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/
[Bioc-devel] Bioc workflows: using rmarkdown as vignette engine
2 messages · Michael Love, 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/