[R] Calling library functions from outside R

[Dirk Eddelbuettel]

On 18 June 2009 at 14:02, Jim Nemesh wrote:
| Actually, I'm going to take by my comments.
| 
| You can use Rscript with multiple -e arguments to do what I was  
| looking for:
| 
| Rscript -e 'library(broadgap.hapmaptools)' -e 'processAllFiles(dir="/ 
| humgen/cnp04/sandbox/steve/1m/hapmap3/genotypes/ftp.hapmap.org/genotypes/2008-07_phaseIII/hapmap_format/forward 
| ", outRootDir="/humgen/cnp04/sandbox/data/snpTagging")'

That file structure reveals that you use a Unix-alike operating system, in
which case you should look at littler (which Gabor already pointed you too).
I use it all the time for scripted wrappers like your case here.  E.g. and
obviously untested:

  $ r -lbroadgap.hapmaptools,getopt \      # this loads you both libraries, silently
      -e'processAllFiles(dir="/humgen/.../forward", outRootDir="/humgen/.../snpTagging")'

where I truncated the paths and indented a line.  [ In tis case we don't even
need getopt, do we ? ]

As a bonus, r starts up faster than Rscript [1]. And it may save you from
pressing six more keys not counting Shift.

Hope this helps,  Dirk

[1] As it embeds R rather than calls it using exec() -- at the cost of not
being portable beyond Linux and OS X.

-- 
Three out of two people have difficulties with fractions.