On 16 Apr 2018, at 10:49, Mike Smith <grimbough at 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.Rainer at 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