[Bioc-devel] Roxygen documentation under windows

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Mon Oct 8 14:55:04 CEST 2018

I think there is a reference here


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.



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