[Bioc-devel] Package reference manuals in html

Hartley, Stephen (NIH/NHGRI) [F] stephen.hartley at nih.gov
Wed Mar 2 17:46:29 CET 2016

I'd like to second this. Currently Bioconductor hosts the pdf reference manuals, but those are often sub-ideal. The page breaks make it harder to read, the fixed width basically makes it either too small or too big depending on your display, you can't navigate cross-package links, and in general using paper-formatted software documentation is just poor form.

Yihui, the creator of knitr, has a blog post where he shows how to do this. There are a lot of ways to do this, and it's generally pretty straightforward.

You can also use a function in knitr, knit_rd(), which builds the examples as well and inserts the output right onto the page. That's what I used to make the docs for QoRTs (http://hartleys.github.io/QoRTs/Rhtml/index.html) and JunctionSeq (http://hartleys.github.io/JunctionSeq/Rhtml/index.html). 

Or you can use the staticdocs package, which does the same basic thing but prettier (see ggplot2's docs: http://docs.ggplot2.org/current/)

The nuclear option, of course, is to do what CRAN does and rebuild R on (one of) the servers using the --enable-prebuilt-html configure option. That might affect other things, though, and might not be ideal.

Does any of this seem like a viable option for Bioconductor? I think it could be an incredibly valuable resource for the community. Are there any technical issues that haven't been considered in the above?

Steve Hartley

-----Original Message-----
From: Laurent Gatto [mailto:lg390 at cam.ac.uk] 
Sent: Tuesday, March 01, 2016 6:42 AM
To: bioc-devel
Subject: [Bioc-devel] Package reference manuals in html

Dear all,

I find the http://www.rdocumentation.org/ site very useful to refer to nicely formatted online man pages individually. Unfortunately, this resource is terribly outdated and not maintained anymore.

I was wondering if Bioconductor had any interest in serving an html version of individual reference manuals in addition to the pdf that are already available on the package landing pages.

Is there anything I or any other members of the community could help with to get this up and running?

Best wishes,


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