[Bioc-devel] RMarkdown for vignettes

James W. MacDonald jmacdon at uw.edu
Fri Oct 3 15:39:32 CEST 2014


Hi Gordon,

Sean Davis has something about this on his blog:

http://watson.nci.nih.gov/~sdavis/blog/convert_from_sweave_to_r_markdown_vignettes/

Best,

Jim



On Fri, Oct 3, 2014 at 9:06 AM, Gordon Ball <gordon.ball at ki.se> wrote:

> Hello
>
> Is it possible to use (RStudio's) rmarkdown package as a vignette
> builder for the upcoming release?
>
> ie, with the (at least locally working) configuration
>
> DESCRIPTION
>
>     Suggests: knitr, rmarkdown, BiocStyle
>     VignetteBuilder: knitr
>
> vignette/vignette.Rmd
>
>     ---
>     title: ...
>     output: BiocStyle::html_document
>     vignette: >
>         %% \VignetteEngine{knitr::rmarkdown}
>         %% \VignetteIndexEntry{...}
>     ----
>
> I couldn't find any explicit reference to markdown vs rmarkdown in the
> package guidelines. The documentation for [BiocStyle] indicates that it
> isn't possible to build package vignettes with the newer rmarkdown - is
> that still correct?
>
> I note that the newer [rmarkdown] is now in CRAN, so presumably can be
> used by the builders - but do they have the non-R dependency (pandoc)
> available?
>
> The rationale for wanting rmarkdown instead markdown is support for a
> few extended features, particularly being able to cite from a bibtex
> file (which as far as I know isn't possible with the older markdown).
>
> Thanks
>
> Gordon Ball
> Computational Medicine Group
> Karolinska Institute
>
>
>
> [BiocStyle]:
>
> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
>
> [rmarkdown]: http://cran.r-project.org/web/packages/rmarkdown/
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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