rlinuxcommand-line-interfacecommand-line-argumentsrscript

Why are "--slave" and "--no-restore" being used by commandArgs when I call my R file with Rscript

I am running an R script using Rscript from the command line (linux) like this:

Rscript myscript.R inputfile1.csv inputfile.csv integerArg

My command args are structured like this

  cmd_args <- commandArgs() 
  infile1 <- cmd_args[1]
  infile2 <- cmd_args[2]
  intArg <- cmd_args[3]

  main_func<-function(infile1, infile2, intArg){
  print(infile1)
  print(infile2)
  print(intArg)
  }

  main_func(infile1, infile2, intArg)

This prints out

[1] "/home/miniconda3/envs/bionano_python3.0/lib/R/bin/exec/R" [1] "--slave" [1] "--no-restore"

I guess I don't have to tell you that the script gives an error the first time it hits one of the input arguments.

I have also tried running the script like this and it gives the exact same output/error

R --slave --no-restore --file=myscript.R --args inputfile1.csv inputfile.csv integerArg

I'm confused because I am not setting these flags when I call Rscript so why are they appearing, and how can I make the commandArgs read only the designated input parameters? Any ideas on how to solve this issue? I can't seem to find any information about why this could be happening and I'm clearly just missing something. Thanks so much in advance.

Solution

  • "That's just the way it is" with Rscript.

    One fix: use commandArgs(trailingOnly=TRUE)

    Another fix: use littler (see littler at CRAN which prunes the arguments similar to trailingOnly=TRUE and leaves them in `argv[]

    And another fix: use eg docopt which standardizes option process (see docopt at CRAN.

    There are a bunch of examples combining littler and docopt in the littler repo in inst/examples. I have used a number of those daily for many years. "Works for me" as they say.