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

[Dan Tenenbaum]

----- Original Message -----
> From: "Michael Love" <michaelisaiahlove at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>, bioc-devel at r-project.org
> Sent: Friday, August 14, 2015 10:29:18 AM
> Subject: Bioc workflows: using rmarkdown as vignette engine
> 
> 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?

At this point it is not possible.
I'll see what I can do, but may not be able to get to it in the short term.

Dan


> 
> 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/
>