[Bioc-devel] Reference manual as HTML

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Sep 26 02:53:22 CEST 2019

Oops, I said 'vignettes' but meant the reference manual. Html vignettes (from appropriate Rmd files) are have been available for a number of years.


On 9/25/19, 5:10 PM, "Martin Morgan" <mtmorgan.bioc using gmail.com> wrote:

    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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