[Rd] R's parsing of command line arguments using commandArgs()

[Prof Brian D Ripley]

On Mon, 26 Sep 2005, Marc Schwartz (via MN) wrote:

> On Fri, 2005-09-23 at 15:37 -0500, Marc Schwartz (via MN) wrote:
> > Hi all,
> >
> > I am setting up some R program files for use by our DB programmers to
> > enable them to utilize some R functions which will be called from within
> > TCL code. R has been installed on an RHEL server and R will process the
> > results of SQL queries against an Oracle database.
> >
> > In some cases, they will generate a data file to be read in and
> > processed by R, in others they will simply make the tabulated results
> > available.
> >
> > I know that I could do the SQL queries from within R, however, this is
> > the approach that has been defined for now for various reasons.
> >
> > I wanted to provide some flexibility for them, by passing some of the
> > tabulated results via command line arguments to R functions, rather than
> > via environment variables, which is easier for them to do in TCL it
> > would seem. They would create these values at run time, based upon specs
> > that I give them.
> >
> > Using the following as an example:
> >
> > $ R --slave --vanilla --args "c(5,5)" "c(.5,.5)" < RScript.R
> >
> > I can then process "c(5,5)" and "c(.5,.5)" as two arguments, via:
> >
> > Args <- commandArgs()
> >
> > where the two arguments are Args[5] and Args[6], respectively. I can
> > then of course pass these as "eval(parse(text = Args[5]))" to other R
> > functions.
> >
> >
> > However, if there is any whitespace in the two arguments, such as:
> >
> > R --slave --vanilla --args "c(5, 5)" "c(.5, .5)" < RScript.R
> >
> > even though surrounded by double quotes (or single quotes or
> > backquotes), the two arguments are parsed as four.
> >
> > Is this behavior expected? I was under the impression, from other C
> > based programs and bash shell scripts for example, that the use of the
> > double quotes would wrap such text and thus be parsed as a single
> > argument.

Sort of.  Unfortunately both the R front-end script and the R executable
get to play here, so once the front-end has parsed the args the quoting
gets lost.  You might hope that double quoting would help, but it does not.

> >
> > This is using:
> >
> > Version 2.1.1 Patched (2005-09-22) on FC4.
>
>
> Apologies for replying to my own post here, but I wanted to follow up
> with a solution provided by Robert McGehee, which works here.
>
> The solution is as follows:
>
> echo "a <- c(5, 5); b <- c(0.5, 0.5)" | cat - RScript.R | R --slave \
> --vanilla
>
>
> This uses echo and cat to pre-pend the 'a' and 'b' vector assignments to
> the R program file, before passing the whole thing to R.
>
> This then allows for arguments with embedded whitespace to be passed as
> required at run time.
>
> Thanks Robert!
>
> Marc
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595