[Bioc-devel] Package reference manuals in html

Laurent Gatto lg390 at cam.ac.uk
Fri Dec 23 18:16:14 CET 2016

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.


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.oles at 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.Morgan at 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-bounces at r-project.org> on behalf
>>         of Hartley, Stephen (NIH/NHGRI) [F] <stephen.hartley at 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: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,
>>         Laurent
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Laurent Gatto | @lgatt0

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