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).
jo > On 16 Apr 2018, at 10:49, Mike Smith <grimbo...@gmail.com> wrote: > > 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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel