Hopefully they'll remedy these problems. They've clearly put a enormous
effort on this.
It sounds like a non-trivial effort to generate the tens of thousands of
Bioconductor man pages in HTML and keep them in sync with whatever comes
out of the nightly builds every day. Plus, if we want the links in the
man pages to work, we would need to also generate and host the HTML man
pages of all CRAN dependencies. I'm not sure we (the core team) have the
resource for that. Maybe an easier/cheaper path is to rely on some
already existing resource like rdrr.io (and maybe help them by reporting
problems etc...)
Best,
H.
On 9/26/19 22:35, Laurent Gatto wrote:
> 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 and buggy (examples don't run, despite the Run button and outdated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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_biocLite.R&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=g7u2I_OwcuL2CSwFfDGK-FX8zsC54IyHxCxV78Zy4kk&e=
> ")`)
>
> Laurent
>
> ________________________________________
> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Pages, Herve
> <hpa...@fredhutch.org>
> Sent: 27 September 2019 00:14
> To: Martin Maechler; Martin Morgan
> Cc: bioc-devel@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://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Frdrr.io-252Fbioc-252FDESeq2-252Fman-252FDESeq.html-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3D82CPHhbrpMfjL1iZy8OMBO6T-252FBt0Kgms3VauzT-252FxlqQ-253D-26amp-3Breserved-3D0&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=E9M_UM64RYYAPZvTbx0XaGVwWY-g9je6xgvHj9Xs6qU&e=
>
> 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__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5FR-2D2Dmanual-5F-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253DC4NHQqM1TjSqBsj4QBM8g6rtiU4U-5FxgOigegtYPO8pc-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3DDujWDlOjIMeiA-252FDSh9IyBdfDwqvisOHu8vY9qTrbkHc-253D-26amp-3Breserved-3D0-3D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=NhxQUIrorkTLVJqvSA_BXQ033CzLPBmbKEeeljVfkX0&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__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5FR-2D2Dmanual-5FR-2D2Ddevel-5Fdoc-5Fhtml-5Fpackages.html-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253DQocHf4AchWBuoEVZC-2DHLffWkIbqQKnBCRhuovHpI4lI-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3Dh43tcLTXczYDUsZRCDZgrAxxgjqacXbRhp-252FOmIULkag-253D-26amp-3Breserved-3D0-3D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=whVthWQxSLPHIXmYqhg3Vx1wd2RLsroluMCrLbrloAA&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__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Frdrr.io-5Fbioc-5FDESeq2-5Fman-5FDESeq.html-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253DsHA2r6mT4RdU-2D4xFyz7-2DaE0PH2f-5FrygY4C5S3QToH-5FE-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3Dm2tonNHuf9DWKWclzPxfLs5hZSOWBnvW5wHGH3Yu1lY-253D-26amp-3Breserved-3D0-3D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=UVpKGa8NF8NIdjl1LUsn3aVICpK42SdrSQuT6UgcjjI&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__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5Fmailman-5Flistinfo-5Fbioc-2D2Ddevel-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253D1vQt-5F1VkcxKSPxoc2fKM0H9PT8bo0ZmM-5Fb5QfLvzUP0-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3DGAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q-253D-26amp-3Breserved-3D0-3D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=BuIrhsD360TIj0KOFh1wzAzNW179bakbVj6F-z_KBRM&e=
>>
>> > _______________________________________________
>> > Bioc-devel@r-project.org mailing list
>> >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5Fmailman-5Flistinfo-5Fbioc-2D2Ddevel-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253D1vQt-5F1VkcxKSPxoc2fKM0H9PT8bo0ZmM-5Fb5QfLvzUP0-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3DGAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q-253D-26amp-3Breserved-3D0-3D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=BuIrhsD360TIj0KOFh1wzAzNW179bakbVj6F-z_KBRM&e=
>>
>> > _______________________________________________
>> > Bioc-devel@r-project.org mailing list
>> >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5Fmailman-5Flistinfo-5Fbioc-2D2Ddevel-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253D1vQt-5F1VkcxKSPxoc2fKM0H9PT8bo0ZmM-5Fb5QfLvzUP0-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3DGAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q-253D-26amp-3Breserved-3D0-3D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=BuIrhsD360TIj0KOFh1wzAzNW179bakbVj6F-z_KBRM&e=
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fstat.ethz.ch-5Fmailman-5Flistinfo-5Fbioc-2D2Ddevel-2526d-253DDwIDaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253Dc4VdSQh-5FZ9zl5XbA2uoUx-2DcLMNMKpPP7NOvfAEo82ms-2526s-253D1vQt-5F1VkcxKSPxoc2fKM0H9PT8bo0ZmM-5Fb5QfLvzUP0-2526e-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265489883-26amp-3Bsdata-3DGAZHzVYfTl80ZEs7qEDvph4f3xEMHjqGBNKXbDNeE2Q-253D-26amp-3Breserved-3D0-3D&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=BuIrhsD360TIj0KOFh1wzAzNW179bakbVj6F-z_KBRM&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://urldefense.proofpoint.com/v2/url?u=https-3A__eur03.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fstat.ethz.ch-252Fmailman-252Flistinfo-252Fbioc-2Ddevel-26amp-3Bdata-3D02-257C01-257Claurent.gatto-2540uclouvain.be-257Ceab709733a714ae52f1d08d742cf05d4-257C7ab090d4fa2e4ecfbc7c4127b4d582ec-257C0-257C0-257C637051329265499877-26amp-3Bsdata-3D7mvx2ZxNdAVGDgI4EJMlFOhNS3MQKMiZu7ZwBK1qBJU-253D-26amp-3Breserved-3D0&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ&s=W-OKbs64mpUrNyIXnMmuLkYMdqdAmI8EHMRvD7r0eCk&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
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