Charles,

If you put your scripts (or any file) in inst/folder within your package
structure you can always get the path to them by doing
system.file("folder/<filename>", package="<packagename>") regardless of
install location for the package. In other words, system.file can see all
folders in your inst directory, not just specific ones like extdata.

For your other question I don't know of any other ways to call perl from R
besides system calls, but I haven't needed that functionality so that
doesn't mean there aren't any (a quick google didn't turn up anything
though).

HTH,
~G


On Wed, Oct 23, 2013 at 10:58 AM, Warden, Charles <cwarden@coh.org> wrote:

> Hi,
>
> I would like to develop a Bioconductor package that calls Perl scripts for
> certain functions.  I currently have a standalone program written in Perl
> that calls Rscript at certain steps, so I would like to switch this around.
>
> It looks like I can call Perl scripts using the 'system' command, but I am
> wondering if there is a better way to call the Perl scripts as part of an R
> package.  For example, I know data files should be stored in "data", demo
> files should be called using system.file (for files located in
> "inst/extdata").  Is there a folder where I should save external scripts
> and a systematic way to call those scripts, so that I don't need to know
> the full installation path?  I'm assuming that I shouldn't be saving Perl
> scripts in the 'R' folder.
>
> Thanks,
> Charles
>
>
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-- 
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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