[Bioc-devel] Roxygen documentation under windows

[Leonardo Collado Torres]

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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