[Bioc-devel] Reference manual as HTML

[Martin Maechler]

>>>>> Martin Morgan 
>>>>>     on Wed, 25 Sep 2019 21:10:24 +0000 writes:

    > 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...)

Yes, by default.
But you may (or not) remember that for R itself, I (and my
university, ETH Zurich) have provided static HTML help pages and
manuals since "forever" -> https://stat.ethz.ch/R-manual/
and my cron job that creates (and daily updates) them "starts
with"

  ../R/configure --with-prebuilt-html

As it does provide static html help pages for all "base R" +
Recommended packages,

 see, e.g., https://stat.ethz.ch/R-manual/R-devel/doc/html/packages.html

it should not be hard to have it do the same for all other
packages in principle.

"The other R Core" Martin

Martin Maechler
ETH Zurich


    > 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
    
    > [[alternative HTML version deleted]]
    
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