[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

	[[alternative HTML version deleted]]

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


---------------------------------------------------------------------
*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]]

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

	[[alternative HTML version deleted]]

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


---------------------------------------------------------------------
*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)
---------------------------------------------------------------------


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