rcmd: Run an R CMD command

In callr: Call R from R

Run an ⁠R CMD⁠ command

Description

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().

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.

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).

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.

See Also

Other R CMD commands: rcmd_bg(), rcmd_copycat()

Examples

rcmd("config", "CC")

callr documentation built on June 22, 2024, 6:48 p.m.