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

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.

CodePudding user response：

"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.