Re: [Bioc-devel] Roxygen documentation under windows
Hi,
Thanks for the quick and helpful comments! As suggested, I used the the
following code
\code{\link[BiocParallel:BiocParallelParam-class]{BiocParallelParam}}
And it worked perfectly and all warnings are gone now! But im still puzzled why
it only gave a warning on windows and not on linux.
Thanks again,
Christian
> On 8. Oct 2018, at 07:14, Leonardo Collado Torres wrote:
>
> Hi,
>
> Adding the -class part will help for most. To get the correct name,
> check the top left part of the help page for the function you want to
> link to. For example, if you type
>
> library(GenomicRanges)
> ?GRanges
>
> you'll see GRanges-class {GenomicRanges} on the top left (I'm on a Mac
> right now).
>
> Here are some examples that I fixed on my packages
> https://github.com/lcolladotor/derfinder/commit/2dee40434b8916a2e8acc717e3300c07ad5236b2
>
> Best,
> Leo
>
> On Mon, Oct 8, 2018 at 9:00 AM Shepherd, Lori
> wrote:
>>
>> I think there is a reference here
>>
>> https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi
>>
>>
>> Where the actual name of the man file that has BiocParallelParam is
>> BiocParallelParm-class and BiocParallelParam is an alias.
>>
>>
>> I believe if you change the link to be
>>
>> \code{\link[BiocParallel:BiocParallelParam-class]{BiocParallelParam}} It
>> should remedy the issue.
>>
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>>
>> From: Bioc-devel on behalf of Christian
>> Mertes
>> Sent: Sunday, October 7, 2018 9:01:35 PM
>> To: bioc-devel
>> Subject: [Bioc-devel] Roxygen documentation under windows
>>
>> Hey all,
>>
>> I have a question. My package builds perfectly on Linux and MacOS, but fails
>> to link my documentation correctly on Windows, which results in a warning.
>>
>> The exact error which I get is:
>> Rd warning:
>> C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpei0FPy/R.INSTALL215c42273ec6/OUTRIDER/man/OUTRIDER.Rd:22:
>> file link 'BiocParallelParam' in package 'BiocParallel' does not exist and
>> so has been treated as a topic
>> The line in my code which generates this is:
>>
>> #' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
>>
>> The error can also be found here:
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html
>>
>> <http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html>
>>
>> For me it looks odd since it compiles without any error on Linux and MacOS
>> but not on Windows. So I�m not sure if its a bug on Windows or the way I�m
>> linking it in my Roxygen2 documentation.
>>
>> Any help is appreciated.
>>
>> Thanks,
>>
>> Christian
>>
>>
>>[[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information. If you are not the intended recipient(s), or the employee or
>> agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited. If you have
>> received this message in error, please notify the sender immediately by
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Re: [Bioc-devel] Roxygen documentation under windows
Hi,
Adding the -class part will help for most. To get the correct name,
check the top left part of the help page for the function you want to
link to. For example, if you type
library(GenomicRanges)
?GRanges
you'll see GRanges-class {GenomicRanges} on the top left (I'm on a Mac
right now).
Here are some examples that I fixed on my packages
https://github.com/lcolladotor/derfinder/commit/2dee40434b8916a2e8acc717e3300c07ad5236b2
Best,
Leo
On Mon, Oct 8, 2018 at 9:00 AM Shepherd, Lori
wrote:
>
> I think there is a reference here
>
> https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi
>
>
> Where the actual name of the man file that has BiocParallelParam is
> BiocParallelParm-class and BiocParallelParam is an alias.
>
>
> I believe if you change the link to be
>
> \code{\link[BiocParallel:BiocParallelParam-class]{BiocParallelParam}} It
> should remedy the issue.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> From: Bioc-devel on behalf of Christian
> Mertes
> Sent: Sunday, October 7, 2018 9:01:35 PM
> To: bioc-devel
> Subject: [Bioc-devel] Roxygen documentation under windows
>
> Hey all,
>
> I have a question. My package builds perfectly on Linux and MacOS, but fails
> to link my documentation correctly on Windows, which results in a warning.
>
> The exact error which I get is:
> Rd warning:
> C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpei0FPy/R.INSTALL215c42273ec6/OUTRIDER/man/OUTRIDER.Rd:22:
> file link 'BiocParallelParam' in package 'BiocParallel' does not exist and
> so has been treated as a topic
> The line in my code which generates this is:
>
> #' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
>
> The error can also be found here:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html
>
> <http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html>
>
> For me it looks odd since it compiles without any error on Linux and MacOS
> but not on Windows. So I�m not sure if its a bug on Windows or the way I�m
> linking it in my Roxygen2 documentation.
>
> Any help is appreciated.
>
> Thanks,
>
> Christian
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Roxygen documentation under windows
I think there is a reference here
https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi
Where the actual name of the man file that has BiocParallelParam is
BiocParallelParm-class and BiocParallelParam is an alias.
I believe if you change the link to be
\code{\link[BiocParallel:BiocParallelParam-class]{BiocParallelParam}} It
should remedy the issue.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel on behalf of Christian
Mertes
Sent: Sunday, October 7, 2018 9:01:35 PM
To: bioc-devel
Subject: [Bioc-devel] Roxygen documentation under windows
Hey all,
I have a question. My package builds perfectly on Linux and MacOS, but fails to
link my documentation correctly on Windows, which results in a warning.
The exact error which I get is:
Rd warning:
C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpei0FPy/R.INSTALL215c42273ec6/OUTRIDER/man/OUTRIDER.Rd:22:
file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so
has been treated as a topic
The line in my code which generates this is:
#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
The error can also be found here:
http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html
<http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html>
For me it looks odd since it compiles without any error on Linux and MacOS but
not on Windows. So I�m not sure if its a bug on Windows or the way I�m linking
it in my Roxygen2 documentation.
Any help is appreciated.
Thanks,
Christian
[[alternative HTML version deleted]]
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This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
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[Bioc-devel] Roxygen documentation under windows
Hey all,
I have a question. My package builds perfectly on Linux and MacOS, but fails to
link my documentation correctly on Windows, which results in a warning.
The exact error which I get is:
Rd warning:
C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmpei0FPy/R.INSTALL215c42273ec6/OUTRIDER/man/OUTRIDER.Rd:22:
file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so
has been treated as a topic
The line in my code which generates this is:
#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} instance
The error can also be found here:
http://bioconductor.org/checkResults/devel/bioc-LATEST/OUTRIDER/tokay1-checksrc.html
For me it looks odd since it compiles without any error on Linux and MacOS but
not on Windows. So I’m not sure if its a bug on Windows or the way I’m linking
it in my Roxygen2 documentation.
Any help is appreciated.
Thanks,
Christian
[[alternative HTML version deleted]]
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