[Bioc-devel] Running Perl Scripts from R package

[Warden, Charles]

Ok - thank you all for your feedback!

Best,
Charles

-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: Wednesday, October 23, 2013 12:02 PM
To: Gabriel Becker
Cc: bioc-devel at r-project.org; Warden, Charles
Subject: Re: [Bioc-devel] Running Perl Scripts from R package



----- Original Message -----
> From: "Gabriel Becker" <gmbecker at ucdavis.edu>
> To: "Charles Warden" <cwarden at coh.org>
> Cc: bioc-devel at r-project.org
> Sent: Wednesday, October 23, 2013 11:55:05 AM
> Subject: Re: [Bioc-devel] Running Perl Scripts from R package
> 
> 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).
> 

There is system2() which is a bit more flexible, depending on what you need.
Dan


> 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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> 
> 
> --
> Gabriel Becker
> Graduate Student
> Statistics Department
> University of California, Davis
> 
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