[Bioc-devel] org-mode vignettes

Yihui Xie xie at yihui.name
Sat Aug 31 04:28:26 CEST 2013

IMHO, Sweave handlers (drivers) were a bad design in the sense that
extensions based on Sweave have to copy a large amount of source code
from the utils package. You can compare
https://github.com/eusebe/ascii/blob/master/R/RweaveAscii.r to
That is probably why most Sweave extensions (ascii, cacheSweave,
pgfSweave, ...) have been struggling to survive but eventually could
not catch up with the constant changes in Sweave.

The real value of the ascii package in my eyes lies in its wide
support to the conversion of R objects to different markup languages.
To use that in knitr, all you need is the chunk option results='asis'.
No custom drivers required. In the future you may not even need
results='asis' (that is on the knitr agenda).

Yihui Xie <xieyihui at gmail.com>
Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

On Fri, Aug 30, 2013 at 4:47 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Wed, Aug 28, 2013 at 5:50 AM, Wolfgang Huber <whuber at embl.de> wrote:
>> 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.
> I have used the ascii package available on CRAN and described here:
> http://eusebe.github.io/ascii/
> for org files before.  While not providing org-babel integration, it
> allows a subset of the org (or asciidoc, textile, restructuredText,
> ...) markup to be used instead of latex by supplying sweave handlers
> for those markups.
> Sean

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