Capture output of system command within a function in R

Question

I'm working with a function in a package that uses system2() to run a command within the function. This particular command prints some stuff to standard out. I want to capture the output of that system2() call, however capture.output() does not work. I understand how to run system2() directly and capture the standard output, but not how to get it in this specific situation.

Simple example:

my_ls <- function() {
  system2("ls")
  return("Hello")
}
my_ls()
output <- capture.output(my_ls())
output

when in doubt ?system2. you would have seen that using the argument stdout = T captures the output as a string. — JeremyS
– JeremyS, Commented Mar 17, 2016 at 6:17
the returned value of my_ls will always be just "Hello". There's no point in trying capture.output., Either use return() around the system2` call or reverse the order of those commands inside the function. — IRTFM
– IRTFM, Commented Mar 17, 2016 at 6:33
@JeremyS Yes, I am aware of that already. The point of my question is that the system2 call is within a function in a package and I am not able to edit the function to set stdout = T, so I'm looking for a workaround. — Matt SM
– Matt SM, Commented Mar 17, 2016 at 6:48
You are able to edit the function in a way. If the function is MyFoo then type MyFoo, note no brackets, and you get the R code of the function, copy it and make your changes and save it as a new function MyFoo2 for example — JeremyS
– JeremyS, Commented Mar 17, 2016 at 7:10
help(stdin) talks about "the console" and "the C-level 'stdin'" - capture.output gets "the console" output and system2 outputs to "the C-level stdout' I reckon. — Spacedman
– Spacedman, Commented Mar 17, 2016 at 16:29

Spacedman · Accepted Answer · 2016-03-17 17:26:19Z

1

Here's a solution... But be warned, it works for me on Linux, might work on a Mac, and I doubt it works on Windows...

Create two Rcpp functions:

library(Rcpp)
cppFunction('void redir(){FILE* F=freopen("/tmp/capture.txt","w+",stdout);}')
cppFunction('void resetredir(){FILE* F=freopen("/dev/tty","w+",stdout);}')

The first will send everything to that file. The second will reset it. The problem is that interactively after the first you'll not be able to see anything. So beware...

So initially system2 sends to the console:

> system2("echo", "hello")
hello

But wrapping a call in redir/resetredir sends it to the file:

> redir(); system2("echo","hello world this time") ; resetredir()
> # prompt returns!

Now we have:

$ cat /tmp/capture.txt 
hello world this time

and if this is the output from some other package you'll have to read it in with R's file I/O routines.

The dodgy bit is the use of /dev/tty in the reset code - I'm not sure it works on a Mac or Windows. If you don't care about resetting the stdout then skip it, and just make sure you know how to quite R without seeing what you type. I'm also unsure if this will work in RStudio which probably has a different concept of the console....

answered Mar 17, 2016 at 17:26

Spacedman

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2 Comments

Matt SM Over a year ago

Very cool, thanks for this. You're right that resetredir() doesn't seem to work on a Mac/RStudio, but it doesn't matter for my purposes.

tomaz Over a year ago

The function redir() works fine on Windows. resetredir(), however, should be defined as cppFunction('void resetredir(){FILE* F=freopen("CON","w+",stdout);}')

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