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

[Kasper Daniel Hansen]

see Henrik's answer.  Just adding that I would also like to see support for
multiple formats, particularly HTML and PDF from a single source.

Best,
Kasper

On Wed, Aug 17, 2016 at 1:02 PM, Henrik Bengtsson <
henrik.bengtsson at gmail.com> wrote:

> 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
>
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