Invoke a System Command

Description

system invokes the OS command specified by command.

Usage

system(command, intern = FALSE,
       ignore.stdout = FALSE, ignore.stderr = FALSE,
       wait = TRUE, input = NULL, show.output.on.console = TRUE,
       minimized = FALSE, invisible = TRUE)

Arguments

Details

command is parsed as a command plus arguments separated by spaces. So if the path to the command (or an argument) contains spaces, it must be quoted e.g. by shQuote. Only double quotes are allowed on Windows: see the examples. (Note: a Windows path name cannot contain a double quote, so we do not need to worry about escaping embedded quotes.)

command must be an executable (extensions ‘.exe’, ‘.com’) or a batch file (extensions ‘.cmd’ and ‘.bat’): these extensions are tried in turn if none is supplied.) This means that redirection, pipes, DOS internal commands, ... cannot be used: see shell.

The search path for command may be system-dependent: it will include the R ‘bin’ directory, the working directory and the Windows system directories before PATH.

The ordering of arguments after the first two has changed from time to time: it is recommended to name all arguments after the first.

There are many pitfalls in using system to ascertain if a command can be run — Sys.which is more suitable.

Value

If intern = TRUE, a character vector giving the output of the command, one line per character string. (Output lines of more than 8095 bytes will be split.) If the command could not be run an R error is generated. Under the Rgui console intern = TRUE also captures stderr unless ignore.stderr = TRUE. If command runs but gives a non-zero exit status this will be reported with a warning and in the attribute "status" of the result: an attribute "errmsg" may also be available

If intern = FALSE, the return value is an error code (0 for success), given the invisible attribute (so needs to be printed explicitly). If the command could not be run for any reason, the value is 127. Otherwise if wait = TRUE the value is the exit status returned by the command, and if wait = FALSE it is 0 (the conventional success value). Some Windows commands return out-of-range status values (e.g. -1) and so only the bottom 16 bits of the value are used.

If intern = FALSE, wait = TRUE, show.output.on.console = TRUE the ‘stdout’ and ‘stderr’ (unless ignore.stdout = TRUE or ignore.stderr = TRUE) output from a command that is a ‘console application’ should appear in the R console (Rgui) or the window running R (Rterm).

Not all Windows executables properly respect redirection of output, or may only do so from a console application such as Rterm and not from Rgui: for example, ‘fc.exe’ was among these in the past, but we have had more success recently.

Interaction with the command

Precisely what is seen by the user depends on the optional parameters, whether Rgui or Rterm is being used, and whether a console command or GUI application is run by the command.

By default nothing will be seen in either front-end until the command finishes and the output is displayed.

For console commands Rgui will open a new ‘console’, so if invisible = FALSE, a commands window will appear for the duration of the command. For Rterm a separate commands window will appear for console applications only if wait = FALSE and invisible = FALSE.

GUI applications will not display in either front-end unless invisible is false.

It is possible to interrupt a running command being waited for from the keyboard (using the Esc key in Rgui or Ctrl-C in Rterm) or from the Rgui menu: this should at least return control to the R console. R will attempt to shut down the process cleanly, but may need to force it to terminate, with the possibility of losing unsaved work, etc.

Do not try to run console applications that require user input from Rgui setting intern = TRUE or show.output.on.console = TRUE. They will not work.

Differences between Unix and Windows

How processes are launched differs fundamentally between Windows and Unix-alike operating systems, as do the higher-level OS functions on which this R function is built. So it should not be surprising that there are many differences between OSes in how system behaves. For the benefit of programmers, the more important ones are summarized in this section.

• 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.

• What happens to stdout and stderr when not captured depends on how R is running: Windows batch commands behave like a Unix-alike, but from the Windows GUI they are generally lost. system(intern=TRUE) captures ‘stderr’ when run from the Windows GUI console unless ignore.stderr = TRUE.

• The behaviour on error is different in subtle ways (and has differed between R versions).

• The quoting conventions for command differ, but shQuote is a portable interface.

• Arguments show.output.on.console, minimized, invisible only do something on Windows (and are most relevant to Rgui there).

See Also

system2.

shell or shell.exec for a less raw interface.

.Platform for platform-specific variables.

pipe to set up a pipe connection.

Examples

# launch an editor, wait for it to quit
## Not run: system("notepad myfile.txt")
# launch your favourite shell:
## Not run: system(Sys.getenv("COMSPEC"))
## Not run: 
## note the two sets of quotes here:
system(paste('"c:/Program Files/Mozilla Firefox/firefox.exe"',
             '-url cran.r-project.org'), wait = FALSE)
## End(Not run)