R/run_batch.R

In shug0131/cctu: In-House Functions for Report Writing at Cambridge Clinical Trials Unit

#' Runs a script in batch mode directly from within R.
#'
#' This function is to allow R CMD BATCH to be called interactively, without
#' needing to start up a command line terminal and change directories etc.
#' It calls the R CMD BATCH from the current working directory. Hence its value
#'  is in producing the side-effects: whatever happens when the script is run.
#' Plus a log file will be created in the working directory with the same name
#' as the script but with the suffix changed to '.Rout'.
#'
#' The command will not run in environments where \code{\link{interactive}}
#' is false, so as to prevent infinite loops.
#'
#'
#' @param filename character string of the name or path of the script
#' (relative to the working directory).
#' @param ... other arguments to pass to \code{\link{system}}
#'
#' @return  see \code{\link{system}} which is called.
#'
#' @seealso \code{\link{BATCH}} and \code{rcmd} from the callr package,
#' which might already do this....
#'
#' @seealso \code{check_failures} from the devtools package for future ideas
#'  for a function to check the log file for errors or warnings.
#' @export





run_batch <- function(filename, ...) {
  if (!rlang::is_interactive()) {
    warning("run_batch() only works in interactive mode")
  } else {
    warning("Make certain you only have the project open on one computer",
      immediate. = TRUE
    )
    warning("If using renv for package management, you have to have renv::load() in your script at the start",
      immediate. = TRUE
    )
    # belt and braces approach to use full filepaths with quotes.
    # It did work  with just "R CMD BATCH --vanilla filename", in a simple example.
    command <- paste0(
      '"', R.home("bin"),
      '/R" CMD BATCH --vanilla "',
      normalizePath(filename),
      '"'
    )
    system(command, ...)
    # tools::Rcmd(c("BATCH","--vanilla", normalizePath(filename)))
    # still doesn't fix the testing problem with UNC path
  }
}