[Bioc-devel] Reference manual as HTML

Laurent Gatto |@urent@g@tto @end|ng |rom uc|ouv@|n@be
Wed Sep 25 15:43:48 CEST 2019

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,


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




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,


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