[Bioc-devel] org-mode vignettes

[Dan Tenenbaum]

On Wed, Aug 28, 2013 at 8:25 AM, Martin Morgan <mtmorgan at 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 <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 _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
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>>> Computational Biology / Fred Hutchinson Cancer Research Center
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>>>
>>> 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
>
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