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

Gabor

I agree with you. There's Travis CI, and r-travis -- an attempt to integrate
R package testing with Travis. Pushing back to GitHub is possible, but the
setup is somewhat difficult. Also, this can be subject to race conditions
because each push triggers a test run and they can happen in parallel even
for the same repository.

How do you handle branches?

It would be really great to be able to execute custom R code before
building. Perhaps in a PreBuild: section in DESCRIPTION?

Cheers

Kirill




On 12/12/2013 02:21 AM, G?bor Cs?rdi wrote:

Hi,

this is maybe mostly a personal preference, but I prefer not to put
generated files in the vc repository. Changes in the generated files,
especially if there is many of them, pollute the diffs and make them
less useful.

If you really want to be able to install the package directly from
github, one solution is to
1. create another repository, that contains the complete generated
package, so that install_github() can install it.
2. set up a CI service, that can download the package from github,
build the package or the generated files (check the package, while it
is at it), and then push the build stuff back to github.
3. set up a hook on github, that invokes the CI after each commit.

I have used this setup in various projects with jenkins-ci and it
works well. Diffs are clean, the package is checked and built
frequently, and people can download it without having to install the
tools that generate the generated files.

The only downside is that you need to install a CI, so you need a
"server" for that. Maybe you can do this with travis-ci, maybe not, I
am not familiar with it that much.

Best,
Gabor

On Wed, Dec 11, 2013 at 7:39 PM, Kirill M?ller
<kirill.mueller at ivt.baug.ethz.ch> 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.


Cheers

Kirill

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