[Bioc-devel] RMarkdown for vignettes

From: "Henrik Bengtsson" <hb at biostat.ucsf.edu>
To: jmacdon at u.washington.edu
Cc: bioc-devel at r-project.org
Sent: Friday, October 3, 2014 6:56:59 AM
Subject: Re: [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]:

http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html

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

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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