[Bioc-devel] Running Perl Scripts from R package

[Dan Tenenbaum]

----- 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
> >
> >
> > ---------------------------------------------------------------------
> > *SECURITY/CONFIDENTIALITY WARNING:
> > This message and any attachments are intended solely for the
> > individual or
> > entity to which they are addressed. This communication may contain
> > information that is privileged, confidential, or exempt from
> > disclosure
> > under applicable law (e.g., personal health information, research
> > data,
> > financial information). Because this e-mail has been sent without
> > encryption, individuals other than the intended recipient may be
> > able to
> > view the information, forward it to others or tamper with the
> > information
> > without the knowledge or consent of the sender. If you are not the
> > intended
> > recipient, or the employee or person responsible for delivering the
> > message
> > to the intended recipient, any dissemination, distribution or
> > copying of
> > the communication is strictly prohibited. If you received the
> > communication
> > in error, please notify the sender immediately by replying to this
> > message
> > and deleting the message and any accompanying files from your
> > system. If,
> > due to the security risks, you do not wi!
> >  sh to receive further communications via e-mail, please reply to
> >  this
> > message and inform the sender that you do not wish to receive
> > further
> > e-mail from the sender. (fpc5p)
> > ---------------------------------------------------------------------
> >
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> 
> 
> 
> --
> Gabriel Becker
> Graduate Student
> Statistics Department
> University of California, Davis
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>