On Wed, Aug 28, 2013 at 8:25 AM, Martin Morgan <mtmor...@fhcrc.org> wrote: > 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!". >
See also http://yihui.name/knitr/demo/org/ Dan > Martin > > > >> Best wishes, Wolfgang >> >> On 28 Aug 2013, at 14:28, Martin Morgan <mtmor...@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 _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>> >>> >>> -- >>> 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 >> >> > > > -- > 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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
