[Rd] Strategies for keeping autogenerated .Rd files out of a Git tree

Brian Diggs brian.s.diggs at gmail.com
Fri Dec 13 18:09:53 CET 2013

On 12/11/2013 4:39 PM, Kirill Müller wrote:
> Hi
> Quite a few R packages are now available on GitHub long before they
> appear on CRAN, installation is simple thanks to
> devtools::install_github(). However, it seems to be common practice to
> keep the .Rd files (and NAMESPACE and the Collate section in the
> DESCRIPTION) in the Git tree, and to manually update it, even if they
> are autogenerated from the R code by roxygen2. This requires extra work
> for each update of the documentation and also binds package development
> to a specific version of roxygen2 (because otherwise lots of bogus
> changes can be added by roxygenizing with a different version).
> What options are there to generate the .Rd files during build/install?
> In https://github.com/hadley/devtools/issues/43 the issue has been
> discussed, perhaps it can be summarized as follows:
> - The devtools package is not the right place to implement
> roxygenize-before-build
> - A continuous integration service would be better for that, but
> currently there's nothing that would be easy to use
> - Roxygenizing via src/Makefile could work but requires further
> investigation and an installation of Rtools/xcode on Windows/OS X
> Especially the last point looks interesting to me, but since this is not
> widely used there must be pitfalls I'm not aware of. The general idea
> would be:
> - Place code that builds/updates the .Rd and NAMESPACE files into
> src/Makefile
> - Users installing the package from source will require infrastructure
> (Rtools/make)
> - For binary packages, the .Rd files are already generated and added to
> the .tar.gz during R CMD build before they are submitted to
> CRAN/WinBuilder, and they are also generated (in theory) by R CMD build
> --binary
> I'd like to hear your opinion on that. I have also found a thread on
> package development workflow
> (https://stat.ethz.ch/pipermail/r-devel/2011-September/061955.html) but
> there was nothing on un-versioning .Rd files.

One downside I can see with this third approach is that by making the 
package documentation generation part of the build process, you must 
then make the package depend/require roxygen (or whatever tools you are 
using to generate documentation). This dependence, though, is just to 
build the package, not to actually use the package. And by pushing this 
dependency onto the end users of the package, you have transferred the 
problem you mentioned ("... and also binds package development to a 
specific version of roxygen2 ...") to the many end users rather than the 
few developers.

> Cheers
> Kirill

Brian S. Diggs, PhD
Senior Research Associate, Department of Surgery
Oregon Health & Science University

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