[Bioc-devel] Package reference manuals in html

Laurent Gatto lg390 at cam.ac.uk
Fri Dec 23 17:36:12 CET 2016

Dear all,

I'm following up re my online references suggestion with my recent
experience with Hadley's pkgdown package


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,


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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