very late answer, maybe the library is newer than your question, but what about optparse or getopt?

install.packages('optparse')
?optparse
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I tried to get it working (I come from Python and I'm used to the syntax) but in the end I settled for the easier (and working) 'getopt' solution:

install.packages('getopt')
.
.
.
  if(require("getopt", quietly=TRUE)) {
    opt <- getopt(matrix(c('path', 'p', 1, "character"),
                         ncol=4, byrow=TRUE))
    if(!is.null(opt$path))
      path <- opt$path
  }
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