[Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2>

[Rainer Johannes]

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 <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
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>