On Wed, Aug 28, 2013 at 5:28 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 08/28/2013 02:50 AM, Wolfgang Huber wrote:
>
>>
>> Hi
>>
>> is there already a best practice (example?) for how to deliver vignettes
>> written in org-mode (http://orgmode.org) in Bioconductor packages?
>>
>
> Three possibilities come to mind.
>
> Implement the equivalent of the knitr package, preferably without external
> dependencies (sounds like a fun exercise ;)) and simply add the package to
> the VignetteBuilder: tag to the DESCRIPTION file (as in Writing R
> Extensions).
>
>
If one was actually ambitious enough to go this far, why not extend knitr
directly? It's designed to handle multiple input formats, and presumably
would offer some things for free. Apparently there is an org-mode parser
for pretty much every language except R, so there's an opportunity here ;)
Running emacs in batch mode would be the easiest path, especially given
ravel, but then there's dependencies.



> Do the two-step of transforming org-mode to an intermediate form, e.g.,
> markdown, then using standard tools. The transformation would be the
> maintainer's responsibility, prior to svn commit. This is essentially how
> roxygen2 is being used for man pages.
>
> (Even as an emacs user I find it weird to tie documentation to an
> application.)
>
> Martin
>
>
>
>> (This would also require that emacs and its ESS and org modes are
>> installed
>> on the build servers.)
>>
>> Best wishes Wolfgang ______________________________**_________________
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>>
>>
>
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