r: Evaluate an expression in another R session

In MangoTheCat/callr: Call R from R

Evaluate an expression in another R session

Description

From callr version 2.0.0, r() is equivalent to r_safe(), and tries to set up a less error prone execution environment. In particular:

• Ensures that at least one reasonable CRAN mirror is set up.

• Adds some command line arguments to avoid saving .RData files, etc.

• Ignores the system and user profiles (by default).

• Sets various environment variables: CYGWIN to avoid warnings about DOS-style paths, R_TESTS to avoid issues when callr is invoked from unit tests, R_BROWSER and R_PDFVIEWER to avoid starting a browser or a PDF viewer. See rcmd_safe_env().

Usage

r(
  func,
  args = list(),
  libpath = .libPaths(),
  repos = default_repos(),
  stdout = NULL,
  stderr = NULL,
  poll_connection = TRUE,
  error = getOption("callr.error", "error"),
  cmdargs = c("--slave", "--no-save", "--no-restore"),
  show = FALSE,
  callback = NULL,
  block_callback = NULL,
  spinner = show && interactive(),
  system_profile = FALSE,
  user_profile = "project",
  env = rcmd_safe_env(),
  timeout = Inf,
  package = FALSE,
  arch = "same",
  ...
)

r_safe(
  func,
  args = list(),
  libpath = .libPaths(),
  repos = default_repos(),
  stdout = NULL,
  stderr = NULL,
  poll_connection = TRUE,
  error = getOption("callr.error", "error"),
  cmdargs = c("--slave", "--no-save", "--no-restore"),
  show = FALSE,
  callback = NULL,
  block_callback = NULL,
  spinner = show && interactive(),
  system_profile = FALSE,
  user_profile = "project",
  env = rcmd_safe_env(),
  timeout = Inf,
  package = FALSE,
  arch = "same",
  ...
)

Arguments

func	Function object to call in the new R process. The function should be self-contained and only refer to other functions and use variables explicitly from other packages using the :: notation. By default the environment of the function is set to .GlobalEnv before passing it to the child process. (See the package option if you want to keep the environment.) Because of this, it is good practice to create an anonymous function and pass that to callr, instead of passing a function object from a (base or other) package. In particular r(.libPaths) does not work, because .libPaths is defined in a special environment, but r(function() .libPaths()) works just fine.
args	Arguments to pass to the function. Must be a list.
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	The name of the file the standard output of the child R process will be written to. If the child process runs with the --slave option (the default), then the commands are not echoed and will not be shown in the standard output. Also note that you need to call print() explicitly to show the output of the command(s). IF NULL, then standard output is not returned, but it is recorded and included in the error object if an error happens. Various special values for this argument such as "|" are explained in the stdout argument of processx::process.
stderr	The name of the file the standard error of the child R process will be written to. In particular message() sends output to the standard error. If nothing was sent to the standard error, then this file will be empty. This argument can be the same file as stdout, in which case they will be correctly interleaved. If this is the string "2>&1", then standard error is redirected to standard output. IF NULL, then standard output is not returned, but it is recorded and included in the error object if an error happens. Various special values for this argument such as "|" are explained in the stdout argument of processx::process.
poll_connection	Whether to have a control connection to the process. This is used to transmit messages from the subprocess to the main process.
error	What to do if the remote process throws an error. See details below.
cmdargs	Command line arguments to pass to the R process. Note that c("-f", rscript) is appended to this, rscript is the name of the script file to run. This contains a call to the supplied function and some error handling code.
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.
package	Whether to keep the environment of func when passing it to the other package. Possible values are: FALSE: reset the environment to .GlobalEnv. This is the default. TRUE: keep the environment as is. pkg: set the environment to the pkg package namespace.
arch	Architecture to use in the child process, for multi-arch builds of R. By default the same as the main process. See supported_archs(). If it contains a forward or backward slash character, then it is taken as the path to the R executable. Note that on Windows you need the path to Rterm.exe.
...	Extra arguments are passed to processx::run().

Details

The r() function from before 2.0.0 is called r_copycat() now.

Value

Value of the evaluated expression.

Error handling

callr handles errors properly. If the child process throws an error, then callr throws an error with the same error message in the main process.

The error expert argument may be used to specify a different behavior on error. The following values are possible:

• error is the default behavior: throw an error in the main process, with a prefix and the same error message as in the subprocess.

• stack also throws an error in the main process, but the error is of a special kind, class callr_error, and it contains both the original error object, and the call stack of the child, as written out by utils::dump.frames(). This is now deprecated, because the error thrown for "error" has the same information.

• debugger is similar to stack, but in addition to returning the complete call stack, it also start up a debugger in the child call stack, via utils::debugger().

The default error behavior can be also set using the callr.error option. This is useful to debug code that uses callr.

callr uses parent errors, to keep the stacks of the main process and the subprocess(es) in the same error object.

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.

Transporting objects

func and args are copied to the child process by first serializing them into a temporary file using saveRDS() and then loading them back into the child session using readRDS(). The same strategy is used to copy the result of calling func(args) to the main session. Note that some objects, notably those with externalptr type, won't work as expected after being saved to a file and loaded back.

For performance reasons compress=FALSE is used when serializing with saveRDS(), this can be disabled by setting options(callr.compress_transport = TRUE).

See Also

Other callr functions: r_copycat(), r_vanilla()

Examples

# Workspace is empty
r(function() ls())

# library path is the same by default
r(function() .libPaths())
.libPaths()

MangoTheCat/callr documentation built on Aug. 29, 2024, 2:32 a.m.