[Bioc-devel] RMarkdown for vignettes

Henrik Bengtsson hb at biostat.ucsf.edu
Fri Oct 3 15:56:59 CEST 2014


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/
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> --
> 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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>
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>

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