[Bioc-devel] org-mode vignettes

Charles Berry ccberry at ucsd.edu
Wed Aug 28 17:34:43 CEST 2013

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.)


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


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 

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


The part that gets turned into Sweave starts at the line 

'* Sweave Example 1'.



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