Package 'callr'

Description

This function allows users of callr to specify functions that get invoked whenever an R session is launched. The function can modify the environment variables and command line arguments.

Usage

add_hook(...)

Arguments

Details

The prototype of the hook function is ⁠function (options)⁠, and it is expected to return the modified options.

Value

add_hook is called for its side-effects.

Description

callr sets the repos option in subprocesses, to make sure that a CRAN mirror is set up. This is because the subprocess cannot bring up the menu of CRAN mirrors for the user to choose from.

Usage

default_repos()

Value

Named character vector, the default value of the repos option in callr subprocesses.

Examples

default_repos()

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

r(.libPaths)

r(function() .libPaths())

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()

Description

Starts evaluating an R function call in a background R process, and returns immediately. Use p$get_result() to collect the result or to throw an error if the background computation failed.

Usage

r_bg(
  func,
  args = list(),
  libpath = .libPaths(),
  repos = default_repos(),
  stdout = "|",
  stderr = "|",
  poll_connection = TRUE,
  error = getOption("callr.error", "error"),
  cmdargs = c("--slave", "--no-save", "--no-restore"),
  system_profile = FALSE,
  user_profile = "project",
  env = rcmd_safe_env(),
  supervise = FALSE,
  package = FALSE,
  arch = "same",
  ...
)

Arguments

r(.libPaths)

r(function() .libPaths())

Value

An r_process object, which inherits from process, so all process methods can be called on it, and in addition it also has a get_result() method to collect the result.

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.

Examples

rx <- r_bg(function() 1 + 2)

# wait until it is done
rx$wait()
rx$is_alive()
rx$get_result()

Description

Differences to r():

• No extra repositories are set up.

• The --no-save, --no-restore command line arguments are not used. (But --slave still is.)

• The system profile and the user profile are loaded.

• No extra environment variables are set up.

Usage

r_copycat(
  func,
  args = list(),
  libpath = .libPaths(),
  repos = getOption("repos"),
  cmdargs = "--slave",
  system_profile = TRUE,
  user_profile = TRUE,
  env = character(),
  ...
)

Arguments

r(.libPaths)

r(function() .libPaths())

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 callr functions: r(), r_vanilla()

Description

An R process that runs in the background. This is an R6 class that extends the processx::process class. The process starts in the background, evaluates an R function call, and then quits.

Super class

processx::process -> r_process

Methods

Public methods

• r_process$new()

• r_process$get_result()

Method new()

Start a new R process in the background.

Usage

r_process$new(options)

Arguments

Returns

A new r_process object.

Method get_result()

Return the result, an R object, from a finished background R process. If the process has not finished yet, it throws an error. (You can use wait() method (see processx::process) to wait for the process to finish, optionally with a timeout.) You can also use processx::poll() to wait for the end of the process, together with other processes or events.

Usage

r_process$get_result()

Returns

The return value of the R expression evaluated in the R process.

Examples

## List all options and their default values:
r_process_options()

## Start an R process in the background, wait for it, get result
opts <- r_process_options(func = function() 1 + 1)
rp <- r_process$new(opts)
rp$wait()
rp$get_result()

Create options for an r_process object

Description

Create options for an r_process object

Usage

r_process_options(...)

Arguments

Value

A list of options.

r_process_options() creates a set of options to initialize a new object from the r_process class. Its arguments must be named, the names are used as option names. The options correspond to (some of) the arguments of the r() function. At least the func option must be specified, this is the R function to run in the background.

Examples

## List all options and their default values:
r_process_options()

Description

A permanent R session that runs in the background. This is an R6 class that extends the processx::process class.

The process is started at the creation of the object, and then it can be used to evaluate R function calls, one at a time.

Super class

processx::process -> r_session

Public fields

Methods

Public methods

• r_session$new()

• r_session$run()

• r_session$run_with_output()

• r_session$call()

• r_session$poll_process()

• r_session$get_state()

• r_session$get_running_time()

• r_session$read()

• r_session$close()

• r_session$traceback()

• r_session$debug()

• r_session$attach()

• r_session$print()

Method new()

creates a new R background process. It can wait for the process to start up (wait = TRUE), or return immediately, i.e. before the process is actually ready to run. In the latter case you may call the poll_process() method to make sure it is ready.

Usage

r_session$new(options = r_session_options(), wait = TRUE, wait_timeout = 3000)

Arguments

Returns

An r_session object.

Method run()

Similar to r(), but runs the function in a permanent background R session. It throws an error if the function call generated an error in the child process.

Usage

r_session$run(func, args = list(), package = FALSE)

Arguments

Returns

The return value of the R expression.

Method run_with_output()

Similar to ⁠$run()⁠, but returns the standard output and error of the child process as well. It does not throw on errors, but returns a non-NULL error member in the result list.

Usage

r_session$run_with_output(func, args = list(), package = FALSE)

Arguments

Returns

A list with the following entries.

• result: The value returned by func. On error this is NULL.

• stdout: The standard output of the process while evaluating

• stderr: The standard error of the process while evaluating the func call.

• error: On error it contains an error object, that contains the error thrown in the subprocess. Otherwise it is NULL.

• code, message: These fields are used by call internally and you can ignore them.

Method call()

Starts running a function in the background R session, and returns immediately. To check if the function is done, call the poll_process() method.

Usage

r_session$call(func, args = list(), package = FALSE)

Arguments

Method poll_process()

Poll the R session with a timeout. If the session has finished the computation, it returns with "ready". If the timeout is reached, it returns with "timeout".

Usage

r_session$poll_process(timeout)

Arguments

Returns

Character string "ready" or "timeout".

Method get_state()

Return the state of the R session.

Usage

r_session$get_state()

Returns

Possible values:

• "starting": starting up,

• "idle": ready to compute,

• "busy": computing right now,

• "finished": the R process has finished.

Method get_running_time()

Returns the elapsed time since the R process has started, and the elapsed time since the current computation has started. The latter is NA if there is no active computation.

Usage

r_session$get_running_time()

Returns

Named vector of POSIXct objects. The names are "total" and "current".

Method read()

Reads an event from the child process, if there is one available. Events might signal that the function call has finished, or they can be progress report events.

This is a low level function that you only need to use if you want to process events (messages) from the R session manually.

Usage

r_session$read()

Returns

NULL if no events are available. Otherwise a named list, which is also a callr_session_result object. The list always has a code entry which is the type of the event. See also r_session$public_fields$status for symbolic names of the event types.

• 200: (DONE) The computation is done, and the event includes the result, in the same form as for the run() method.

• 201: (STARTED) An R session that was in 'starting' state is ready to go.

• 202: (ATTACH_DONE) Used by the attach() method.

• 301: (MSG) A message from the subprocess. The message is a condition object with class callr_message. (It typically has other classes, e.g. cli_message for output from the cli package.)

• 500: (EXITED) The R session finished cleanly. This means that the evaluated expression quit R.

• 501: (CRASHED) The R session crashed or was killed.

• 502: (CLOSED) The R session closed its end of the connection that callr uses for communication.

Method close()

Terminate the current computation and the R process. The session object will be in "finished" state after this.

Usage

r_session$close(grace = 1000)

Arguments

Method traceback()

The traceback() method can be used after an error in the R subprocess. It is equivalent to the base::traceback() call, in the subprocess.

On callr version 3.8.0 and above, you need to set the callr.traceback option to TRUE (in the main process) to make the subprocess save the trace on error. This is because saving the trace can be costly for large objects passed as arguments.

Usage

r_session$traceback()

Returns

The same output as from base::traceback()

Method debug()

Interactive debugger to inspect the dumped frames in the subprocess, after an error. See more at r_session_debug.

On callr version 3.8.0 and above, you need to set the callr.traceback option to TRUE (in the main process) to make the subprocess dump frames on error. This is because saving the frames can be costly for large objects passed as arguments.

Usage

r_session$debug()

Method attach()

Experimental function that provides a REPL (Read-Eval-Print-Loop) to the subprocess.

Usage

r_session$attach()

Method print()

Print method for an r_session.

Usage

r_session$print(...)

Arguments

Examples

rs <- r_session$new()

rs$run(function() 1 + 2)

rs$call(function() Sys.sleep(1))
rs$get_state()

rs$poll_process(-1)
rs$get_state()
rs$read()

Description

The r_session$debug() method is an interactive debugger to inspect the stack of the background process after an error.

Details

Note that on callr version 3.8.0 and above, you need to set the callr.traceback option to TRUE (in the main process) to make the subprocess dump the frames on error. This is because saving the frames can be costly for large objects passed as arguments.

⁠$debug()⁠ starts a REPL (Read-Eval-Print-Loop), that evaluates R expressions in the subprocess. It is similar to browser() and debugger() and also has some extra commands:

• .help prints a short help message.

• .where prints the complete stack trace of the error. (The same as the ⁠$traceback()⁠ method.

• ⁠.inspect <n>⁠ switches the "focus" to frame ⁠<n>⁠. Frame 0 is the global environment, so ⁠.inspect 0⁠ will switch back to that.

To exit the debugger, press the usual interrupt key, i.e. CTRL+c or ESC in some GUIs.

Here is an example session that uses ⁠$debug()⁠ (some output is omitted for brevity):

# ----------------------------------------------------------------------
> rs <- r_session$new()
> rs$run(function() knitr::knit("no-such-file"))
Error in rs_run(self, private, func, args) :
 callr subprocess failed: cannot open the connection

> rs$debug()
Debugging in process 87361, press CTRL+C (ESC) to quit. Commands:
  .where       -- print stack trace
  .inspect <n> -- inspect a frame, 0 resets to .GlobalEnv
  .help        -- print this message
  <cmd>        -- run <cmd> in frame or .GlobalEnv

3: file(con, "r")
2: readLines(input2, encoding = "UTF-8", warn = FALSE)
1: knitr::knit("no-such-file") at #1

RS 87361 > .inspect 1

RS 87361 (frame 1) > ls()
 [1] "encoding"  "envir"     "ext"       "in.file"   "input"     "input.dir"
 [7] "input2"    "ocode"     "oconc"     "oenvir"    "oopts"     "optc"
[13] "optk"      "otangle"   "out.purl"  "output"    "quiet"     "tangle"
[19] "text"

RS 87361 (frame 1) > input
[1] "no-such-file"

RS 87361 (frame 1) > file.exists(input)
[1] FALSE

RS 87361 (frame 1) > # <CTRL + C>
# ----------------------------------------------------------------------

Create options for an r_session object

Description

Create options for an r_session object

Usage

r_session_options(...)

Arguments

Value

Named list of options.

The current options are:

• libpath: Library path for the subprocess. By default the same as the current library path. I.e. not necessarily the library path of a fresh R session.)

• repos: repos option for the subprocess. By default the current value of the main process.

• stdout: Standard output of the sub-process. This can be NULL or a pipe: "|". If it is a pipe then the output of the subprocess is not included in the responses, but you need to poll and read it manually. This is for experts. Note that this option is not used for the startup phase that currently always runs with stdout = "|".

• stderr: Similar to stdout, but for the standard error. Like stdout, it is not used for the startup phase, which runs with stderr = "|".

• error: See 'Error handling' in r().

• cmdargs: See the same argument of r(). (Its default might be different, though.)

• system_profile: See the same argument of r().

• user_profile: See the same argument of r().

• env: See the same argument of r().

• load_hook: NULL, or code (quoted) to run in the sub-process at start up. (I.e. not for every single run() call.)

• extra: List of extra arguments to pass to processx::process.

Call r_session_options() to see the default values. r_session_options() might contain undocumented entries, you cannot change these.

Examples

r_session_options()

Description

It tries to mimic a fresh R installation. In particular:

• No library path setting.

• No CRAN(-like) repository is set.

• The system and user profiles are not run.

Usage

r_vanilla(
  func,
  args = list(),
  libpath = character(),
  repos = c(CRAN = "@CRAN@"),
  cmdargs = "--slave",
  system_profile = FALSE,
  user_profile = FALSE,
  env = character(),
  ...
)

Arguments

r(.libPaths)

r(function() .libPaths())

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 callr functions: r(), r_copycat()

Examples

# Compare to r()
r(function() .libPaths())
r_vanilla(function() .libPaths())

r(function() getOption("repos"))
r_vanilla(function() getOption("repos"))

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

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")

Description

The child process is started in the background, and the function return immediately.

Usage

rcmd_bg(
  cmd,
  cmdargs = character(),
  libpath = .libPaths(),
  stdout = "|",
  stderr = "|",
  poll_connection = TRUE,
  repos = default_repos(),
  system_profile = FALSE,
  user_profile = "project",
  env = rcmd_safe_env(),
  wd = ".",
  supervise = FALSE,
  ...
)

Arguments

Value

It returns a process 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.

See Also

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

Description

This function is similar to rcmd(), but it has slightly different defaults:

• The repos options is unchanged.

• No extra environment variables are defined.

Usage

rcmd_copycat(
  cmd,
  cmdargs = character(),
  libpath = .libPaths(),
  repos = getOption("repos"),
  env = character(),
  ...
)

Arguments

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(), rcmd_bg()

Description

An ⁠R CMD *⁠ command that runs in the background. This is an R6 class that extends the processx::process class.

Super class

processx::process -> rcmd_process

Methods

Public methods

• rcmd_process$new()

• rcmd_process$clone()

Method new()

Start an ⁠R CMD⁠ process.

Usage

rcmd_process$new(options)

Arguments

Returns

A new rcmd_process object.

Method clone()

The objects of this class are cloneable with this method.

Usage

rcmd_process$clone(deep = FALSE)

Arguments

Examples

options <- rcmd_process_options(cmd = "config", cmdargs = "CC")
rp <- rcmd_process$new(options)
rp$wait()
rp$read_output_lines()

Create options for an rcmd_process object

Description

Create options for an rcmd_process object

Usage

rcmd_process_options(...)

Arguments

Value

A list of options.

rcmd_process_options() creates a set of options to initialize a new object from the rcmd_process class. Its arguments must be named, the names are used as option names. The options correspond to (some of) the arguments of the rcmd() function. At least the cmd option must be specified, to select the ⁠R CMD⁠ subcommand to run. Typically cmdargs is specified as well, to supply more arguments to ⁠R CMD⁠.

Examples

## List all options and their default values:
rcmd_process_options()

rcmd_safe_env returns a set of environment variables that are more appropriate for rcmd_safe(). It is exported to allow manipulating these variables (e.g. add an extra one), before passing them to the rcmd() functions.

Description

It currently has the following variables:

• CYGWIN="nodosfilewarning": On Windows, do not warn about MS-DOS style file names.

• R_TESTS="" This variable is set by ⁠R CMD check⁠, and makes the child R process load a startup file at startup, from the current working directory, that is assumed to be the ⁠/test⁠ directory of the package being checked. If the current working directory is changed to something else (as it typically is by testthat, then R cannot start. Setting it to the empty string ensures that callr can be used from unit tests.

• R_BROWSER="false": typically we don't want to start up a browser from the child R process.

• R_PDFVIEWER="false": similarly for the PDF viewer.

Usage

rcmd_safe_env()

Details

Note that callr also sets the R_ENVIRON, R_ENVIRON_USER, R_PROFILE and R_PROFILE_USER environment variables appropriately, unless these are set by the user in the env argument of the r, etc. calls.

Value

A named character vector of environment variables.

Description

It uses the Rscript program corresponding to the current R version, to run the script. It streams stdout and stderr of the process.

Usage

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

Arguments

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.

Description

An ⁠Rscript script.R⁠ command that runs in the background. This is an R6 class that extends the processx::process class.

Super class

processx::process -> rscript_process

Methods

Public methods

• rscript_process$new()

• rscript_process$clone()

Method new()

Create a new Rscript process.

Usage

rscript_process$new(options)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

rscript_process$clone(deep = FALSE)

Arguments

Examples

options <- rscript_process_options(script = "script.R")
rp <- rscript_process$new(options)
rp$wait()
rp$read_output_lines()

Create options for an rscript_process object

Description

Create options for an rscript_process object

Usage

rscript_process_options(...)

Arguments

Value

A list of options.

rscript_process_options() creates a set of options to initialize a new object from the rscript_process class. Its arguments must be named, the names are used as option names. The options correspond to (some of) the arguments of the rscript() function. At least the script option must be specified, the script file to run.

Examples

## List all options and their default values:
rscript_process_options()

Description

This function uses a heuristic, which might fail, so its result should be taken as a best guess.

Usage

supported_archs()

Value

Character vector of supported architectures. If the current R build is not a multi-architecture build, then an empty string scalar is returned.

Examples

supported_archs()