[Bioc-devel] Reference manual as HTML

Stuart Lee |ee@@ @end|ng |rom weh|@edu@@u
Wed Sep 25 23:27:45 CEST 2019

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?


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,


    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




    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,


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