[Bioc-devel] Roxygen documentation under windows

[Christian Mertes]

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 <lcollado using jhu.edu> 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
> <Lori.Shepherd using roswellpark.org> 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 <bioc-devel-bounces using r-project.org> on behalf of Christian Mertes <mertes using in.tum.de>
>> 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
>> 
>> 
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