[Bioc-devel] Reference manual as HTML

[Martin Morgan]

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

Martin

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?
    
    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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