[Bioc-devel] Bioc workflows: using rmarkdown as vignette engine

[Michael Love]

hi Dan,

(I add bioc-devel as this might be useful info for others)

Is it possible to specify rmarkdown as the vignette engine for workflows?

The citation functionality [1] of rmarkdown would be useful, as there
is discussion to have workflows possible submitted as peer reviewed
papers.

I tried adding:

<!--
%\VignetteEngine{knitr::rmarkdown}
-->

as recommended here [2] but the auto package builder adds this on top:

<!--
 %\VignetteEngine{knitr::knitr}
-->

and my test of using a citation fails [3] (although locally running
rmarkdown::render(), the citation and bibliography works). My test
citation look like: [@love2014]

best,

Mike

[1] http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html
[2] http://www.bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
[3] http://bioconductor.org/help/workflows/rnaseqGene/