Thanks Mike,

I somehow missed the discussion you mentioned. I would really not like to 
include the name of the Rd file I want to link to. The *default* way that works 
on Linux and macOS should also work on Windows - otherwise what's the matter of 
the alias? Interestingly, on my Windows test machine (Windows 7) I don't get 
these warnings (R-devel from 2018-01-07 r74091).


> On 16 Apr 2018, at 10:49, Mike Smith <> wrote:
> Hi Johannes,
> xcms is certainly not alone with the warning, and it was discussed in 
> 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 <> 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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