shell: Invoke a command in the system command-line shell

In acidgenomics/r-acidbase: Acid Genomics Base Functions

Invoke a command in the system command-line shell

Description

Invoke a command in the system command-line shell

Usage

shell(
  command,
  args = character(),
  env = NULL,
  wd = getwd(),
  print = TRUE,
  stderrFile = NULL,
  stdoutFile = NULL,
  stderrToStdout = FALSE,
  returnStdout = FALSE
)

Arguments

command	character(1). Name of program to run.
args	character. Arguments passed to command.
env	character or NULL. Environment variables of the child process. If NULL, the parent environment is inherited. To append new environment variables to the ones set in the current process, specify "current" in env, without a name, and the appended ones with names. The appended ones can overwrite the current ones.
wd	character(1). Working directory path inside process.
print	logical(1). Whether to print (echo) the commands to the console.
stdoutFile, stderrFile	character(1) or NULL. File path to log stdout and/or stderr. Disabled when set NULL.
stderrToStdout	logical(1). Whether to redirect standard error (stderr) to standard output (stdout). Similar to ⁠2>&1⁠ in POSIX or ⁠&>⁠ in Bash.
returnStdout	logical(1). Whether to return stdout as a character vector, split by "\n".

Value

Invisible list. Contains named elements: "status", "stdout", "stderr", "timeout".

Note

Updated 2023-11-04.

See Also

• processx::run().

• base::system2(), our previously used legacy approach.

Examples

x <- shell(
    command = "printf",
    args = c("%s\n", "hello", "world"),
    print = TRUE
)
print(x)

acidgenomics/r-acidbase documentation built on June 13, 2025, 7:06 p.m.