How to capture the output of system()

Question

This question was motivated by Rmarkdown not outputting results of system command to html file. For some reason, the output of system() in R (or system2()

Answer 1

You could add a function knitr::system that masks base::system. Users could work with it like it was system::base, but the output can be captured by capture.output:

system <- function(...) {
  stopifnot(!any(names(list(...)) %in% "intern"))
  result <- base::system(..., intern = TRUE)
  print(result)
}

I admit, that this is somewhat hacky, and to be honest, I'm not sure about possible side effects. But I think it could be worth a try.

Answer 2

I don't think you can do this (at least on *nix systems; I don't have a Windows/Mac system handy) because system appears to invisibly return the value returned by the command executed, and R doesn't appear to redirect the command's output to the R console.

This is because the stdout of your terminal is not the same as the R console "stdout". What you see from within your R session is the mix of the terminal's stdout and the R process output. capture.output is looking for the R process' output, not all output to stdout from the parent process.

You can start a process that prints to stdout, put it in the background, then start R... and you'll see that process' output in your "R output", similar to if you had run system("ping -c5 8.8.8.8") from R.

josh@computer: /home/josh
> ping -c5 8.8.8.8 & R
[1] 5808
PING 8.8.8.8 (8.8.8.8) 56(84) bytes of data.
64 bytes from 8.8.8.8: icmp_seq=1 ttl=46 time=39.9 ms

R version 3.2.4 Revised (2016-03-16 r70336) -- "Very Secure Dishes"
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> 64 bytes from 8.8.8.8: icmp_seq=2 ttl=46 time=38.1 ms
64 bytes from 8.8.8.8: icmp_seq=3 ttl=46 time=38.3 ms
64 bytes from 8.8.8.8: icmp_seq=4 ttl=46 time=38.4 ms
64 bytes from 8.8.8.8: icmp_seq=5 ttl=46 time=38.3 ms

--- 8.8.8.8 ping statistics ---
5 packets transmitted, 5 received, 0% packet loss, time 4003ms
rtt min/avg/max/mdev = 38.176/38.656/39.986/0.703 ms

> q()
Save workspace image? [y/n/c]: n
[1]+  Done                    ping -c5 8.8.8.8

josh@computer: /home/josh
>