Run a command in a conda environment

Source: R/conda.R

This function runs a command in a chosen conda environment.

conda_run2(
  cmd,
  args = c(),
  conda = "auto",
  envname = NULL,
  cmd_line = paste(shQuote(cmd), paste(args, collapse = " ")),
  intern = FALSE,
  echo = !intern
)

Arguments

cmd

The system command to be invoked, as a character string.

args

A character vector of arguments to the command. The arguments should be quoted e.g. by shQuote() in case they contain space or other special characters (a double quote or backslash on Windows, shell-specific special characters on Unix).

conda

The path to a conda executable. Use "auto" to allow reticulate to automatically find an appropriate conda binary. See Finding Conda and conda_binary() for more details.

envname

The name of, or path to, a conda environment.

cmd_line

The command line to be executed, as a character string. This is automatically generated from cmd and args, but can be provided directly if needed (if provided, it overrides cmd and args).

intern

A logical (not NA) which indicates whether to capture the output of the command as an R character vector. If FALSE (the default), the return value is the error code (0 for success).

echo

A logical (not NA) which indicates whether to echo the command to the console before running it.

Value

conda_run2() runs a command in the desired conda environment. If intern = TRUE the output is returned as a character vector; if intern = FALSE (the deafult), then the return value is the error code (0 for success). See shell() (on windows) or system2() on macOS or Linux for more details.

Details

Note that, whilst the syntax is similar to system2(), the function dynamically generates a shell script with commands to activate the chosen conda environent. This avoids issues with quoting, as discussed in this GitHub issue.

See also

conda-tools