[Bioc-devel] Running Perl Scripts from R package

Hervé Pagès hpages at fhcrc.org
Wed Oct 23 21:23:08 CEST 2013


On 10/23/2013 11:55 AM, Gabriel Becker wrote:
> 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>")

This is not portable. Better use:

   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 at 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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Hervé Pagès

Program in Computational Biology
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