Yes, this seems like a time where using a non-standard site directory on Github is useful, or as Sean said, using a separate branch to serve the html content.
-Robert On Fri, Dec 23, 2016 at 12:19 PM Sean Davis <seand...@gmail.com> wrote: > Github allows you to set the branch for the docs directory if I recall. > Perhaps a separate branch with a docs directory (not master) is a viable > way to go? > > Sean > > > On Dec 23, 2016, at 12:16 PM, Laurent Gatto <lg...@cam.ac.uk> wrote: > > > > > > There's actually another side-effect for Bioconductor. The package > > website is (by default) generated in the package's ./docs > > directory. This is very handy, as it can be set directly on Github as a > > Github page and becomes available as https://username.github.io/pkgname. > > > > This also means that the docs directory (which is about 5.5M for > > MSnbase) ends up on hedgehog. It is easy for it not to be part of the > > package build artefact using .Rbuildignore, but I am not sure how to > > easily push it to github but not hedgehog when using git-svn. > > > > Laurent > > > > On 23 December 2016 16:36, Laurent Gatto wrote: > > > >> Dear all, > >> > >> I'm following up re my online references suggestion with my recent > >> experience with Hadley's pkgdown package > >> > >> https://github.com/hadley/pkgdown > >> > >> It doesn't address the cross-package issue (which is a difficult one > >> anyway), but does pretty much everything else (with some caveats though, > >> see below). > >> > >> Here are 2 examples > >> > >> - MSnbase: http://lgatto.github.io/MSnbase/ > >> - hpar: http://lgatto.github.io/hpar/ > >> > >> It uses the REAMDE file as index page, creates html documents for all Rd > >> files in man, an article tab for vignettes (but see below) and a News > >> tab (but see below) > >> > >> The biggest caveats is that only Rmd vignettes are taken into account; > >> Rnw are completely ignored (they don't show up at all in the Articles > >> tab). This is not going to be tackled by the developer [1]. > >> > >> [1] https://github.com/hadley/pkgdown/issues/220 > >> > >> I had a quick look at the code and patching pkgdown (and probably > >> rmarkdown) to build Rnw/pdf vignettes would take too much time I could > >> devote at the moment. I would be satisfied if the Rnw were not build but > >> at least there were links in the Articles tab pointing to the vignettes > >> Bioconductor landing pages. On the other hand, I am migrating to > >> BiocStyle's html_document2 with the nice floating table of contents... > >> > >> Regarding the News tab, only NEWS.md (markdown format) are considered; > >> NEWS in Rd are ignored too. > >> > >> Hope this helps. > >> > >> Best wishes, > >> > >> Laurent > >> > >> On 16 March 2016 23:33, Andrzej Oleś wrote: > >> > >>> Hi all, > >>> > >>> I had a discussion earlier today with Martin and Dan on providing > >>> online man pages for Bioconductor packages. As we dived into > >>> implementation details, it turned out that this idea is a little bit > >>> more complex and resource-intensive than originally anticipated. > >>> > >>> The main problem in generating man pages in a repository-wide fashion > >>> seems to be the cross-linking of packages. Briefly, in order to > >>> generate the links, apparently one needs to generate the html pages in > >>> an R installation which is aware of the other packages. For example, > >>> the Rd macro \linkS4class{ClassName} takes as argument only the class > >>> name, and the corresponding package containing the class definition is > >>> "automagically" resolved by R. I'm not sure how this could be done > >>> manually, on a per-package basis. So by the end of the day, in order to > >>> generate static man pages, we would need to maintain a complete BioC > >>> repo installation, possibly on a system with the --enable-prebuilt-html > >>> configure option. Unfortunately, it seems unfeasible to exploit the > >>> build servers for this, as this would significantly increase the > >>> computational burden. This is because currently only around 2/5 of all > >>> software and data packages are actually being installed by the build > >>> system. The rest which does not have any reverse dependencies is > >>> skipped. Installing the remaining 3/5 of packages on a regular basis, > >>> not to mention the heavy annotation packages, is a little bit of an > >>> overkill. So piggy-backing on the existing infrastructure doesn't seem > >>> realistic. > >>> > >>> On top of this, even if we would have access to a machine with a > >>> complete, up-to-date BioC installation (maybe by just updating the > >>> packages after the repo gets rebuild rather than re-installing them > >>> each time from scratch), it remains an open question how "external" > >>> links to, let's say, CRAN packages, or even base R packages, should be > >>> handled. > >>> > >>> A lightweight and easy to implement alternative for those willing to > >>> share self-hosted documentation of their packages, could be to provide > >>> in the package DESCRIPTION file a "Documentation" field containing a > >>> link to external resource, which would then appear on the package > >>> landing page next to the vignettes and pdf manual. The obvious > >>> downsides of this solution are: 1. no package cross-links, and 2. the > >>> burden of keeping the documentation in sync with the package version on > >>> BioC would be in maintainer's hands... > >>> > >>> I will try to contact the authors of rdocumentation.org - maybe they > >>> have some useful comments or even code which they would be willing to > >>> share. In any case, it would be good to know what their experience is > >>> and why did they stop maintaining their service. Maybe the BioC > >>> community could jump in and help them to resolve the bottlenecks and > >>> keep the website up to date. > >>> > >>> Cheers, > >>> Andrzej > >>> > >>> > >>> On Tue, Mar 8, 2016 at 4:36 PM, Andrzej Oleś <andrzej.o...@gmail.com> > >>> wrote: > >>> > >>> Hi Martin, > >>> > >>> thank you for your suggestions - I would be happy to contribute to > >>> this! I could help with developing the scripts for generating man > >>> pages, and integrating them with the website layout. > >>> > >>> As for rendering the man pages, I suggest that we try a similar > >>> approach to the one used by knitr::knit_rd() rather than plain > >>> tools::Rd2HTML(). It has the advantage that the examples are > >>> actually run, and the results, e.g. plots, are included in the > >>> output documents. I hope you can appreciate the added value by > >>> comparing the following man page rendered using tools::Rd2HTML() > >>> and knitr::knit_rd(), respectively. > >>> http://www.huber.embl.de/users/aoles/man/Image.html > >>> http://www.huber.embl.de/users/aoles/man/Image-knitr.html > >>> Regarding the additional dependencies: we kind of already rely on > >>> knitr when compiling vignettes, so this this shouldn't add much to > >>> the maintenance burden. > >>> > >>> 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 > > > > > > -- > > Laurent Gatto | @lgatt0 > > http://cpu.sysbiol.cam.ac.uk/ > > http://lgatto.github.io/ > > > > _______________________________________________ > > 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
