[Bioc-devel] BiocStyle and R markdown

[Kasper Daniel Hansen]

What exactly do you mean by numbering.  As far as I understand, numbering
is already there in devel:

https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html

Kasper

On Wed, Jul 29, 2015 at 10:39 PM, Thomas Girke <thomas.girke at ucr.edu> wrote:

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

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