Run an R CMD command form within R. This will usually start another R process, from a shell script.

Usage

rcmd(
cmd,
cmdargs = character(),
libpath = .libPaths(),
repos = default_repos(),
stdout = NULL,
stderr = NULL,
poll_connection = TRUE,
echo = FALSE,
show = FALSE,
callback = NULL,
block_callback = NULL,
spinner = show && interactive(),
system_profile = FALSE,
user_profile = "project",
env = rcmd_safe_env(),
timeout = Inf,
wd = ".",
fail_on_status = FALSE,
...
)

rcmd_safe(
cmd,
cmdargs = character(),
libpath = .libPaths(),
repos = default_repos(),
stdout = NULL,
stderr = NULL,
poll_connection = TRUE,
echo = FALSE,
show = FALSE,
callback = NULL,
block_callback = NULL,
spinner = show && interactive(),
system_profile = FALSE,
user_profile = "project",
env = rcmd_safe_env(),
timeout = Inf,
wd = ".",
fail_on_status = FALSE,
...
)

Arguments

cmd

Command to run. See R --help from the command line for the various commands. In the current version of R (3.2.4) these are: BATCH, COMPILE, SHLIB, INSTALL, REMOVE, build, check, LINK, Rprof, Rdconv, Rd2pdf, Rd2txt, Stangle, Sweave, Rdiff, config, javareconf, rtags.

cmdargs

Command line arguments.

libpath

The library path.

repos

The repos option. If NULL, then no repos option is set. This options is only used if user_profile or system_profile is set FALSE, as it is set using the system or the user profile.

stdout

Optionally a file name to send the standard output to.

stderr

Optionally a file name to send the standard error to. It may be the same as stdout, in which case standard error is redirected to standard output. It can also be the special string "2>&1", in which case standard error will be redirected to standard output.

poll_connection

Whether to have a control connection to the process. This is used to transmit messages from the subprocess to the parent.

echo

Whether to echo the complete command run by rcmd.

show

Logical, whether to show the standard output on the screen while the child process is running. Note that this is independent of the stdout and stderr arguments. The standard error is not shown currently.

callback

A function to call for each line of the standard output and standard error from the child process. It works together with the show option; i.e. if show = TRUE, and a callback is provided, then the output is shown of the screen, and the callback is also called.

block_callback

A function to call for each block of the standard output and standard error. This callback is not line oriented, i.e. multiple lines or half a line can be passed to the callback.

spinner

Whether to show a calming spinner on the screen while the child R session is running. By default it is shown if show = TRUE and the R session is interactive.

system_profile

Whether to use the system profile file.

user_profile

Whether to use the user's profile file. If this is "project", then only the profile from the working directory is used, but the R_PROFILE_USER environment variable and the user level profile are not. See also "Security considerations" below.

env

Environment variables to set for the child process.

timeout

Timeout for the function call to finish. It can be a base::difftime object, or a real number, meaning seconds. If the process does not finish before the timeout period expires, then a system_command_timeout_error error is thrown. Inf means no timeout.

wd

Working directory to use for running the command. Defaults to the current working directory.

fail_on_status

Whether to throw an R error if the command returns with a non-zero status code. By default no error is thrown.

...

Extra arguments are passed to processx::run().

Value

A list with the command line $command), standard output ($stdout), standard error (stderr), exit status ($status) of the external R CMD command, and whether a timeout was reached ($timeout).

Details

Starting from callr 2.0.0, rcmd() has safer defaults, the same as the rcmd_safe() default values. Use rcmd_copycat() for the old defaults.

Security considerations

callr makes a copy of the user's .Renviron file and potentially of the local or user .Rprofile, in the session temporary directory. Avoid storing sensitive information such as passwords, in your environment file or your profile, otherwise this information will get scattered in various files, at least temporarily, until the subprocess finishes. You can use the keyring package to avoid passwords in plain files.