the shell script and tail command but not the R script. Sounds simple right?

I've produced a simplified example below, but I don't understand why this doesn't work. Whenever I kill the shell script the R script is also killed despite apparently running in the background. I've tried nohup, disown etc with no success.

example.R

for(i in 1:1000){
   Sys.sleep(1)
   print(i)
}

wrapper.sh

#!/bin/bash

Rscript example.R > logfile &

tail -f logfile

Thanks in advance!

Answer 1

The following seems to work on my Ubuntu machine:

#!/bin/bash

setsid Rscript example.R > logfile.txt &

tail -f logfile.txt

---

Here are some of the relevant processes before sending SIGINT to wrapper.sh:

 5361 pts/10   00:00:00 bash
 6994 ?        00:00:02 update-notifier
 8519 pts/4    00:00:00 wrapper.sh
 8520 ?        00:00:00 R
 8521 pts/4    00:00:00 tail

and after Ctrl+C, you can see that R is still running, but wrapper.sh and tail have been killed:

 5361 pts/10   00:00:00 bash
 6994 ?        00:00:02 update-notifier
 8520 ?        00:00:00 R

---

Although appending your Rscript [...] command with & will send it to the background, it is still part of the same process group, and therefore receives SIGINT as well.

---

I'm not sure if it was your intention, but since you are calling tail -f, if not interrupted with Ctrl+c, your shell that is running wrapper.sh will continue to hang even after the R process completes. If you want to avoid this, the following should work,

#!/bin/bash

setsid Rscript example.R > logfile.txt &

tail --pid="$!" -f logfile.txt

where "$!" is the process id of the last background process executed (the Rscript [...] call).