[Bioc-devel] Reference manual as HTML

[Pages, Herve]

and let's not forget the rdrr site that provides HTML versions of all R 
package man pages in the known world:

   https://rdrr.io/bioc/DESeq2/man/DESeq.html

Unfortunately the links across man pages are not clickable :-/

H.


On 9/26/19 06:19, Martin Maechler wrote:
>>>>>> 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 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://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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-- 
Hervé Pagès

Program in Computational Biology
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