[Bioc-devel] org-mode vignettes

On 08/28/2013 07:38 AM, Wolfgang Huber wrote:

Hi Martin,
thanks! Both of these sound doable, we'll explore. What was the third one?

To clarify, the intermediate form in option 2 should ideally still contain
executable code chunks -- Rmd or Rnw, rather than md or tex. One drawback of
this option (and of using roxygen2)  is that others (e.g., Bioc maintainers
trying to help out with routine maintenance, or the hit-by-a-bus replacement
maintainer) trip over the intended work flow, e.g., updating the
intermediate file rather than the org file, or spend time learning org mode
(and emacs!).

The parenthetical comment came from passing some festive commentary through
a civility filter -- option three is "don't do it!".

Martin

        Best wishes, Wolfgang

On 28 Aug 2013, at 14:28, Martin Morgan <mtmorgan at 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).

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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--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793