[Bioc-devel] Reference manual as HTML

[Henrik Bengtsson]

On Wed, Sep 25, 2019 at 2:28 PM Stuart Lee <lee.s using wehi.edu.au> wrote:
>
> Chiming in to say +1 to this. I also use pkgdown for the same purpose as Laurent. With some kind of CI service you can automate the build of the website after a successful R CMD CHECK. Not sure how tricky this would be to integrate with Bioconductor's build system.

FYI, 'pkgdown' only supports vignettes that are written in the
Rmarkdown format (https://github.com/r-lib/pkgdown/issues/781).

/Henrik

> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Martin Morgan <mtmorgan.bioc using gmail.com>
> Sent: Thursday, 26 September 2019 7:10 AM
> To: Laurent Gatto <laurent.gatto using uclouvain.be>; Ludwig Geistlinger <Ludwig.Geistlinger using sph.cuny.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Reference manual as HTML
>
> Our recollection is that there is no 'flag' in R CMD build to create HTML rather than PDF vignettes; without that it would be non-trivial to create html output, e.g., links across pages. (I *think* the installed package html help pages are generated on the fly...)
>
> What is your experience with pkgdown?
>
> Martin
>
> On 9/25/19, 9:44 AM, "Bioc-devel on behalf of Laurent Gatto" <bioc-devel-bounces using r-project.org on behalf of laurent.gatto using uclouvain.be> wrote:
>
>     I think this would be very useful. This is one of the reasons I create pkgdown sites for my packages: manual pages, news and html vignettes are readily available for all (including me) to browse.
>
>     Best wishes,
>
>     Laurent
>
>     ________________________________________
>     From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Ludwig Geistlinger <Ludwig.Geistlinger using sph.cuny.edu>
>     Sent: 25 September 2019 13:31
>     To: bioc-devel using r-project.org
>     Subject: [Bioc-devel] Reference manual as HTML
>
>     Dear Bioc-Team,
>
>
>     I repeatedly wondered whether it would be possible to display the reference manual
>     as HTML instead of PDF on a package's landing page. This is already possible for vignettes.
>
>     HTML reference manuals have at least two advantages:
>
>     1. links to functions of other package in the man pages of my package would
>     actually work. Links to functions / classes of other packages of the form
>
>     \code{\link{p.adjust}}
>
>     or
>
>     \code{\linkS4class{SummarizedExperiment}}
>
>     within the pdf reference manual currently point nowhere (bring me back to the
>     first page of the pdf). Within the html reference manual
>
>     help(package="myPackage", help_type="html")
>
>     these links work as expected, ie bring me to the help pages of functions / classes
>     of other packages.
>
>     2. I could easily refer users to the documentation link of a specific function
>     (without them having to search through the pdf) such as "check the documentation of
>     the DESeq function here: https://rdrr.io/bioc/DESeq2/man/DESeq.html".
>
>     (where the link would be preferably: bioconductor.org/packages/DESeq2/man/DESeq.html).
>
>
>     Thank you,
>
>     Ludwig
>
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