This might be off base, but would using --args help?  It means "ignore
everything else, Mr. R executable".  However you can still parse it within
the R environment.


I use something like this in my startup file (.site file):

if("--args" %in% commandArgs()){
    i=grep("--args", commandArgs())
    args=commandArgs()[(i+1):length(commandArgs)]
}



On Mon, Mar 14, 2011 at 3:27 PM, Fong Chun Chan <fongchun@interchange.ubc.ca
> wrote:

> Hi,
>
> I have a bunch of R scripts which have the hash bang !/usr/bin/env Rscript
> and I typically run these scripts by passing in some parameters like this:
>
> ./nameOfRScript arg1 arg2 ...
>
> I know Rscript has the option to run in --vanilla.  Where exactly do I
> insert the --vanilla option?  When I do something like this:
>
> ./nameOfRScript --vanilla arg1 arg2 ...
>
> And I try to access the commandArgs, the first argument is --vanilla which
> isn't what I want.  I tried to do commandArgs(trailingOnly=TRUE) with
>
> ./nameOfRScript --vanilla --args arg1 arg2 ...
>
> But I sitll have the first argument as --vanilla.  Does anyone know how to
> get around this?  Thanks,
>
> Fong
>
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>
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