[Bioc-devel] Reference manual as HTML
But it has been badly out-of-data in the past, not sure devel is available and buggy (examples don't run, despite the Run button and outdated installation instructions still using `source("https://bioconductor.org/biocLite.R")`)
Laurent
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Pages, Herve <hpages at fredhutch.org>
Sent: 27 September 2019 00:14
To: Martin Maechler; Martin Morgan
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Reference manual as HTML
Sent: 27 September 2019 00:14
To: Martin Maechler; Martin Morgan
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Reference manual as HTML
and let's not forget the rdrr site that provides HTML versions of all R package man pages in the known world: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fbioc%2FDESeq2%2Fman%2FDESeq.html&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=82CPHhbrpMfjL1iZy8OMBO6T%2FBt0Kgms3VauzT%2FxlqQ%3D&reserved=0 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_R-2Dmanual_%26d%3DDwIDaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3Dc4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms%26s%3DC4NHQqM1TjSqBsj4QBM8g6rtiU4U_xgOigegtYPO8pc%26e&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=DujWDlOjIMeiA%2FDSh9IyBdfDwqvisOHu8vY9qTrbkHc%3D&reserved=0= > 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_R-2Dmanual_R-2Ddevel_doc_html_packages.html%26d%3DDwIDaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3Dc4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms%26s%3DQocHf4AchWBuoEVZC-HLffWkIbqQKnBCRhuovHpI4lI%26e&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=h43tcLTXczYDUsZRCDZgrAxxgjqacXbRhp%2FOmIULkag%3D&reserved=0= > > 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__rdrr.io_bioc_DESeq2_man_DESeq.html%26d%3DDwIDaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3Dc4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms%26s%3DsHA2r6mT4RdU-4xFyz7-aE0PH2f_rygY4C5S3QToH_E%26e&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=m2tonNHuf9DWKWclzPxfLs5hZSOWBnvW5wHGH3Yu1lY%3D&reserved=0= ". > > > (where the link would be preferably: bioconductor.org/packages/DESeq2/man/DESeq.html). > > > > Thank you, > > > Ludwig > > > [[alternative HTML version deleted]] > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwIDaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3Dc4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms%26s%3D1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0%26e&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=GAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q%3D&reserved=0= > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwIDaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3Dc4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms%26s%3D1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0%26e&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=GAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q%3D&reserved=0= > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwIDaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3Dc4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms%26s%3D1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0%26e&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=GAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q%3D&reserved=0= > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwIDaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3Dc4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms%26s%3D1vQt_1VkcxKSPxoc2fKM0H9PT8bo0ZmM_b5QfLvzUP0%26e&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883&sdata=GAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q%3D&reserved=0= > -- Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel at r-project.org mailing list https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265499877&sdata=7mvx2ZxNdAVGDgI4EJMlFOhNS3MQKMiZu7ZwBK1qBJU%3D&reserved=0