[R] reading file names for R batch process

[Duncan Temple Lang]

Thomas Lumley wrote:
> On Thu, 6 Dec 2001, Sven Garbade wrote:
> 
> > Prof Brian D Ripley wrote:
> > >
> > > On Thu, 6 Dec 2001, Sven Garbade wrote:
> > >
> > > > Hi all,
> > > >
> > > > I've written a function that takes several filenames as arguments, does
> > > > some calculations and write new files. Now I want to write a shell
> > > > script (under Linux) that determines the files for the R process and
> > > > starts R with the filenames as arguments. But how can I commit the
> > > > filenames to the R process?
> > >
> > > via enviroment variables, most easily.
> > >
> > > Read by Sys.getenv.
> >
> > Ah, this is very easy and works! Thanks, Sven
> 
> I believe you could also use the commandArgs() function.
> 
> 	-thomas


Using commandArgs() would, in theory, be both a better and simpler
mechanism. It doesn't require you to come up with names for the
environment variables and agree on those in both the shell script and
the R code.  Additionally, the values will not be passed on to any
applications run from within the R session and so avoid any potential
conflicts between the use of environment variables by different
applications.

For your application, since file names are typically single words,
this should work.

  echo 'print(commandArgs())' | R --save file1 file2

However, the way the R script is set up at present, the commandArgs()
doesn't work in general, at least with the obvious usage. For example,

  echo 'print(commandArgs())' | R --save 'my first argument' argument2
 
produces 
ARGUMENT 'my' __ignored__
ARGUMENT 'first' __ignored__
ARGUMENT 'argument' __ignored__
ARGUMENT 'argument2' __ignored__
[1] "/home3/duncan/R/R-cvs/bin/R.bin" "--slave"
[3] "my"                              "first"
[5] "argument"                        "argument2"

So we get warning messages from the R executable (not script) and also
it breaks the single argument 'my first argument' into 3 distinct arguments.

In the future, this might be fixed by a) using a -- separator for
arguments that leaves anything past that uninterpreted by R.
and b) preserving the quotes around arguments.

So a command like
  echo 'print(commandArgs())' | R --save -- 'my first argument' argument2
would print 
[1] "/home3/duncan/R/R-cvs/bin/R.bin" "--slave"
[3] "my first argument"               "argument2"


But that will have to wait.

 D.


-- 
_______________________________________________________________

Duncan Temple Lang                duncan at research.bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-3217
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