[R] Calling library functions from outside R

[Jim Nemesh]

I did look at ?Rscript.  My question there was:
>> 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?

I could write an Rscript client file, but it's still poor CLI support  
compared to other languages, and I still have to distribute an Rscript  
client.  I'd like to just load a library and make 1 call to it on the  
command line.  Is there any way to do that with the -e param?

-Jim

On Jun 18, 2009, at 1:39 PM, Gabor Grothendieck wrote:

> 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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