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

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Mon Apr 16 13:16:54 CEST 2018

This was also discussed in this thread a few weeks ago


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Mike Smith <grimbough at gmail.com>
Sent: Monday, April 16, 2018 6:13:38 AM
To: Rainer Johannes; bioc-devel
Subject: Re: [Bioc-devel] Windows <Problems with Rd links to other packages on Tokay2>

Martin mentioned that he changed the wording in
, so more recently than your version of R-devel.


On 16 April 2018 at 11:57, Rainer Johannes <Johannes.Rainer at eurac.edu>

> 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
> >

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