[Bioc-devel] RMarkdown for vignettes

Gordon Ball gordon.ball at ki.se
Fri Oct 3 15:06:07 CEST 2014


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


    Suggests: knitr, rmarkdown, BiocStyle
    VignetteBuilder: knitr


    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)

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).


Gordon Ball
Computational Medicine Group
Karolinska Institute


[rmarkdown]: http://cran.r-project.org/web/packages/rmarkdown/

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