Hi Johannes,
xcms is certainly not alone with the warning, and it was discussed in
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
I think you should be able to get round it by including the name of Rd file
you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
(I haven't actually tested this though).
Mike
On 16 April 2018 at 09:06, Rainer Johannes <johannes.rai...@eurac.edu>
wrote:
> Dear all,
>
> we're experiencing WARNINGS in xcms on Tokay2 that are all related to
> links in Rd files to functions and methods in other packages.
> Example:
> we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd
> that links to the method in MSnbase, that works nicely on Linux and macOS
> build machines, but on tokay2 we get:
>
> Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw7qeJw/R.
> INSTALL1e704df56ca9/xcms/man/XCMSnExp-inherited-methods.Rd:59: file link
> 'pickPeaks' in package 'MSnbase' does not exist and so has been treated as
> a topic
>
> is there any other solution to removing all links to external packages?
>
> thanks, jo
>
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