[Bioc-devel] Running Perl Scripts from R package

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).

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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