R help - Oct 2009 - What is the most efficient practice to develop an R package?

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")

2. Run the following command in shell to install
R CMD INSTALL -l /path/to/library linmod

On 10/26/2009 10:29 AM, 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")
> 
> 2. Run the following command in shell to install
> R CMD INSTALL -l /path/to/library linmod
You only do step 1 once, and you missed step 1.5:  edit the files, which 
comes before step 2.

I usually cycle between steps 1.5 and 2 multiple times.  Sometimes I 
will not repeat step 2, I'll put together a small script that includes

source('linmod.R')
environment(somefunction) <- environment(linmod::somefunction)

and source that instead.  The second line makes somefunction look for 
functions in the namespace of the package; it's only useful if my edits 
only affect one function, and the functions in the package never call 
it:  so usually I do the full install.

Duncan Murdoch

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.

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