[Bioc-devel] RMarkdown for vignettes
I think it requires Bioc core to make a statement that pandoc will be added to the list of external software that can be assume to exist on the servers. If it is also expected that users should be able to rebuild all vignettes/documents themselves, then that assumption has to be extended to the users as well. BTW, is there such an assumption on LaTeX-dependent packages today? Installing pandoc is not that hard and lightweight (much smaller than LaTeX), but it does add one more installation. On the other hand, it opens up for doing lots of other neat things. Henrik
On Oct 3, 2014 6:40 AM, "James W. MacDonald" <jmacdon at uw.edu> wrote:
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]:
[rmarkdown]: http://cran.r-project.org/web/packages/rmarkdown/
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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099
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