[Bioc-devel] BiocStyle and R markdown
thomas.girke at ucr.edu
Thu Jul 30 04:39:07 CEST 2015
Perfect, if your update in Bioc-devel eliminates the awkward bullets in
front of the numbers. The lack of numbered content tables in Bioc-release
may be something we have to live with until the next Bioc release? I don't
want to overstretch Dan's or the Bioc team's patience with overly picky
On Wed, Jul 29, 2015 at 6:49 PM Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:
> When I roll that styles.css into the bioconductor.css file shipping with
> BiocStyle, it gets rid of the bullets.
> Its added to BiocStyle 1.7.5
> On Wed, Jul 29, 2015 at 9:37 PM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>> This is just reporting what I see using Bioc-devel:
>> I get a TOC where each line looks like
>> <BULLET> <SECTION_NUMBER_AS_LINK> <SECTION_TITLE_AS_LINK>
>> 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>
> 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
>>> 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
>>> 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:
>>> 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.
>> Bioc-devel at r-project.org mailing list
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