[Bioc-devel] org-mode vignettes

Yihui Xie xie at yihui.name
Fri Aug 30 05:18:44 CEST 2013

My impression is that org-mode was designed for very general purposes,
and it might be too general for R package vignettes, so is Dexy. For
vignettes, we use only one language (R) and one document format
(historically LaTeX, and nowadays also Markdown/HTML) in most cases.
Multiple input/output formats sounds fantastic, but in practice it is
not necessarily a big plus (as Michael mentioned, knitr also supports
that and is extensible; you may even play with the new cool kid Julia
http://rpubs.com/yihui/julia-knitr but I'm not sure how many people
will really do that). This is off-topic somehow...

Personally I think the better approach is to translate *.org to
*.Rnw/*.Rmd, etc, and hand it over to Sweave or knitr, which has been
well-supported by R 3.0. You only need to specify the VignetteBuilder
in DESCRIPTION and \VignetteEngine{} in vignettes. R will build
vignettes using your vignette engine.

If we stick to .org, that will require server support to install
additional software packages, or you just play with it locally. Given
Emacs + org-mode are available on the build server, you can write
custom vignette engines to process .org files; since the custom
engines are essentially R functions, you can do whatever you want; see
the R-exts manual.

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

> From: "Wolfgang Huber" <whuber at embl.de>
> Date: Aug 28, 2013 2:51 AM
> Subject: [Bioc-devel] org-mode vignettes
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Cc: "Paul Theodor Pyl" <pyl at embl.de>
> 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.)
>         Best wishes
>         Wolfgang

More information about the Bioc-devel mailing list