[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
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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel at 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 at 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/
More information about the Bioc-devel
mailing list