[R] What is the most efficient practice to develop an R package?

[Martin Morgan]

Dirk Eddelbuettel wrote:
> On 26 October 2009 at 13:29, Peng Yu wrote:
> | On Mon, Oct 26, 2009 at 11:22 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
> | >
> | > On 26 October 2009 at 07:57, Martin Morgan wrote:
> | > | Peng Yu wrote:
> | > | > I am reading Section 5 and 6 of
> | > | > http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
> | > | >
> | > | > It seems that I have to do the following two steps in order to make an
> | > | > R package. But when I am testing these package, these two steps will
> | > | > run many times, which may take a lot of time. So when I still develop
> | > | > the package, shall I always source('linmod.R') to test it. Once the
> | > | > code in linmod.R is finalized, then I run the following two steps?
> | > | >
> | > | > I'm wondering what people usually do when developing packages.
> | > | >
> | > | >
> | > | > 1. Run the following command in R to create the package
> | > | > package.skeleton(name="linmod", code_files="linmod.R")
> | > |
> | > | Do this once, to get a skeleton. Then edit the R source etc in the
> | > | created package.
> | > |
> | > | > 2. Run the following command in shell to install
> | > | > R CMD INSTALL -l /path/to/library linmod
> | > |
> | > | see R CMD INSTALL --help and use options that minimize the amount of
> | > | non-essential work, e.g., no vignettes or documentation until that is
> | > | the focus of your development, or --libs-only if you are working on C
> | > | code. Use --clean to avoid stale package components. Develop individual
> | > | functions interactively, but write a script
> | > |
> | > |   library(MyPackage)
> | > |   someFunction()
> | > |
> | > | so that R -f myscript.R allows you to easily load your package and test
> | > | specific functionality in a clean R session.
> | >
> | > With littler you can do without the one-off script as
> | >
> | >     $ r -lMyPackage -e'print(someFunction())'
> | >
> | > runs both commands you would have put into script.  Hence, I often do
> | > something like
> | >
> | >     $ R CMD INSTALL MyPackage/ && r -lMyPackage -e'print(someFunction())'
> | 
> | What does the small case 'r' do?
> 
> It is a scripting front-end to R and useful for e.g. writing scripts with a
> so-called shebang line (i.e #!/usr/bin/r in the first line), or for quickly
> evaluating command-line expression as I showed you here, or running R scripts
> instead of calling R followed by source() --- see the web page at
> 
> 	http://dirk.eddelbuettel.com/code/littler.html 
> 
> for more.
> 
> Litter (aka 'r') is similar to Rscript which came a few months later, starts
> a little slower but runs on more platforms.

and for the record

  R -e "library(MyPackage); someFunction()"

though probably a better practice is to add --vanilla (or --quiet or
--slave) too.

Martin

> 
> Dirk
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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