R and System calls

Question

I have used R in the past to do very basic calls to the commmand line. The example can be found here.

This time around, I am looking to mimic this code which runs successfully from the command line in Windows:

> cd C:\Documents and Settings\BTIBERT\My Documents\My Dropbox\Eclipse\Projects\R\MLB\retrosheet\rawdata
> bgame -y 2010 2010bos.eva >2010bos.txt

This is the code I am trying to run inside of R. I have already set the working directory inside of R.

dir <- paste("cd", getwd(), sep=" ")
system(dir)
system("bgame -y 2010 2010bos.eva >2010bos.txt")

I am sure this is user error, but what am I doing wrong? It appears to work initially, but returns the following error. I very well could be doing something wrong, but I believe I am using the same commands.

Expanded game descriptor, version 109(185) of 05/08/2008.
  Type 'bgame -h' for help.
Copyright (c) 2001 by DiamondWare.
[Processing file 2010bos.eva.]
>2010bos.txt: can't open.
Warning message:
running command 'bgame -y 2010 2010bos.eva >2010bos.txt' had status 2

Any help you can provide will be appreciated.

Joshua Ulrich · Accepted Answer · 2011-04-21T15:14:00.823

You need to issue all commands in one system() call:

system(paste("cd",getwd() "&& bgame -y 2010 2010bos.eva >2010bos.txt",sep=" "))

You should already be in your working directory, so I'm not sure the cd getwd() is necessary. And you may need quotes around your path because it contains spaces. The error may be resolved by putting spaces around >.

If I were in your shoes, I would try this:

system("bgame -y 2010 2010bos.eva > 2010bos.txt")

UPDATE:

And you should probably heed this advice in the "Differences between Unix and Windows" section of ?system that says you should use shell:

    • The most important difference is that on a Unix-alike
      ‘system’ launches a shell which then runs ‘command’.  On
      Windows the command is run directly - use ‘shell’ for an
      interface which runs ‘command’ _via_ a shell (by default the
      Windows shell ‘cmd.exe’, which has many differences from the
      POSIX shell).

      This means that it cannot be assumed that redirection or
      piping will work in ‘system’ (redirection sometimes does, but
      we have seen cases where it stopped working after a Windows
      security patch), and ‘system2’ (or ‘shell’) must be used on
      Windows.

Thanks for the help. I followed your advice and ignored the directory, but found that I had to include shQuote inside a shell call for it to behave differently. That said, it appears to have worked, but I am getting an error code 1 now, which is bizarre as the file looks OK and the command is identical what I would type in on the command line outside of R. — Btibert3, Apr 21 '11 at 16:51
would you guys know how to accomplish the same task on Linux? See my [question](http://stackoverflow.com/questions/36431465/warning-running-command-had-status-127-when-trying-to-run-exe-from-r) — Antoine, Apr 06 '16 at 08:38
I would like to run multiple system commands like this. In the commands, there can be a command would be failed when being executed. How can R ignore "execution halted" and continue to execute the next command? — , Mar 28 '18 at 04:50

CJB · Answer 2 · 2015-06-12T12:17:50.873

Has no-one else found that system("dir", intern = T) for example doesn't work, but that you need system("cmd.exe /c dir", intern = T)? Only the latter works for me. I found this at the discussion site here (William Dunlap's post, about a third of the way down).

Also, it doesn't work with the "cd" command, but you can use the setwd() function within R and then the command will be executed within that directory.

I created the following functions for convenience, for executing programmes and running commands:

#the subject is an input file that a programme might require
execute <- function(programme, subject.spec = "", intern = FALSE, wait = FALSE){
  if(!identical(subject.spec, "")){subject.spec <- paste0(" ", subject.spec)} #put space before the subject if it exists
  system(paste0("cmd.exe /c ", programme, subject.spec), intern = intern, wait = wait)
}


command <- function(command, intern = TRUE, wait = FALSE){
  system(paste("cmd.exe /c", command), intern = T, wait = wait)
}

This is true, but (as quoted in the accepted answer) the better way to go is to use `shell` instead of `system` in windows. `shell("dir", intern=T` works just fine for me. — Nat, Jul 03 '19 at 22:42

kpie · Answer 3 · 2015-01-10T17:43:35.060

Does it break your code when you get error 1 or does execution continue?

Whenever executing system commands through another language it is useful to print the system call before you call it to see exactly what is happening, pull up the shell you are intending to use and check for the same error. As the command is executed correctly this could be a hickup in bgame or R.

If you look at http://astrostatistics.psu.edu/datasets/R/html/base/html/shell.html you can see the variable flag passed to the system call."flag the switch to run a command under the shell. If the shell is bash or tcsh the default is changed to "-c"."

Also "the shell to be used can be changed by setting the configure variable R_SHELL to a suitable value (a full path to a shell, e.g. /usr/local/bin/bash)."

R and System calls

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