From simon.urbanek at r-project.org  Fri Dec 13 21:14:18 2013
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Fri, 13 Dec 2013 15:14:18 -0500
Subject: [Rd] Strategies for keeping autogenerated .Rd files out of a
	Git tree
In-Reply-To: <52AB10EF.9070503@ivt.baug.ethz.ch>
References: <52A905CB.4020701@ivt.baug.ethz.ch>
	<CABtg=KkgGqaQOYSfzAnXfdgfK0UojLEjsd=amzc=BThS4EV7+w@mail.gmail.com>
	<52AAE990.1050102@ivt.baug.ethz.ch>
	<175312B6-9672-4C71-AB2F-AFA05A06162C@r-enthusiasts.com>
	<52AB10EF.9070503@ivt.baug.ethz.ch>
Message-ID: <0C2772D3-C8CD-4437-B112-4DD0AD7D084C@r-project.org>

FWIW this is essentially what RForge.net provides. Each GitHub commit triggers a build (branches are supported as the branch info is passed in the WebHook) which can be either "classic" R CMD build or a custom shell script (hence you can do anything you want). The result is a tar ball (which includes the generated files) and that tar ball gets published in the R package repository. R CMD  check is run as well on the tar ball and the results are published.
This way you don't need devtools, users can simply use install.packages() without requiring any additional tools.

There are some talks about providing the above as a cloud service, so that anyone can run and/or use it.

Cheers,
Simon


On Dec 13, 2013, at 8:51 AM, Kirill M?ller <kirill.mueller at ivt.baug.ethz.ch> wrote:

> On 12/13/2013 12:50 PM, Romain Francois wrote:
>> Pushing back to github is not so difficult. See e.g 
>> http://blog.r-enthusiasts.com/2013/12/04/automated-blogging.html
> Thanks for the writeup, I'll try this. Perhaps it's better to push the 
> results of `R CMD build`, though.
>> You can manage branches easily in travis. You could for example decide 
>> to do something different if you are on the master branch ...
> That's right. But then no .Rd files are built when I'm on a branch, so I 
> can't easily preview the result.
> 
> The ideal situation would be:
> 
> 1. I manage only R source files on GitHub, not Rd files, NAMESPACE nor 
> the "Collate" section of DESCRIPTION. Machine-readable instructions on 
> how to build those are provided with the package.
> 2. Anyone can install from GitHub using devtools::install_github(). This 
> also should work for branches, forks and pull requests.
> 3. I can build the package so that the result can be accepted by CRAN.
> 
> The crucial point on that list is point 2, the others I can easily solve 
> myself.
> 
> The way I see it, point 2 can be tackled by extending devtools or 
> extending the ways packages are built. Extending devtools seems to be 
> the inferior approach, although, to be honest, I'd be fine with that as 
> well.
> 
> 
> -Kirill
> 
>> 
>> Romain
>> 
>> Le 13 d?c. 2013 ? 12:03, Kirill M?ller 
>> <kirill.mueller at ivt.baug.ethz.ch 
>> <mailto:kirill.mueller at ivt.baug.ethz.ch>> a ?crit :
>> 
>>> 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 
>>>> <mailto: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
>>>>> 
>>>>> ______________________________________________
>>>>> R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> 
>>> -- 
>>> _________________________________________________
>>> ETH Z?rich
>>> Institute for Transport Planning and Systems
>>> HIL F 32.2
>>> Wolfgang-Pauli-Str. 15
>>> 8093 Z?rich
>>> 
>>> Phone:       +41 44 633 33 17
>>> Fax:         +41 44 633 10 57
>>> Secretariat: +41 44 633 31 05
>>> E-Mail: kirill.mueller at ivt.baug.ethz.ch 
>>> <mailto:kirill.mueller at ivt.baug.ethz.ch>
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> -- 
> _________________________________________________
> ETH Z?rich
> Institute for Transport Planning and Systems
> HIL F 32.2
> Wolfgang-Pauli-Str. 15
> 8093 Z?rich
> 
> Phone:       +41 44 633 33 17
> Fax:         +41 44 633 10 57
> Secretariat: +41 44 633 31 05
> E-Mail:      kirill.mueller at ivt.baug.ethz.ch
> 
> 
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[Rd] Strategies for keeping autogenerated .Rd files out of a Git tree
Simon Urbanek