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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>
> ___
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>
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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.
> ___
>
> [[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]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
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]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
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] Error building Vignnette in Bioconductor Windows server when Submitting a new package
Often this means that there is some resource in your vignette that has not been terminated correctly, e.g., a parallel process that has not be stopped or a graphical device that is still open. Martin On 9/25/19, 4:46 AM, "Bioc-devel on behalf of Alberto Valdeolivas" wrote: Hello all, I am submitting the following new package to Bioconductor: https://github.com/Bioconductor/Contributions/issues/1263 R CMD BUILD is reporting the following ERROR when running in Windows server: Error: processing vignette 'OmnipathR.Rnw' failed with diagnostics: Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'OmnipathR'. The following files exist in directory '.': 'Bioc.bib', 'OmnipathR-concordance.tex', 'OmnipathR-fig2.pdf', 'OmnipathR-fig3.pdf', 'OmnipathR-fig4.pdf', 'OmnipathR.Rnw', 'OmnipathR.tex' --- failed re-building 'OmnipathR.Rnw' http://bioconductor.org/spb_reports/OmnipathR_buildreport_20190925041516.html The package pass R CMD BUILD and R CMD CHECK with no issues in the other systems. I have googled the error and found some related topics. However, the solution does not seem very clear to me. https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html They commented that these build error could be transient. However, I resubmitted and had the same problem again. Any clue about what to do? just keep submitting? Many thanks and best regards, Alberto. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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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___
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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]]
___
Bioc-devel@r-project.org mailing list
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[Bioc-devel] Error building Vignnette in Bioconductor Windows server when Submitting a new package
Hello all, I am submitting the following new package to Bioconductor: https://github.com/Bioconductor/Contributions/issues/1263 R CMD BUILD is reporting the following ERROR when running in Windows server: Error: processing vignette 'OmnipathR.Rnw' failed with diagnostics: Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'OmnipathR'. The following files exist in directory '.': 'Bioc.bib', 'OmnipathR-concordance.tex', 'OmnipathR-fig2.pdf', 'OmnipathR-fig3.pdf', 'OmnipathR-fig4.pdf', 'OmnipathR.Rnw', 'OmnipathR.tex' --- failed re-building 'OmnipathR.Rnw' http://bioconductor.org/spb_reports/OmnipathR_buildreport_20190925041516.html The package pass R CMD BUILD and R CMD CHECK with no issues in the other systems. I have googled the error and found some related topics. However, the solution does not seem very clear to me. https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html They commented that these build error could be transient. However, I resubmitted and had the same problem again. Any clue about what to do? just keep submitting? Many thanks and best regards, Alberto. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
