[Bioc-devel] Reference manual as HTML

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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_R-2Dmanual_&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms&s=C4NHQqM1TjSqBsj4QBM8g6rtiU4U_xgOigegtYPO8pc&e=
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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_R-2Dmanual_R-2Ddevel_doc_html_packages.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms&s=QocHf4AchWBuoEVZC-HLffWkIbqQKnBCRhuovHpI4lI&e=

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 at r-project.org on behalf of laurent.gatto at 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 at r-project.org> on behalf of Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
     > Sent: 25 September 2019 13:31
     > To: bioc-devel at 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://urldefense.proofpoint.com/v2/url?u=https-3A__rdrr.io_bioc_DESeq2_man_DESeq.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms&s=sHA2r6mT4RdU-4xFyz7-aE0PH2f_rygY4C5S3QToH_E&e= ".

     > (where the link would be preferably: bioconductor.org/packages/DESeq2/man/DESeq.html).

     > Thank you,

     > Ludwig

     > [[alternative HTML version deleted]]

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