John Pellman
2013-May-24 17:27 UTC
[R] Creating an R function wrapper for a bash shell script
Hi! I'm trying to set up an R library for a common analysis that my lab does. This analysis involves the use of an external bash script, which I would like to encapsulate within the R library. I have been looking at tutorials that detail how to create packages, and many of them mention an experimental "exec" directory where one can store Perl, Java, bash scripts, etc. I was wondering how one might tell an R function to execute a shell script in this directory (I've been thinking along the lines of using system() to execute the script, but I am uncertain what the path to 'exec' would be; my best guess is that the path to 'exec' might be found using the .libPaths() command). Many thanks, John Pellman [[alternative HTML version deleted]]
Greg Snow
2013-May-24 18:05 UTC
[R] Creating an R function wrapper for a bash shell script
Look at the 'system.file' function. On Fri, May 24, 2013 at 11:27 AM, John Pellman < john.samoylovich.pellman@gmail.com> wrote:> Hi! > > I'm trying to set up an R library for a common analysis that my lab does. > This analysis involves the use of an external bash script, which I would > like to encapsulate within the R library. I have been looking at tutorials > that detail how to create packages, and many of them mention an > experimental "exec" directory where one can store Perl, Java, bash scripts, > etc. I was wondering how one might tell an R function to execute a shell > script in this directory (I've been thinking along the lines of using > system() to execute the script, but I am uncertain what the path to 'exec' > would be; my best guess is that the path to 'exec' might be found using the > .libPaths() command). > > Many thanks, > John Pellman > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Gregory (Greg) L. Snow Ph.D. 538280@gmail.com [[alternative HTML version deleted]]