cmd_run: Execute command

In blit: Bioinformatics Library for Integrated Tools

Execute command

Description

• cmd_run: Run the command.

• cmd_help: Print the help document for this command.

• cmd_background: Run the command in the background. This function is provided for completeness. Instead of using this function, we recommend using cmd_parallel(), which can run multiple commands in the background while ensuring that all processes are properly cleaned up when the process exits.

Usage

cmd_run(
  command,
  stdout = TRUE,
  stderr = TRUE,
  stdin = TRUE,
  stdout_callback = NULL,
  stderr_callback = NULL,
  timeout = NULL,
  spinner = FALSE,
  verbose = TRUE
)

cmd_help(
  command,
  stdout = TRUE,
  stderr = TRUE,
  stdout_callback = NULL,
  stderr_callback = NULL,
  verbose = TRUE
)

cmd_background(
  command,
  stdout = FALSE,
  stderr = FALSE,
  stdin = NULL,
  verbose = TRUE
)

Arguments

command	A command object.
stdout, stderr	Specifies how the output/error streams of the child process are handled. Possible values include: FALSE/NULL: Suppresses the output/error stream. TRUE: Prints the child process output/error to the R console. If a standard output/error stream exists, "" is used; otherwise, "|" is used. string: An empty string "" inherits the standard output/error stream from the main R process (Printing in the R console). If the main R process lacks a standard output/error stream, such as in RGui on Windows, an error is thrown. A string "|" prints to the standard output connection of R process (Using cat()). Alternative, a file name or path to redirect the output/error. If a relative path is specified, it remains relative to the current working directory, even if a different directory is set using cmd_wd(). connection: A writable R connection object. If the connection is not open(), it will be automatically opened. For stderr, use string "2>&1" to redirect it to the same connection (i.e. pipe or file) as stdout. For cmd_help(), use FALSE/NULL will do nothing, since it always want to display the help document. For cmd_background(), connection cannot be used, and TRUE and "|" will fallback to the empty string "". When using a connection (if not already open) or a string, wrapping it with I() prevents overwriting existing content.
stdin	should the input be diverted? Possible values include: FALSE/NULL: no standard input. TRUE: If a standard input stream exists, "" is used; otherwise, NULL is used. string: An empty string "" inherits the standard input stream from the main R process. If the main R process lacks a standard input stream, such as in RGui on Windows, an error is thrown. Alternative, a file name or path to redirect the input. If a relative path is specified, it remains relative to the current working directory, even if a different directory is set using cmd_wd().
stdout_callback, stderr_callback	Possible values include: NULL: no callback function. function: A function invoked for each line of standard output or error. Non-text (non-character) output will be ignored. The function should accept two arguments: one for the standard output or error and another for the running process object.
timeout	Timeout in seconds. This is a limit for the elapsed time running command in the separate process.
spinner	Whether to show a reassuring spinner while the process is running.
verbose	A single boolean value indicating whether the command execution should be verbose.

Value

• cmd_run: Exit status invisiblely.

• cmd_help: The input command invisiblely.

• cmd_background: A process object.

See Also

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_conda()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

blit documentation built on April 12, 2025, 1:16 a.m.