r2dup2

Author: rchaput.pro@gmail.com

Description

r2dup2 is a R package that allows you to redirect streams, especially stdout and stderr, at the system level in R.

Its main rationale is that the default r utils::capture.output function only redirects R messages: it does not truly redirect the system streams, and thus fails with sub-processes, such as pandoc when using RMarkdown.

See for example:

capture.output(file = "error.txt", type = "message", {
    cat("This will be printed to error.txt", file = stderr())
    message("This will also be printed to error.txt")
    system("echo But this will be printed to R Console instead of error.txt! >&2")
})

r2dup2 instead uses the dup2 C function to effectively redirect streams in R.

Installation

Important: this packages requires a POSIX-compliant system, such as Linux, or macOS. It will not work on Windows, as it uses low-level system calls that are specific to POSIX.

It is recommended to use either remotes or devtools to install this package:

install.packages("remotes")
remotes::install_github("rchaput/r2dup2")

or, alternatively:

install.packages("devtools")
devtools::install_github("rchaput/r2dup2")

How to use

The main function of this package is with_redirect_stderr. It can be used to:

• Redirect to a new file (truncates any existing content):

with_redirect_stderr(file = "my_new_file.err", {
  # Place here any command that outputs to stderr
  system("echo This line will be printed to my_new_file.err >&2")
  system("echo This line will be printed after the first one >&2")
})

• Redirect to an existing file (appending new content):

with_redirect_stderr(file = "existing_file.err", append = TRUE, {
  system("echo This line will be appended to existing_file.err >&2")
  system("echo And this one too >&2")
})

• Capture stderr to a variable:

stderr <- with_redirect_stderr({
  system("echo The variable stderr will contain this line")
})

See the documentation r ?with_redirect_stderr for more details.