[Bioc-devel] org-mode vignettes

[Charles Berry]

Wolfgang Huber <whuber <at> embl.de> writes:

> 
> 
> Hi
> 
> is there already a best practice (example?) for how to deliver vignettes
written in org-mode
> (http://orgmode.org) in Bioconductor packages?
> 
> (This would also require that emacs and its ESS and org modes are
installed on the build servers.)


Wolfgang, 

ravel will translate org-mode to Sweave, knitr, or similar formats. See

https://github.com/chasberry/orgmode-accessories

As currently implemented, it usually requires that the chunk options 
be manually added to the org-mode source blocks in a header line.

That is, the org-mode header arguments are not translated to Sweave/knitr
chunk options. This can be automated, but I've not had a reason to do so 
yet.

You can see the 'example-1.Rnw' from the Sweave manual rendered as org-mode
that ravel can translate back to Sweave at:

https://raw.github.com/chasberry/orgmode-accessories/master/example-1-Rnw.org

The part that gets turned into Sweave starts at the line 

'* Sweave Example 1'.

HTH,

Chuck
==