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

________________________________
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
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.

Mike

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

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

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