[R] Calling library functions from outside R

[Gabor Grothendieck]

See the getopt R package and have a look at ?Rscript

Also on Windows see Rscript.bat and #Rscript.bat in
http://batchfiles.googlecode.com

and on Linux see:
http://dirk.eddelbuettel.com/code/littler.html

On Thu, Jun 18, 2009 at 1:25 PM, Jim Nemesh<nemesh at broad.mit.edu> wrote:
> I develop quite a bit of R code that I tend to distribute, or let
> other people embed in their software.  One of the things I'd really
> like to do is find a way to load an R library I've developed, and call
> one function with arguments.
>
> Currently, I achieve that by building a separate R client file, which
> reads in the command line arguments, loads the library, and calls the
> main function. The commandLineArgs function below uses commandArgs(),
> and searches the vector for the keys/values to make life easier.
>
> (code available at inside "birdsuite executables" at http://www.broad.mit.edu/science/programs/medical-and-population-genetics/birdsuite/birdsuite-downloads-0)
>
> Example:
> ---
> library (broadgap.utils)
> pedigreeFile<-commandLineArg("pedigreeFile", verbose=T)
> outPedigreeFile<-commandLineArg("outPedigreeFile", verbose=T)
> relabelPedigree(pedigreeFile, outPedigreeFile)
> ---
> called by:
>
> R CMD BATCH --pedigreeFile="foo" --outPedigreeFile="bar"
> example_client.R
>
> What I'd like to do is find a way to achieve the above, but without
> writing the client file, so I can avoid distributing these wrapper
> client files.  While the above works, it's not terribly robust, and a
> user needs to know what they are doing. To make this robust, there
> would have to be a fair bit of work to properly validate arguments,
> and print help files appropriately. Python would be an obvious choice
> for writing CLI's, as it has great CLI support and is easy to
> distribute and build executables.
>
> I've looked at the following options:
>
> RPy (setup is difficult, some users don't even know R, much less being
> capable of the setup required here, which looks like it needs root)
> RSPython (same problems as RPy)
>
> These are reasonable for me to use for my own personal fooling around,
> but not for distributing software to 1000's of users.
>
> Rscript looks like it could be a possibility:
>  >Rscript -e 'library(broadgap. utils)' -e 'ls()'
> character(0)
>
> Unfortunately, it looks like each expression is evaluated separately.
> Is there a way to evaluate multiple expressions in the same
> environment to make the above work?  If so, I could then wrap R in
> whatever language of choice I'd like, and only have to make a user
> install a library.
>
> Are there other options I'm missing?
>
> Thanks for help/input on this.
>
> -Jim Nemesh
>        [[alternative HTML version deleted]]
>
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