[R] commandArgs usage and --args invokation
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sun Apr 1 09:18:22 CEST 2007
On Sat, 31 Mar 2007, ivo welch wrote:
> Dear R experts:
> I am a bit stymied by how the argument picking-off works in R batch file
You seem to mean 'R CMD BATCH' usage (there are other ways to run R in
batch), and also I will assume you are talking only about a Unix-alike
(these things are somewhat different on Windows). Please do follow the R
posting guide and provide basic information (and read the help).
In R 2.5.0 you probably want to use 'Rscript' instead for this sort of
> $ cat commandArgs.R
> cat(" Command Line Arguments were ", commandArgs(), "\n");
We don't want the trailing ';': this is R not C.
> $ /usr/bin/R CMD BATCH commandArgs.R --args 1 2 3
> $ /usr/bin/R --args 1 CMD BATCH commandArgs.R
> ... I am now getting into interactive mode ?! I guess it really is
> skipping the rest of the command line
Yes, that is what --args is documented to do, skip the rest of the command
line. Try R --help
> $ /usr/bin/R CMD BATCH commandArgs.R --args 1
> $ ls -lt | head
> total 1628148
> -rw-rw-r-- 1 ivo ivo 827 Mar 31 21:47 --args
Please DO read the help here:
gannet% R CMD BATCH --help
Usage: R CMD BATCH [options] infile [outfile]
so you have 'options' in the wrong place, and --args is matching
'outfile'. As is says that only arguments starting with '-' are
considered to be options, you cannot use '1' here as an option. What you
can do is
R CMD BATCH '--args 1' commandArgs.R
Once again, this is doing what it is documented to do.
> Could someone please let me know?
> [also, are there multi-core versions of R? my guess is no, but since
> I have a second processor lying around, I am trying to get it into the
> A working example would be appreciated.
R is not multithreaded, but you can make use of multithreaded BLASes: see
the R-admin installation manual.
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
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