[Bioc-devel] RMarkdown for vignettes

[Andrzej Oleś]

Hi Gordon, James,

thank you for pointing this out! At the time BiocStyle for markdown
documents was developed 'rmarkdown' was not yet on CRAN and couldn't
be used as a vignette builder engine.
As things changed in the meantime, the approach described by Gordon
should be just fine. I will update the BiocStyle vignette accordingly.

Best,
Andrzej

On Fri, Oct 3, 2014 at 4:51 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>
> ----- 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
>> >
>>
>>       [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel