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-boun...@r-project.org on behalf of laurent.ga...@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-boun...@r-project.org> on behalf of > Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> > > Sent: 25 September 2019 13:31 > > To: bioc-devel@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]] > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms&s=1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0&e= > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms&s=1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0&e= > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms&s=1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0&e= > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms&s=1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel