[Bioc-devel] BiocStyle and R markdown
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
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