[Bioc-devel] Is it OK for Rmd package vignettes to be rendered as PDF?

[Henrik Bengtsson]

R CMD build, which is what triggers vignette  building, only supports one
output file (HTML or PDF) per vignette. It will basically ignore duplicate
output formats. This is by design / legacy reasons. Technically it wouldn't
be hard to add support for multiple output formats, but that would require
changes to R itself - I think it could be a useful feature.

A related question is where some prefer to have access to also the
intermediate plain Markdown / TeX rather than the final HTML / PDF product,
e.g. because they work better with screen readers.

The only way I see you can have a PDF and a HTML version at the same time
is to create to identical vignettes each outputting a specific format.

Henrik

On Aug 17, 2016 12:17, "Ramon Diaz-Uriarte" <rdiaz02 at gmail.com> wrote:

>
> Dear All,
>
> I am considering rewriting the vignette of one BioC package I maintain as
> Rmd (it is currently Rnw). But I would like that the entry under
> "Documentation" contain a PDF of the vignette; it can ideally also contain
> the HTML version too, but I do not want it to not have the PDF[1].
>
>
> I know I can add entries to the document header such as
>
> output:
>   BiocStyle::pdf_document:
>     toc: true
>   BiocStyle::html_document:
>     toc: true
>
>
> that will, when run locally via "render('file.Rmd', output_format =
> 'all')", produce both formats.
>
>
>
> I've googled around, but I am not sure about:
>
> 1. If I have both output formats specified in the document header, will the
> BioC page of the package actually show both the PDF and the HTML of the
> vignette?
>
>
> 2. Is it OK (in conforming with BioC policies, sensible[1], whatever) to
> even try/want this? My reading of the doc for the BiocStyle
> (https://www.bioconductor.org/packages/devel/bioc/vignettes/
> BiocStyle/inst/doc/HtmlStyle.html)
> seems to suggest that the "natural" thing for Rmd vignettes is to be
> rendered as HTML, but I have not seen that producing PDF is discouraged
> explicitly.
>
>
> Best,
>
>
> R.
>
>
> [1] Why do I want to get a PDF if I am using Rmd? I want a PDF because this
> is a fairly long document that some users want to be able to print. I want
> HTML because some users prefer HTML and because I'd like to also place the
> vignette as HTML in Github Pages. I think that the only way to accomplish
> both is to use Rmd (not Rnw, even if I really, really, prefer LaTeX :-).
>
>
>
>
>
>
>
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
>
> Phone: +34-91-497-2412
>
> Email: rdiaz02 at gmail.com
>        ramon.diaz at iib.uam.es
>
> http://ligarto.org/rdiaz
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]