Hi, this is just to clarify the relation between the two github repos https://github.com/Bioconductor-mirror/BiocStyle and https://github.com/Bioconductor/BiocStyle mentioned by Martin: actually, these two are perfectly in sync right now. The "This branch is 3 commits ahead, 3 commits behind Bioconductor-mirror:master." message is just an inevitable(?) artifact of using the bioc git mirrors approach ( https://www.bioconductor.org/developers/how-to/git-mirrors/). Bioconductor-mirror/BiocStyle is a read-only mirror automatically synchronized with the bioc svn, whereas its fork Bioconductor/BiocStyle is the proper place to which pull requests and issues should be submitted, and where any development should happen.
Cheers, Andrzej On Fri, Mar 4, 2016 at 2:20 PM, Morgan, Martin < martin.mor...@roswellpark.org> wrote: > One thing about accessing the html versions locally (e.g., via ? with > options(help_type="html")] or help.start() or Rstudio) is that you get the > version relevant to your R / Bioconductor, rather than whatever is at the > top of google; I guess the same applies to the pdf versions, and the reason > that there isn't more current confusion is because the online pdf versions > are not as useful as the off-line help system. > > I think Laurent was interested in an integration of help pages across > packages (which is the appeal of rdocumentation.org?), not just rendering > the help pages in html rather than pdf? An integration of help pages would > definitely be a big job with substantial development and maintenance; we > will not be undertaking this ourselves. > > For the more limited case of adding a (directory of) html files for the > the manual, it's not impossible that we could find the resources to do this > in the next 6 months. > > One intermediate and helpful step for those willing to help would be to > develop the code to process help pages into a style consistent with the > bioconductor web site. One place where this could be implemented would be > the BiocStyle package (https://github.com/Bioconductor-mirror/BiocStyle > but hmm, seems like there's a slightly out of sync version at > https://github.com/Bioconductor/BiocStyle that would be more > convenient...). Perhaps this really means only developing a css style sheet > and R's tools::Rd2HTML() (I'm very reluctant to introduce dependencies into > the build system, and am very conservative about inclusion of fancy > features in the html -- these become significant maintenance burdens moving > forward). > > The web site is generated by > https://github.com/Bioconductor/bioconductor.org, with the style sheet at > https://github.com/Bioconductor/bioconductor.org/blob/master/assets/style/bioconductor.css. > The package landing pages are templated using > layouts/_bioc_views_package_detail.html. The idea would be to end up with > layouts/_bioc_man_index.html and _bioc_man_body.html that wrapped output > from BiocStyle in the overall bioc page. > > The implementation suggestions above are just a sketch and could be quite > misguided. If there's interest then probably we should set up a hangout to > discuss in a little more detail. > > Martin > > ________________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Hartley, > Stephen (NIH/NHGRI) [F] <stephen.hart...@nih.gov> > Sent: Wednesday, March 2, 2016 11:46 AM > To: Laurent Gatto; bioc-devel > Subject: Re: [Bioc-devel] Package reference manuals in html > > 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. > http://yihui.name/en/2012/10/build-static-html-help/ > > 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? > > Regards, > Steve Hartley > > -----Original Message----- > From: Laurent Gatto [mailto:lg...@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, > > Laurent > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > _______________________________________________ > 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