Re: [Bioc-devel] Reference manual as HTML
Thanks a lot for the insights.
I think I am then indeed resorting to pkgdown and the rdrr site.
Ludwig
From: Bioc-devel on behalf of Pages, Herve
Sent: Friday, September 27, 2019 2:02 AM
To: Laurent Gatto; Martin Maechler; Martin Morgan
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Reference manual as HTML
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 and buggy (examples don't run, despite the Run button and outdated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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=g7u2I_OwcuL2CSwFfDGK-FX8zsC54IyHxCxV78Zy4kk=
> ")`)
>
> Laurent
>
>
> From: Bioc-devel on behalf of Pages, Herve
>
> 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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=E9M_UM64RYYAPZvTbx0XaGVwWY-g9je6xgvHj9Xs6qU=
>
> 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 + 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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=NhxQUIrorkTLVJqvSA_BXQ033CzLPBmbKEeeljVfkX0=
>> 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-2DHL
Re: [Bioc-devel] Reference manual as HTML
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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=g7u2I_OwcuL2CSwFfDGK-FX8zsC54IyHxCxV78Zy4kk=
> ")`)
>
> Laurent
>
>
> From: Bioc-devel on behalf of Pages, Herve
>
> 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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=E9M_UM64RYYAPZvTbx0XaGVwWY-g9je6xgvHj9Xs6qU=
>
> 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 + 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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V2DMbdkOnMOEDmM-NTXRK2Upst5xq5TTNfoiTX4FlbQ=NhxQUIrorkTLVJqvSA_BXQ033CzLPBmbKEeeljVfkX0=
>> 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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYb
Re: [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 on behalf of Pages, Herve
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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fbioc%2FDESeq2%2Fman%2FDESeq.htmldata=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883sdata=82CPHhbrpMfjL1iZy8OMBO6T%2FBt0Kgms3VauzT%2FxlqQ%3Dreserved=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 + 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%26edata=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883sdata=DujWDlOjIMeiA%2FDSh9IyBdfDwqvisOHu8vY9qTrbkHc%3Dreserved=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%26edata=02%7C01%7Claurent.gatto%40uclouvain.be%7Ceab709733a714ae52f1d08d742cf05d4%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637051329265489883sdata=h43tcLTXczYDUsZRCDZgrAxxgjqacXbRhp%2FOmIULkag%3Dreserved=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"
>
> 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 on behalf of
> Ludwig Geistlinger
> > 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
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://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 + 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_=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms=C4NHQqM1TjSqBsj4QBM8g6rtiU4U_xgOigegtYPO8pc=
> 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=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms=QocHf4AchWBuoEVZC-HLffWkIbqQKnBCRhuovHpI4lI=
>
> 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"
>
> 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 on behalf of
> Ludwig Geistlinger
> > 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=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms=sHA2r6mT4RdU-4xFyz7-aE0PH2f_rygY4C5S3QToH_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=DwIDaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=c4VdSQh_Z9zl5XbA2uoUx-cLMNMKpPP7NOvfAEo82ms=1vQt_1Vkc
Re: [Bioc-devel] Reference manual as HTML
>>>>> Martin Morgan
>>>>> on Wed, 25 Sep 2019 21:10:24 + 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://stat.ethz.ch/R-manual/
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://stat.ethz.ch/R-manual/R-devel/doc/html/packages.html
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"
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 on behalf of Ludwig
Geistlinger
> 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://rdrr.io/bioc/DESeq2/man/DESeq.html;.
> (where the link would be preferably:
bioconductor.org/packages/DESeq2/man/DESeq.html).
> Thank you,
> Ludwig
> [[alternative HTML version deleted]]
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Re: [Bioc-devel] Reference manual as HTML
My experience with pkgdown is very positive. As mentioned by Stuart, I use
travis to automatically build the webpage after a successful check and serve it
as a gh-page.
I find it particularly useful as it displays the devel version of the vignettes
and individual manual pages, which often come handy to answer questions related
to new features or bug fixes and to add a link to the relevant manual page
(rather than a large pdf) or vignette section. The webpage is also a good
starting point to learn about new packages, as all the documentation sources,
README, vignettes and individual man pages (which can easily be overwhelming
for large packages) are readily available to read and search.
Laurent
From: Martin Morgan
Sent: 25 September 2019 23:10
To: Laurent Gatto; Ludwig Geistlinger; bioc-devel@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"
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 on behalf of Ludwig
Geistlinger
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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frdrr.io%2Fbioc%2FDESeq2%2Fman%2FDESeq.htmldata=02%7C01%7Claurent.gatto%40uclouvain.be%7Ce38d0811b2c94f5450f808d741fcc9a6%7C7ab090d4fa2e4ecfbc7c4127b4d582ec%7C0%7C0%7C637050426278839970sdata=hEk11QlPbH1cNC1xvidpDjKtdU9lqrkxBdvK0u2qYxM%3Dreserved=0;.
(where the link would be preferably:
bioconductor.org/packages/DESeq2/man/DESeq.html).
Thank you,
Ludwig
[[alternative HTML version deleted]]
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Re: [Bioc-devel] Reference manual as HTML
Oops, I said 'vignettes' but meant the reference manual. Html vignettes (from
appropriate Rmd files) are have been available for a number of years.
Martin
On 9/25/19, 5:10 PM, "Martin Morgan" wrote:
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"
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 on behalf of Ludwig
Geistlinger
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://rdrr.io/bioc/DESeq2/man/DESeq.html;.
(where the link would be preferably:
bioconductor.org/packages/DESeq2/man/DESeq.html).
Thank you,
Ludwig
[[alternative HTML version deleted]]
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Re: [Bioc-devel] Reference manual as HTML
On Wed, Sep 25, 2019 at 2:28 PM Stuart Lee 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 on behalf of Martin
> Morgan
> Sent: Thursday, 26 September 2019 7:10 AM
> To: Laurent Gatto ; Ludwig Geistlinger
> ; bioc-devel@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"
>
> 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 on behalf of Ludwig
> Geistlinger
> 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://rdrr.io/bioc/DESeq2/man/DESeq.html;.
>
> (where the link would be preferably:
> bioconductor.org/packages/DESeq2/man/DESeq.html).
>
>
> Thank you,
>
> Ludwig
>
> [[alternative HTML version deleted]]
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
>
> The information in this email is confidential and intended solely for the
> addressee.
> You must not disclose, forward, print or use it without the permission of the
> sender.
>
> The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the
> Kulin
> Nation as the traditional owners of the land where our campuses are located
> and
> the continuing connection to country and community.
> ___
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Reference manual as HTML
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.
From: Bioc-devel on behalf of Martin Morgan
Sent: Thursday, 26 September 2019 7:10 AM
To: Laurent Gatto ; Ludwig Geistlinger
; bioc-devel@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"
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 on behalf of Ludwig
Geistlinger
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://rdrr.io/bioc/DESeq2/man/DESeq.html;.
(where the link would be preferably:
bioconductor.org/packages/DESeq2/man/DESeq.html).
Thank you,
Ludwig
[[alternative HTML version deleted]]
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The information in this email is confidential and intended solely for the
addressee.
You must not disclose, forward, print or use it without the permission of the
sender.
The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the
Kulin
Nation as the traditional owners of the land where our campuses are located and
the continuing connection to country and community.
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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"
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 on behalf of Ludwig
Geistlinger
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://rdrr.io/bioc/DESeq2/man/DESeq.html;.
(where the link would be preferably:
bioconductor.org/packages/DESeq2/man/DESeq.html).
Thank you,
Ludwig
[[alternative HTML version deleted]]
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Re: [Bioc-devel] Reference manual as HTML
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 on behalf of Ludwig
Geistlinger
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://rdrr.io/bioc/DESeq2/man/DESeq.html;.
(where the link would be preferably:
bioconductor.org/packages/DESeq2/man/DESeq.html).
Thank you,
Ludwig
[[alternative HTML version deleted]]
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[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
[[alternative HTML version deleted]]
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