[Bioc-devel] BiocStyle and R markdown

[Thomas Girke]

Yes, they show under Bioc-devel, but not under Bioc-release. Building the
exact same *Rmd source from here
https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
under Bioc-release looks quite different:
http://biocluster.ucr.edu/~tgirke/HtmlStyle.html

Thomas

On Wed, Jul 29, 2015 at 7:58 PM Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

>  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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