[Bioc-devel] Reference manual as HTML

[Stuart Lee]

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.
________________________________
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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