[Bioc-devel] Reference manual as HTML
On Wed, Sep 25, 2019 at 2:28 PM Stuart Lee <lee.s at wehi.edu.au> wrote:
Chiming in to say +1 to this. I also use pkgdown for the same purpose as Laurent. With some kind of CI service you can automate the build of the website after a successful R CMD CHECK. Not sure how tricky this would be to integrate with Bioconductor's build system.
FYI, 'pkgdown' only supports vignettes that are written in the Rmarkdown format (https://github.com/r-lib/pkgdown/issues/781). /Henrik
________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Martin Morgan <mtmorgan.bioc at gmail.com>
Sent: Thursday, 26 September 2019 7:10 AM
To: Laurent Gatto <laurent.gatto at uclouvain.be>; Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Reference manual as HTML
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 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://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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