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
