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 < kasperdanielhan...@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.gi...@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 < >> kasperdanielhan...@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 < >>> kasperdanielhan...@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.gi...@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@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
