[Bioc-devel] BiocStyle and R markdown

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Jul 30 03:37:55 CEST 2015

This is just reporting what I see using Bioc-devel:

I get a TOC where each line looks like


While I agree that the bullet is kind of ugly (and would be great to get
rid of), I do get the section numbering functionality you want.

Note: for this report I am rendering the Rmd file myself, I haven't tested
how it looks when I do it as a vignette.

It would be great to expand on the BiocStyle vignette and discuss citations
and other issues and also include a clear template file.  I am planning on
doing some pull request along those lines soon; I have been testing Rmd ->
HTML extensively for a course I am developing, but I am also new to the
knitr+markdown thing so I am still experimenting.


On Wed, Jul 29, 2015 at 4:44 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:

> A simple formatting issue:
> Since support for table of contents in R markdown vignettes has become
> available, it seems like an amazing solution for many online
> documentation needs in the future.
> What would help me to fully to adopt to it, is a solution to get rid of
> the bullets in a numbered table of content which looks a bit unusual to
> me:
> http://www.bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
> For navigating longer documents numbered tables of contents are an
> essential feature to me, which I believe wasn't available in earlier R
> markdown versions or sometimes they showed up in unacceptable places
> like before the title of a document.
> A prescribed solution to get rid of these bullets from here
> http://stackoverflow.com/questions/28138456/rmarkdown-with-knitr-to-html-how-to-hide-bullets-in-toc-table-of-contents
> didn't work for me.
> Also, it would be nice to be able to generate the exact same vignette
> style in Bioc release and development, but it seems others have
> difficulties with this too, probably due to version differences of R
> markdown as seen here:
> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
> Thanks for making BiocStyle and R markdown available. I really enjoy
> using them. The resulting HTML pages look professionally designed and
> are highly functional while allowing us to focus on generating content
> in a consistent format rather than getting lost in formatting issues.
> Thomas
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> Bioc-devel at r-project.org mailing list
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