[Bioc-devel] BiocStyle and R markdown

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Jul 30 15:28:02 CEST 2015

Well, without really knowing details it could just be that more work has
been done on BiocStyle in devel.

One could backport the change to release, but that would mean that all
packages (which use BiocStyle) need to be version bumped and re-build,
purely for cosmetic issues in the vignette.  While I care about aesthetics,
it is not worth doing a massive update to our stable release branch for

So lets try to hammer BiocStyle before the next release so we can iron out
any issues.

Biocore: could we get a Github version of BiocStyle so we could start
issues etc.  Easy way to keep a todo.


On Thu, Jul 30, 2015 at 12:13 AM, Thomas Girke <thomas.girke at ucr.edu> wrote:

> 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
>>>>>  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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