R: Invoke a System Command

system {base}

R Documentation

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, timeout = 0,
       receive.console.signals = wait)

Arguments

`command`	the system command to be invoked, as a character string.
`intern`	a logical (not `NA`) which indicates whether to capture the output of the command as an R character vector.
`ignore.stdout`, `ignore.stderr`	a logical (not `NA`) indicating whether messages written to ‘stdout’ or ‘stderr’ should be ignored.
`wait`	a logical (not `NA`) indicating whether the R interpreter should wait for the command to finish, or run it asynchronously. This will be ignored (and the interpreter will always wait) if `intern = TRUE`. When running the command asynchronously, no output will be displayed on the `Rgui` console in Windows (it will be dropped, instead).
`input`	if a character vector is supplied, this is copied one string per line to a temporary file, and the standard input of `command` is redirected to the file.
`timeout`	timeout in seconds, ignored if 0. This is a limit for the elapsed time running `command` in a separate process. Fractions of seconds are ignored.
`receive.console.signals`	a logical (not `NA`) indicating whether the command should receive events from the terminal/console that R runs from, particularly whether it should be interrupted by `Ctrl-C`. This will be ignored and events will always be received when `intern = TRUE` or `wait = TRUE`.
`show.output.on.console`, `minimized`, `invisible`	arguments that are accepted on Windows but ignored on this platform, with a warning.

Details

This interface has become rather complicated over the years: see system2 for a more portable and flexible interface which is recommended for new code.

command is parsed as a command plus arguments separated by spaces. So if the path to the command (or a single argument such as a file path) contains spaces, it must be quoted e.g. by shQuote.

Unix-alikes pass the command line to a shell (normally ‘/bin/sh’, and POSIX requires that shell), so command can be anything the shell regards as executable, including shell scripts, and it can contain multiple commands separated by ;.

On Windows, system does not use a shell and there is a separate function shell which passes command lines to a shell.

If intern is TRUE then popen is used to invoke the command and the output collected, line by line, into an R character vector. If intern is FALSE then the C function system is used to invoke the command.

wait is implemented by appending & to the command: this is in principle shell-dependent, but required by POSIX and so widely supported.

When timeout is non-zero, the command is terminated after the given number of seconds. The termination works for typical commands, but is not guaranteed: it is possible to write a program that would keep running after the time is out. Timeouts can only be set with wait = TRUE.

Timeouts cannot be used with interactive commands: the command is run with standard input redirected from ‘/dev/null’ and it must not modify terminal settings. As long as tty tostop option is disabled, which it usually is by default, the executed command may write to standard output and standard error. One cannot rely on that the execution time of the child processes will be included into user.child and sys.child element of proc_time returned by proc.time. For the time to be included, all child processes have to be waited for by their parents, which has to be implemented in the parent applications.

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.

receive.console.signals = TRUE is useful when running asynchronous processes (using wait = FALSE) to implement a synchronous operation. In all other cases it is recommended to use the default.

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 on some systems.) If the command could not be run an R error is generated.

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 and a warning is issued (as from R 3.5.0). 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).

If the command times out, a warning is reported and the exit status is 124.

Stdout and stderr

For command-line R, error messages written to ‘stderr’ will be sent to the terminal unless ignore.stderr = TRUE. They can be captured (in the most likely shells) by

    system("some command 2>&1", intern = TRUE)

For GUIs, what happens to output sent to ‘stdout’ or ‘stderr’ if intern = FALSE is interface-specific, and it is unsafe to assume that such messages will appear on a GUI console (they do on the macOS GUI's console, but not on some others).

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 a 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).

Examples

# list all files in the current directory using the -F flag
## Not run: system("ls -F")

# t1 is a character vector, each element giving a line of output from who
# (if the platform has who)
t1 <- try(system("who", intern = TRUE))

try(system("ls fizzlipuzzli", intern = TRUE, ignore.stderr = TRUE))
# zero-length result since file does not exist, and will give warning.

[Package base version 4.4.1 Index]