[Bioc-devel] RMarkdown for vignettes

[Dan Tenenbaum]

----- Original Message -----
> 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.


Pandoc is installed on the build servers. Several packages use it.

> 
> 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?
> 

Users only need LaTeX (or pandoc) if they are going to build package vignettes from svn. Source packages (as well as binary packages of course) already contain built vignettes.

Dan


> 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
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> 
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